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BMRB: 16485

2KO0

Solution structure of the THAP zinc finger of THAP1 in complex with its DNA target

Authors

Campagne, S., Gervais, V., Saurel, O., Milon, A.

Assembly

THAP RRM1

Entity

1. THAP domain (polymer, Thiol state: free and other bound), 87 monomers, 10170.62 Da Detail

MVQSCSAYGC KNRYDKDKPV SFHKFPLTRP SLCKEWEAAV RRKNFKPTKY SSICSEHFTP DSFKRESNNK LLKENAVPTI FLELVPR

2. RRM1 (polymer, Thiol state: not present), 32 monomers, 9907.274 Da Detail

GCTTGTGTGG GCAGCGCGCT GCCCACACAA GC

3. ZN (non-polymer), 65.409 Da

Total weight

20143.303 Da

Max. entity weight

10170.62 Da

Entity Connection

na 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS5:SG	3:ZN1:ZN
2	na	sing	1:CYS10:SG	3:ZN1:ZN
3	na	sing	1:CYS54:SG	3:ZN1:ZN
4	na	sing	1:HIS57:HE2	3:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

Rigid body docking, Semi flexible simulated annealing, Water refinement

Data set

RDCs, assigned_chemical_shifts, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation

Chem. Shift Complete1

Sequence coverage: 73.1 %, Completeness: 70.1 %, Completeness (bb): 67.3 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	70.1 % (974 of 1389)	60.6 % (536 of 885)	85.1 % (355 of 417)	95.4 % (83 of 87)
Backbone	67.3 % (493 of 732)	42.9 % (168 of 392)	95.0 % (247 of 260)	97.5 % (78 of 80)
Sidechain	76.2 % (566 of 743)	74.6 % (368 of 493)	79.4 % (193 of 243)	71.4 % (5 of 7)
Aromatic	36.9 % (62 of 168)	37.9 % (44 of 116)	33.3 % (17 of 51)	100.0 % (1 of 1)
Methyl	89.0 % (65 of 73)	84.6 % (33 of 39)	94.1 % (32 of 34)

1. THAP domain

MVQSCSAYGC KNRYDKDKPV SFHKFPLTRP SLCKEWEAAV RRKNFKPTKY SSICSEHFTP DSFKRESNNK LLKENAVPTI FLELVPR

2. RRM1

GCTTGTGTGG GCAGCGCGCT GCCCACACAA GC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N13C uniformly labelled THAP domain and unlabelled DNA (protein:DNA 1:1 at 1mM)

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details Unlabelled DNA and protein

#	Name	Isotope labeling	Concentration
6	THAP domain	natural abundance	1 mM
7	RRM1	natural abundance	1 mM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %
10	NaCl	natural abundance	30 mM

Chem. Shift Complete2

Sequence coverage: 40.3 %, Completeness: 49.8 %, Completeness (bb): 52.6 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	49.8 % (1383 of 2778)	50.1 % (886 of 1770)	48.0 % (400 of 834)	55.7 % (97 of 174)
Backbone	52.6 % (770 of 1464)	50.1 % (393 of 784)	54.8 % (285 of 520)	57.5 % (92 of 160)
Sidechain	48.0 % (713 of 1486)	50.1 % (494 of 986)	44.0 % (214 of 486)	35.7 % (5 of 14)
Aromatic	39.6 % (133 of 336)	48.3 % (112 of 232)	19.6 % (20 of 102)	50.0 % (1 of 2)
Methyl	51.4 % (75 of 146)	51.3 % (40 of 78)	51.5 % (35 of 68)

1. THAP domain

MVQSCSAYGC KNRYDKDKPV SFHKFPLTRP SLCKEWEAAV RRKNFKPTKY SSICSEHFTP DSFKRESNNK LLKENAVPTI FLELVPR

2. RRM1

GCTTGTGTGG GCAGCGCGCT GCCCACACAA GC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N13C uniformly labelled THAP domain and unlabelled DNA (protein:DNA 1:1 at 1mM)

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details Unlabelled DNA and protein

#	Name	Isotope labeling	Concentration
6	THAP domain	natural abundance	1 mM
7	RRM1	natural abundance	1 mM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %
10	NaCl	natural abundance	30 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.37 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.37 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 2KO0, Strand ID: A Detail

Heteronucl. T₁

73 T₁ values in 1 lists
Coherence Sz, Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 296 K, pH 6.8 Detail

Heteronucl. T₂

73 T₂ values in 1 lists
Coherence S(+,-), Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 296 K, pH 6.8 Detail

Heteronucl. NOE

73 NOE values in 1 lists
Value type relative intensities, Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 296 K, pH 6.8 Detail

Heteronucl. T₁/T₂

73 T₁/T₂ values in 1 lists
Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 296 K, pH 6.8 Detail

RDC

53 RDC values in 1 lists
Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 296 K, pH 6.8 Detail

Release date

2009-09-07

Citation

Structural determinants of specific DNA-recognition by the THAP zinc finger
Campagne, S., Saurel, O., Gervais, V., Milon, A.
Nucleic Acids Res. (2010), 38, 3466-3476, PubMed 20144952 , DOI 10.1093/nar/gkq053 , Abstract

Related entities 1. THAP domain, : 1 : 1 : 4 : 71 entities Detail

Experiments performed 14 experiments Detail

1 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N13C uniformly labelled THAP domain and unlabelled DNA (protein:DNA 1:1 at 1mM)

