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Found 1 Document (1.076 seconds)

BMRB: 15532

2JP9

Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA

Authors

Stoll, R., Lee, B.M., Debler, E.W., Laity, J.H., Wilson, I.A., Dyson, H.JANE., Wright, P.E.

Assembly

wt1-17mer

Entity

1. wt1-17mer (polymer, Thiol state: all other bound), 119 monomers, 14448.38 Da Detail

ASEKRPFMCA YPGCNKRYFK LSHLQMHSRK HTGEKPYQCD FKDCERRFSR SDQLKRHQRR HTGVKPFQCK TCQRKFSRSD HLKTHTRTHT GEKPFSCRWP SCQKKFARSD ELVRHHNMH

2. ZN (non-polymer), 65.409 × 4 Da

Total weight

14710.016 Da

Max. entity weight

14448.38 Da

Entity Connection

na 16 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS9:SG	2:ZN1:ZN
2	na	sing	1:CYS14:SG	2:ZN1:ZN
3	na	sing	1:HIS27:NE2	2:ZN1:ZN
4	na	sing	1:HIS31:NE2	2:ZN1:ZN
5	na	sing	1:CYS39:SG	2:ZN1:ZN
6	na	sing	1:CYS44:SG	2:ZN1:ZN
7	na	sing	1:HIS57:NE2	2:ZN1:ZN
8	na	sing	1:HIS61:NE2	2:ZN1:ZN
9	na	sing	1:CYS69:SG	2:ZN1:ZN
10	na	sing	1:CYS72:SG	2:ZN1:ZN
11	na	sing	1:HIS85:NE2	2:ZN1:ZN
12	na	sing	1:HIS89:NE2	2:ZN1:ZN
13	na	sing	1:CYS97:SG	2:ZN1:ZN
14	na	sing	1:CYS102:SG	2:ZN1:ZN
15	na	sing	1:HIS115:NE2	2:ZN1:ZN
16	na	sing	1:HIS119:NE2	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.6 %, Completeness: 25.5 %, Completeness (bb): 63.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	25.5 % (234 of 917)	15.6 % (124 of 794)	89.4 % (110 of 123)
Backbone	63.6 % (222 of 349)	47.9 % (113 of 236)	96.5 % (109 of 113)
Sidechain	2.1 % (12 of 568)	2.0 % (11 of 558)	10.0 % (1 of 10)
Aromatic	6.2 % (5 of 81)	5.0 % (4 of 80)	100.0 % (1 of 1)
Methyl	0.0 % (0 of 24)	0.0 % (0 of 24)

1. wt1-17mer

ASEKRPFMCA YPGCNKRYFK LSHLQMHSRK HTGEKPYQCD FKDCERRFSR SDQLKRHQRR HTGVKPFQCK TCQRKFSRSD HLKTHTRTHT GEKPFSCRWP SCQKKFARSD ELVRHHNMH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	wt1	[U-100% 13C; U-100% 15N]	0.6 mM
2	Tris/HCl		10 mM
3	KCl		20 mM
4	ZnSO4		5 uM
5	NaN3		2 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2JP9, Strand ID: A Detail

Release date

2008-02-13

Citation

Structure of the Wilms tumor suppressor protein zinc finger domain bound to DNA
Stoll, R., Lee, B.M., Debler, E.W., Laity, J.H., Wilson, I.A., Dyson, H.JANE., Wright, P.E.
J. Mol. Biol. (2007), 372, 1227-1245, PubMed 17716689 , DOI 10.1016/j.jmb.2007.07.017 , Abstract

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

  BMRB: 15533 released on 2008-02-13
    Title Structure of the Wilms' Tumor Suppressor Protein Zinc Finger Domain Bound to DNA
  Swiss-Prot: P19544 released on 1991-02-01
    Title WT1_HUMAN Entity Wilms tumor protein

