BMRB Entry 19914

Name: NMR Structure of KDM5B PHD1 finger in complex with H3K4me0(1-10aa)
Published: 2014-08-04

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PDB ID: 2mnz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19914
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR Structure of KDM5B PHD1 finger in complex with H3K4me0(1-10aa)

Deposition date:

2014-04-16

Original release date:

2014-08-04

Authors:

Zhang, Yan; Yang, Huirong; Guo, Xue; Rong, Naiyan; Song, Yujiao; Xu, Youwei; Lan, Wenxian; Xu, Yanhui; Cao, Chunyang

Citation:

Citation: Zhang, Yan; Yang, Huirong; Guo, Xue; Rong, Naiyan; Rong, Yujiao; Xu, Youwei; Lan, Wenxian; Xu, Yanhui; Cao, Chunyang. "The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B" Protein Cell ., .-. (2014).
PubMed: 24952722

Assembly members:

Assembly members:
entity_1, polymer, 55 residues, 7360.083 Da.
ZINC ION, non-polymer, 65.409 Da.
entity_3, polymer, 10 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-6p-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AVDLYVCLLCGSGNDEDRLL LCDGCDDSYHTFCLIPPLHD VPKGDWRCPKCLAQE
entity_3: ARTKQTARKS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	165
15N chemical shifts	51
1H chemical shifts	396

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	ZINC ION_1	2
3	ZINC ION_2	2
4	H3K4me0(1-10aa)	3

Entities:

Entity 1, entity_1 55 residues - 7360.083 Da.

1

ALA

VAL

ASP

LEU

TYR

VAL

CYS

LEU

CYS

2

GLY

SER

GLY

ASN

ASP

GLU

ASP

ARG

LEU

3

LEU

CYS

ASP

GLY

CYS

ASP

SER

TYR

HIS

4

THR

PHE

CYS

LEU

ILE

PRO

LEU

HIS

ASP

5

VAL

PRO

LYS

GLY

ASP

TRP

ARG

CYS

PRO

LYS

6

CYS

LEU

ALA

GLN

GLU

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Entity 3, H3K4me0(1-10aa) 10 residues - Formula weight is not available

1

ALA

ARG

THR

LYS

GLN

THR

ALA

ARG

LYS

SER

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 0.8 – 2 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.1 M; pH: 7.4; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

NMR spectrometers:

Varian INOVA 600 MHz

BMRB	19913
PDB	2MNY 2MNZ
DBJ	BAC30898 BAD90482 BAE37363 BAE89761 BAG53706
EMBL	CAB43532 CAB61368 CAB63108 CAH65222
GB	AAD16061 AAH48180 AAH57318 AAI56050 AAI57032
REF	NP_001026200 NP_001100647 NP_001300971 NP_006609 NP_690855
SP	Q5F3R2 Q80Y84 Q9UGL1
TPG	DAA21261
AlphaFold	Q5F3R2 Q80Y84 Q9UGL1