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BMRB: 30705

6VFO

Solution structure of the PHD of mouse UHRF1 (NP95)

Authors

Lemak, A., Houliston, S., Duan, S., Arrowsmith, C.H.

Assembly

E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27)

Entity

1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), entity 1 (polymer, Thiol state: all other bound), 78 monomers, 8682.809 Da Detail

SGPSCRFCKD DENKPCRKCA CHVCGGREAP EKQLLCDECD MAFHLYCLKP PLTSVPPEPE WYCPSCRTDS SEVVQAGE

2. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), entity ZN (non-polymer), 65.409 × 3 Da

Total weight

8879.035 Da

Max. entity weight

8682.809 Da

Entity Connection

na 13 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS5:SG	2:ZN1:ZN
2	na	sing	1:CYS8:SG	2:ZN1:ZN
3	na	sing	1:CYS16:SG	2:ZN1:ZN
4	na	sing	1:CYS19:SG	2:ZN1:ZN
5	na	sing	1:CYS21:SG	2:ZN1:ZN
6	na	sing	1:CYS24:SG	2:ZN1:ZN
7	na	sing	1:HIS44:ND1	2:ZN1:ZN
8	na	sing	1:CYS47:SG	2:ZN1:ZN
9	na	sing	1:CYS36:SG	2:ZN1:ZN
10	na	sing	1:GLU38:OE2	2:ZN1:ZN
11	na	sing	1:CYS39:SG	2:ZN1:ZN
12	na	sing	1:CYS63:SG	2:ZN1:ZN
13	na	sing	1:CYS66:SG	2:ZN1:ZN

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.8 %, Completeness (bb): 96.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.8 % (820 of 865)	96.5 % (441 of 457)	91.9 % (308 of 335)	97.3 % (71 of 73)
Backbone	96.0 % (432 of 450)	98.7 % (149 of 151)	93.5 % (215 of 230)	98.6 % (68 of 69)
Sidechain	91.8 % (449 of 489)	93.1 % (285 of 306)	89.9 % (161 of 179)	75.0 % (3 of 4)
Aromatic	67.9 % (38 of 56)	82.1 % (23 of 28)	51.9 % (14 of 27)	100.0 % (1 of 1)
Methyl	91.7 % (44 of 48)	91.7 % (22 of 24)	91.7 % (22 of 24)

1. entity 1

SGPSCRFCKD DENKPCRKCA CHVCGGREAP EKQLLCDECD MAFHLYCLKP PLTSVPPEPE WYCPSCRTDS SEVVQAGE

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 290 K, pH 7.5, Details 200 uM [U-99% 13C; U-99% 15N] PHD, 5 mM DTT, 2 mM beta-mercaptoethanol, 5 mM TCEP, 150 mM sodium chloride, 50 mM sodium phosphate, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PHD	[U-99% 13C; U-99% 15N]	200 uM
2	DTT	natural abundance	5 mM
3	beta-mercaptoethanol	natural abundance	2 mM
4	TCEP	natural abundance	5 mM
5	sodium chloride	natural abundance	150 mM
6	sodium phosphate	natural abundance	50 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6VFO, Strand ID: A Detail

Release date

2020-05-05

Citation

Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1
Tauber, M., Kreuz, S., Lemak, A., Mandal, P., Yerkesh, Z., Veluchamy, A., Al-Gashgari, B., Aljahani, A., Cortes-Medina, L.V., Azhibek, D., Fan, L., Ong, M.S., Duan, S., Houliston, S., Arrowsmith, C.H., Fischle, W.
Nucleic Acids Res. (2020), 48, 7728-7747, PubMed 32609811 , DOI 10.1093/nar/gkaa520 , Abstract

Related entities 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), entity 1, : 1 : 2 : 37 entities Detail

Interaction partners 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), entity 1, : 4 interactors Detail

More details for 4 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE II - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 290 K, pH 7.5, Details 200 uM [U-99% 13C; U-99% 15N] PHD, 5 mM DTT, 2 mM beta-mercaptoethanol, 5 mM TCEP, 150 mM sodium chloride, 50 mM sodium phosphate, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PHD	[U-99% 13C; U-99% 15N]	200 uM
2	DTT	natural abundance	5 mM
3	beta-mercaptoethanol	natural abundance	2 mM
4	TCEP	natural abundance	5 mM
5	sodium chloride	natural abundance	150 mM
6	sodium phosphate	natural abundance	50 mM

2 2D 1H-13C HSQC

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PHD	[U-99% 13C; U-99% 15N]	200 uM
2	DTT	natural abundance	5 mM
3	beta-mercaptoethanol	natural abundance	2 mM
4	TCEP	natural abundance	5 mM
5	sodium chloride	natural abundance	150 mM
6	sodium phosphate	natural abundance	50 mM

3 3D HNCO

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PHD	[U-99% 13C; U-99% 15N]	200 uM
2	DTT	natural abundance	5 mM
3	beta-mercaptoethanol	natural abundance	2 mM
4	TCEP	natural abundance	5 mM
5	sodium chloride	natural abundance	150 mM
6	sodium phosphate	natural abundance	50 mM

