BMRB Entry 19913

Name: NMR Structure of KDM5B PHD1 finger
Published: 2014-08-04

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PDB ID: 2mny
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19913
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR Structure of KDM5B PHD1 finger

Deposition date:

2014-04-16

Original release date:

2014-08-04

Authors:

Zhang, Y.; Yang, H.; Guo, X.; Rong, N.; Song, Y.; Xu, Y.; Lan, W.; Xu, Y.; Cao, C.

Citation:

Citation: Zhang, Y.; Yang, H.; Guo, X.; Rong, N.; Song, Y.; Xu, Y.; Lan, W.; Xu, Y.; Cao, C.. "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:
PHD1_finger_of_KDM5B, polymer, 55 residues, 6133.026 Da.
ZINC ION, non-polymer, 65.409 Da.

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):
PHD1_finger_of_KDM5B: AVDLYVCLLCGSGNDEDRLL LCDGCDDSYHTFCLIPPLHD VPKGDWRCPKCLAQE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	189
15N chemical shifts	51
1H chemical shifts	301

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PHD1 finger of KDM5B	1
2	ZINC ION_1	2
3	ZINC ION_2	2

Entities:

Entity 1, PHD1 finger of KDM5B 55 residues - 6133.026 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

Samples:

sample_1: PHD1 finger of KDM5B, [U-13C; U-15N], 0.8 mM; Phosphate buffer 50 mM; D2O 10%; H2O 90%

sample_2: PHD1 finger of KDM5B, [U-13C; U-15N], 0.8 mM; Phosphate buffer 50 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 7.2; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D_15N-separated_NOESY	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1

Software:

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

NMR spectrometers:

Agilent DD2 600 MHz

BMRB	19914
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