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

3 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

4 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 950 MHz EU NMR (Frankfort)

Sample

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

6 3D 1H-13C NOESY

Instrument

Bruker Avance - 950 MHz EU NMR (Frankfort)

Sample

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

7 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

8 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

9 2D 1H-1H NOESY

Instrument

Bruker Avance - 950 MHz EU NMR (Frankfort)

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details Unlabelled DNA and protein

#	Name	Isotope labeling	Concentration
6	THAP domain	natural abundance	1 mM
7	RRM1	natural abundance	1 mM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %
10	NaCl	natural abundance	30 mM

10 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details Unlabelled DNA and protein

#	Name	Isotope labeling	Concentration
6	THAP domain	natural abundance	1 mM
7	RRM1	natural abundance	1 mM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %
10	NaCl	natural abundance	30 mM

11 2D IPAP 15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

12 2D 15N HSQC T1

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

13 2D 15N HSQC T2

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

14 2D 15N HSQC Heteronuclear NOE

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	THAP domain	[U-100% 13C; U-100% 15N]	1 mM
2	RRM1	natural abundance	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	NaCl	natural abundance	30 mM

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16485_2ko0.nef
Input source #2: Coordindates	2ko0.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)
1:5:CYS:SG	4:1:ZN:ZN	unknown	unknown	n/a
1:10:CYS:SG	4:1:ZN:ZN	unknown	unknown	n/a
1:54:CYS:SG	4:1:ZN:ZN	unknown	unknown	n/a
1:57:HIS:NE2	4:1: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

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80-------
MVQSCSAYGCKNRYDKDKPVSFHKFPLTRPSLCKEWEAAVRRKNFKPTKYSSICSEHFTPDSFKRESNNKLLKENAVPTIFLELVPR
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MVQSCSAYGCKNRYDKDKPVSFHKFPLTRPSLCKEWEAAVRRKNFKPTKYSSICSEHFTPDSFKRESNNKLLKENAVPTIFLELVPR

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

-------110---------10-----------
CAAGGACCCCGGCTTGTGTGGGCAGCGCTCAC
           ||||||||||||||||     
...........GCTTGTGTGGGCAGCG     
-------------------10------

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

--20--------30--
CGCTGCCCACACAAGC
||||||||||||||||
CGCTGCCCACACAAGC
--------10------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	87	0	0	100.0
C	C	16	0	0	100.0

Content subtype: combined_16485_2ko0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	974		100.0 (chain: A, length: 87)
2	Assigned chemical shifts	Assigned_chem_shifts_list_2	OK	295		53.1 (chain: B, length: 32)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1936 (1)	noe	98.9 (chain: A, length: 87)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	6 (1)	undefined	4.6 (chain: A, length: 87)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	752 (1)	noe	35.6 (chain: A, length: 87), 50.0 (chain: B, length: 32), 100.0 (chain: C, length: 16)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	156 (156)	.	100.0 (chain: A, length: 87)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 539
  - ¹³C chemical shifts: 351
  - ¹⁵N chemical shifts: 84
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
Saveframe: Assigned_chem_shifts_list_2
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 32, Sequence coverage: 53.1%
- Total number of assignments
  - ¹H chemical shifts: 295
- Completeness of assignments
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
29	ARG	HH11	6.689
29	ARG	HH12	6.689
29	ARG	NH1	109.273
65	ARG	HH11	6.998
65	ARG	HH12	6.998
65	ARG	NH1	100.904

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	570	534	93.7
¹³C chemical shifts	417	351	84.2
¹⁵N chemical shifts	93	82	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	168	166	98.8
¹³C chemical shifts	174	159	91.4
¹⁵N chemical shifts	80	77	96.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	402	368	91.5
¹³C chemical shifts	243	192	79.0
¹⁵N chemical shifts	13	5	38.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	34	97.1
¹³C chemical shifts	35	33	94.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	44	84.6
¹³C chemical shifts	51	17	33.3
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 98.9%
- Total number of restraints: 1927
- Weight of restraints: 1.0 (1927)
- Potential type of restraints: lower-bound-parabolic (1), square-well-parabolic (1926)
- Range of distance target values: 1.85, 6.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in 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: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 4.6%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: square-well-parabolic (6)
  - Range of distance target values: 3.52, 3.81 (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: CNS/XPLOR_distance_constraints_4
    - Status: OK
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 35.6%
      - Entity_assembly_ID: B, Chain length: 32, Sequence coverage: 50.0%
      - Entity_assembly_ID: C, Chain length: 16, Sequence coverage: 100.0%
    - Total number of restraints: 752
    - Weight of restraints: 1.0 (752)
    - Potential type of restraints: square-well-parabolic (752)
    - Range of distance target values: 1.7, 5.5 (Å)
    - Histogram of distance target values
    - Histogram of discrepancy in distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
      - Chain_ID: C
      - Chain_ID: D
        None
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 100.0%
- Total number of restraints: 156
- Total number of restraints per polymer type: 156
- Weight of restraints: 1.0 (156)
- Potential type of restraints: square-well-parabolic (156)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA binding domain, Protein-DNA complex, transcription factor, zinc finger, CCCH, Transcription factor, Zinc finger

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Found 1 Document (0.757 seconds)

BMRB: 16485

Sample #1

Sample #2

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. THAP domain, : 1 : 1 : 4 : 71 entities Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 7 contents Detail