Related entities 1. wt1-17mer, : 1 : 2 : 2 : 5 : 428 entities Detail

Interaction partners 1. wt1-17mer, : 14 interactors Detail

More details for 14 interactors identified by 5 citations

Experiments performed 2 experiments Detail

NMR combined restraints 13 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15532_2jp9.nef
Input source #2: Coordindates	2jp9.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
3:9:CYS:SG	4:1:ZN:ZN	unknown	unknown	n/a
3:14:CYS:SG	4:1:ZN:ZN	unknown	unknown	n/a
3:27:HIS:NE2	4:1:ZN:ZN	unknown	unknown	n/a
3:31:HIS:NE2	4:1:ZN:ZN	unknown	unknown	n/a
3:39:CYS:SG	4:2:ZN:ZN	unknown	unknown	n/a
3:44:CYS:SG	4:2:ZN:ZN	unknown	unknown	n/a
3:57:HIS:NE2	4:2:ZN:ZN	unknown	unknown	n/a
3:61:HIS:NE2	4:2:ZN:ZN	unknown	unknown	n/a
3:69:CYS:SG	4:3:ZN:ZN	unknown	unknown	n/a
3:72:CYS:SG	4:3:ZN:ZN	unknown	unknown	n/a
3:85:HIS:NE2	4:3:ZN:ZN	unknown	unknown	n/a
3:89:HIS:NE2	4:3:ZN:ZN	unknown	unknown	n/a
3:97:CYS:SG	4:4:ZN:ZN	unknown	unknown	n/a
3:102:CYS:SG	4:4:ZN:ZN	unknown	unknown	n/a
3:115:HIS:NE2	4:4:ZN:ZN	unknown	unknown	n/a
3:119:HIS:NE2	4:4:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
D	1	ZN	ZINC ION	None
D	2	ZN	ZINC ION	None
D	3	ZN	ZINC ION	None
D	4	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A
Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------20--120-------130-------140
.......................CGCGGGGGCGTCTGCGC
                                        
GCGCAGACGCCCCCGCG.......................

Entity_assembly_ID (NMR): C vs Auth_asym_ID (model): C

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
B	B	17	100.0
C	C	17	100.0
A	A	119	100.0