4 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PHD	[U-99% 13C; U-99% 15N]	200 uM
2	DTT	natural abundance	5 mM
3	beta-mercaptoethanol	natural abundance	2 mM
4	TCEP	natural abundance	5 mM
5	sodium chloride	natural abundance	150 mM
6	sodium phosphate	natural abundance	50 mM

5 3D HNCA

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PHD	[U-99% 13C; U-99% 15N]	200 uM
2	DTT	natural abundance	5 mM
3	beta-mercaptoethanol	natural abundance	2 mM
4	TCEP	natural abundance	5 mM
5	sodium chloride	natural abundance	150 mM
6	sodium phosphate	natural abundance	50 mM

6 3D HCCH-TOCSY

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PHD	[U-99% 13C; U-99% 15N]	200 uM
2	DTT	natural abundance	5 mM
3	beta-mercaptoethanol	natural abundance	2 mM
4	TCEP	natural abundance	5 mM
5	sodium chloride	natural abundance	150 mM
6	sodium phosphate	natural abundance	50 mM

7 3D 1H-15N NOESY

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PHD	[U-99% 13C; U-99% 15N]	200 uM
2	DTT	natural abundance	5 mM
3	beta-mercaptoethanol	natural abundance	2 mM
4	TCEP	natural abundance	5 mM
5	sodium chloride	natural abundance	150 mM
6	sodium phosphate	natural abundance	50 mM

8 3D 1H-13C NOESY aromatic

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PHD	[U-99% 13C; U-99% 15N]	200 uM
2	DTT	natural abundance	5 mM
3	beta-mercaptoethanol	natural abundance	2 mM
4	TCEP	natural abundance	5 mM
5	sodium chloride	natural abundance	150 mM
6	sodium phosphate	natural abundance	50 mM

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PHD	[U-99% 13C; U-99% 15N]	200 uM
2	DTT	natural abundance	5 mM
3	beta-mercaptoethanol	natural abundance	2 mM
4	TCEP	natural abundance	5 mM
5	sodium chloride	natural abundance	150 mM
6	sodium phosphate	natural abundance	50 mM

10 3D HBHA(CO)NH

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PHD	[U-99% 13C; U-99% 15N]	200 uM
2	DTT	natural abundance	5 mM
3	beta-mercaptoethanol	natural abundance	2 mM
4	TCEP	natural abundance	5 mM
5	sodium chloride	natural abundance	150 mM
6	sodium phosphate	natural abundance	50 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30705_6vfo.nef
Input source #2: Coordindates	6vfo.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	2:1:ZN:ZN	unknown	unknown	n/a
1:8:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:16:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:19:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:21:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:24:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:36:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:38:GLU:OE2	2:3:ZN:ZN	unknown	unknown	n/a
1:39:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:44:HIS:ND1	2:2:ZN:ZN	unknown	unknown	n/a
1:47:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:63:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:66:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a

Non-standard residues

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

Sequence alignments

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

-----310-------320-------330-------340-------350-------360-------370-------380
SGPSCRFCKDDENKPCRKCACHVCGGREAPEKQLLCDECDMAFHLYCLKPPLTSVPPEPEWYCPSCRTDSSEVVQAGE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SGPSCRFCKDDENKPCRKCACHVCGGREAPEKQLLCDECDMAFHLYCLKPPLTSVPPEPEWYCPSCRTDSSEVVQAGE
--------10--------20--------30--------40--------50--------60--------70--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	78	0	0	100.0

Content subtype: combined_30705_6vfo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	13		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	814		100.0 (chain: A, length: 78)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	6 (1)	hbond	5.1 (chain: A, length: 78)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	107 (107)	.	98.7 (chain: A, length: 78)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 440
  - ¹³C chemical shifts: 303
  - ¹⁵N chemical shifts: 71
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	457	439	96.1
¹³C chemical shifts	335	303	90.4
¹⁵N chemical shifts	77	71	92.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	151	149	98.7
¹³C chemical shifts	156	140	89.7
¹⁵N chemical shifts	69	68	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	306	290	94.8
¹³C chemical shifts	179	163	91.1
¹⁵N chemical shifts	8	3	37.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	23	92.0
¹³C chemical shifts	25	23	92.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	22	78.6
¹³C chemical shifts	27	13	48.1
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: hbond
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 5.1%
- Total number of restraints: 6
- Weight of restraints: 1.0 (6)
- Potential type of restraints: square-well-parabolic (6)
- Range of distance target values: 2.05, 3.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 98.7%
- Total number of restraints: 107
- Total number of restraints per polymer type: 107
- Weight of restraints: 1.0 (107)
- Potential type of restraints: square-well-parabolic (107)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords H3K9me3, Histone, NP95, PEPTIDE BINDING PROTEIN, Plant Homeodomain

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Found 1 Document (0.566 seconds)

BMRB: 30705

Sample

Related entities 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), entity 1, : 1 : 2 : 37 entities Detail

Interaction partners 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), entity 1, : 4 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 4 contents Detail