Content subtype: combined_15532_2jp9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	16		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	220		91.6 (chain: A, length: 119)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	77 (1)	noe	17.6 (chain: A, length: 119)
2	Distance restraints	DYANA/DIANA_distance_constraints_8	Warning	68 (1)	noe	16.0 (chain: A, length: 119)
3	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	77 (1)	noe	17.6 (chain: A, length: 119)
4	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	77 (1)	noe	17.6 (chain: A, length: 119)
5	Distance restraints	DYANA/DIANA_distance_constraints_10	OK	405 (1)	undefined	76.5 (chain: A, length: 119)
6	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	16 (1)	hbond	10.1 (chain: A, length: 119)
7	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	16 (1)	hbond	10.1 (chain: A, length: 119)
8	Distance restraints	DYANA/DIANA_distance_constraints_9	Warning	16 (1)	hbond	10.1 (chain: A, length: 119)
9	Distance restraints	DYANA/DIANA_distance_constraints_11	Warning	88 (1)	hbond	53.8 (chain: A, length: 119)
10	Distance restraints	DYANA/DIANA_distance_constraints_7	Warning	16 (1)	hbond	10.1 (chain: A, length: 119)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_12	OK	104 (104)	.	63.9 (chain: A, length: 119)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 91.6%
- Total number of assignments
  - ¹H chemical shifts: 110
  - ¹⁵N chemical shifts: 110
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	794	110	13.9
¹⁵N chemical shifts	138	110	79.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	236	109	46.2
¹⁵N chemical shifts	113	109	96.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	558	1	0.2
¹⁵N chemical shifts	25	1	4.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	1	1.3
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 17.6%
- Total number of restraints: 77
- Weight of restraints: 1.0 (77)
- Potential type of restraints: upper-bound-parabolic (77)
- Range of distance target values: 2.0, 5.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
  - Chain_ID: C
    None
  - Chain_ID: D
    None
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_8
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 16.0%
  - Total number of restraints: 68
  - Weight of restraints: 1.0 (68)
  - Potential type of restraints: upper-bound-parabolic (68)
  - Range of distance target values: 2.0, 5.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
    - Chain_ID: C
      None
    - Chain_ID: D
      None
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_6
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 17.6%
    - Total number of restraints: 77
    - Weight of restraints: 1.0 (77)
    - Potential type of restraints: upper-bound-parabolic (77)
    - Range of distance target values: 2.0, 5.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
      - Chain_ID: C
        None
      - Chain_ID: D
        None
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_2
      - Status: Warning
      - Experiment type: noe
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 17.6%
      - Total number of restraints: 77
        Sequential restraints, | i - j | = 1 : 18
        Backbone-backbone: 18
        Medium range restraints, 1 < | i - j | < 5 : 46
        Backbone-backbone: 36
        Backbone-side chain: 10
        Long range restraints, | i - j | >= 5 : 7
        Total hydrogen bond restraints: 6
      - Weight of restraints: 1.0 (77)
        Sequential restraints, | i - j | = 1 : 1.0 (18)
        Backbone-backbone: 1.0 (18)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (46)
        Backbone-backbone: 1.0 (36)
        Backbone-side chain: 1.0 (10)
        Long range restraints, | i - j | >= 5 : 1.0 (7)
        Total hydrogen bond restraints: 1.0 (6)
      - Potential type of restraints: upper-bound-parabolic (77)
        Sequential restraints, | i - j | = 1 : upper-bound-parabolic (18)
        Backbone-backbone: upper-bound-parabolic (18)
        Medium range restraints, 1 < | i - j | < 5 : upper-bound-parabolic (46)
        Backbone-backbone: upper-bound-parabolic (36)
        Backbone-side chain: upper-bound-parabolic (10)
        Long range restraints, | i - j | >= 5 : upper-bound-parabolic (7)
        Total hydrogen bond restraints: upper-bound-parabolic (6)
      - Range of distance target values: 2.0, 5.0 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
        Chain_ID: C
        None
        Chain_ID: D
        None
      - Distance restraints on contact map
      - Saveframe: DYANA/DIANA_distance_constraints_10
        Status: OK
        Experiment type: undefined
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 76.5%
        --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 ASEKRPFMCAYPGCNKRYFKLSHLQMHSRKHTGEKPYQCDFKDCERRFSRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGEKPFSCRWP ||| | | ||||||||||||||||| | ||| | | ||| |||||||||| || | ||| |||||||||||||||||||| || ||||| ......FMC.Y..C.KRYFKLSHLQMHSRKHT.E..YQC.F..C.RRF.RSDQLKRHQR.HT..K.FQC.TCQRKFSRSDHLKTHTRTHT.EK.FSCRW. -------110--------- SCQKKFARSDELVRHHNMH | |||||||||||||||| .C.KKFARSDELVRHHNMH
        Total number of restraints: 405
        Medium range restraints, 1 < | i - j | < 5 : 119
        Backbone-backbone: 13
        Backbone-side chain: 53
        Side chain-side chain: 53
        Long range restraints, | i - j | >= 5 : 286
        Weight of restraints: 1.0 (405)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (119)
        Backbone-backbone: 1.0 (13)
        Backbone-side chain: 1.0 (53)
        Side chain-side chain: 1.0 (53)
        Long range restraints, | i - j | >= 5 : 1.0 (286)
        Potential type of restraints: upper-bound-parabolic (405)
        Medium range restraints, 1 < | i - j | < 5 : upper-bound-parabolic (119)
        Backbone-backbone: upper-bound-parabolic (13)
        Backbone-side chain: upper-bound-parabolic (53)
        Side chain-side chain: upper-bound-parabolic (53)
        Long range restraints, | i - j | >= 5 : upper-bound-parabolic (286)
        Range of distance target values: 3.3, 5.0 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
        Chain_ID: C
        None
        Chain_ID: D
        None
        Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
        Saveframe: DYANA/DIANA_distance_constraints_3
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 10.1%
        Total number of restraints: 16
        Total hydrogen bond restraints: 16
        O...H-x: 8
        O...h-N: 8
        Weight of restraints: 1.0 (16)
        Total hydrogen bond restraints: 1.0 (16)
        O...H-x: 1.0 (8)
        O...h-N: 1.0 (8)
        Potential type of restraints: upper-bound-parabolic (16)
        Total hydrogen bond restraints: upper-bound-parabolic (16)
        O...H-x: upper-bound-parabolic (8)
        O...h-N: upper-bound-parabolic (8)
        Range of distance target values: 2.0, 3.0 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
        Chain_ID: C
        None
        Chain_ID: D
        None
        Distance restraints on contact map
        Saveframe: DYANA/DIANA_distance_constraints_5
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 10.1%
        Total number of restraints: 16
        Total hydrogen bond restraints: 16
        O...H-x: 8
        O...h-N: 8
        Weight of restraints: 1.0 (16)
        Total hydrogen bond restraints: 1.0 (16)
        O...H-x: 1.0 (8)
        O...h-N: 1.0 (8)
        Potential type of restraints: upper-bound-parabolic (16)
        Total hydrogen bond restraints: upper-bound-parabolic (16)
        O...H-x: upper-bound-parabolic (8)
        O...h-N: upper-bound-parabolic (8)
        Range of distance target values: 2.0, 3.0 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
        Chain_ID: C
        None
        Chain_ID: D
        None
        Distance restraints on contact map
        Saveframe: DYANA/DIANA_distance_constraints_9
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 10.1%
        Total number of restraints: 16
        Total hydrogen bond restraints: 16
        O...H-x: 8
        O...h-N: 8
        Weight of restraints: 1.0 (16)
        Total hydrogen bond restraints: 1.0 (16)
        O...H-x: 1.0 (8)
        O...h-N: 1.0 (8)
        Potential type of restraints: upper-bound-parabolic (16)
        Total hydrogen bond restraints: upper-bound-parabolic (16)
        O...H-x: upper-bound-parabolic (8)
        O...h-N: upper-bound-parabolic (8)
        Range of distance target values: 2.0, 3.0 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
        Chain_ID: C
        None
        Chain_ID: D
        None
        Distance restraints on contact map
        Saveframe: DYANA/DIANA_distance_constraints_11
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 53.8%
        --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 ASEKRPFMCAYPGCNKRYFKLSHLQMHSRKHTGEKPYQCDFKDCERRFSRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGEKPFSCRWP | | | | |||||||||||| | | | | |||||||||||| | | | | |||||||||||| | | ......F.C......K.Y.KLSHLQMHSRKH.....Y.C......R.F.RSDQLKRHQRRH.....F.C....R.F.RSDHLKTHTRTH.....F.C... -------110--------- SCQKKFARSDELVRHHNMH | | |||||||||||| ...K.F.RSDELVRHHNMH
        Total number of restraints: 88
        Total hydrogen bond restraints: 88
        O...H-x (too close!): 33
        O...h-N (too close!): 33
        Long range: 22
        O...H-x (too close!): 11
        O...h-N: 8
        O...h-N (too close!): 3
        Weight of restraints: 1.0 (88)
        Total hydrogen bond restraints: 1.0 (88)
        O...H-x (too close!): 1.0 (33)
        O...h-N (too close!): 1.0 (33)
        Long range: 1.0 (22)
        O...H-x (too close!): 1.0 (11)
        O...h-N: 1.0 (8)
        O...h-N (too close!): 1.0 (3)
        Potential type of restraints: upper-bound-parabolic (88)
        Total hydrogen bond restraints: upper-bound-parabolic (88)
        O...H-x (too close!): upper-bound-parabolic (33)
        O...h-N (too close!): upper-bound-parabolic (33)
        Long range: upper-bound-parabolic (22)
        O...H-x (too close!): upper-bound-parabolic (11)
        O...h-N: upper-bound-parabolic (8)
        O...h-N (too close!): upper-bound-parabolic (3)
        Range of distance target values: 1.8, 3.0 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
        Chain_ID: C
        None
        Chain_ID: D
        None
        Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
        Saveframe: DYANA/DIANA_distance_constraints_7
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 10.1%
        Total number of restraints: 16
        Total hydrogen bond restraints: 16
        O...H-x: 8
        O...h-N: 8
        Weight of restraints: 1.0 (16)
        Total hydrogen bond restraints: 1.0 (16)
        O...H-x: 1.0 (8)
        O...h-N: 1.0 (8)
        Potential type of restraints: upper-bound-parabolic (16)
        Total hydrogen bond restraints: upper-bound-parabolic (16)
        O...H-x: upper-bound-parabolic (8)
        O...h-N: upper-bound-parabolic (8)
        Range of distance target values: 2.0, 3.0 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
        Chain_ID: C
        None
        Chain_ID: D
        None
        Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_12
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 63.9%
- Total number of restraints: 104
- Total number of restraints per polymer type: 104
- Weight of restraints: 1.0 (104)
- Potential type of restraints: square-well-parabolic (104)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA binding, NMR, nucleic acid recognition, residual dipolar coupling, X-ray, zinc finger

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Found 1 Document (1.076 seconds)

BMRB: 15532

Sample

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

Related entities 1. wt1-17mer, : 1 : 2 : 2 : 5 : 428 entities Detail

Interaction partners 1. wt1-17mer, : 14 interactors Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 13 contents Detail