BMRB Entry 16778

Name: Solution structure of the CBX7 chromodomain in complex with a H3K27me2 peptide
Published: 2011-05-26

Click here to enlarge.

PDB ID: 2kvm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16778
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Solution structure of the CBX7 chromodomain in complex with a H3K27me2 peptide

Deposition date:

2010-03-17

Original release date:

2011-05-26

Authors:

Yap, Kyoko; Zeng, Lei; Zhou, Ming-Ming

Citation:

Citation: Yap, Kyoko; Li, Side; Munoz-Cabello, Ana; Raguz, Selina; Zeng, Lei; Mujtaba, Shiraz; Gil, Jesus; Walsh, Martin; Zhou, Ming-Ming. "Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a" Mol. Cell 38, 662-674 (2010).
PubMed: 20541999

Assembly members:

Assembly members:
CBX7_chromodomain, polymer, 71 residues, 8555.949 Da.
H3K27me2_peptide, polymer, 16 residues, 1726.093 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CBX7_chromodomain: MELSAIGEQVFAVESIRKKR VRKGKVEYLVKWKGWPPKYS TWEPEEHILDPRLVMAYEEK EERDRASGYRK
H3K27me2_peptide: APRKQLATKAARXSAP

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	308
15N chemical shifts	68
1H chemical shifts	631

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CBX7_chromodomain	1
2	H3K27me2_peptide	2

Entities:

Entity 1, CBX7_chromodomain 71 residues - 8555.949 Da.

1

MET

GLU

LEU

SER

ALA

ILE

GLY

GLU

GLN

VAL

2

PHE

ALA

VAL

GLU

SER

ILE

ARG

LYS

ARG

3

VAL

ARG

LYS

GLY

LYS

VAL

GLU

TYR

LEU

VAL

4

LYS

TRP

LYS

GLY

TRP

PRO

LYS

TYR

SER

5

THR

TRP

GLU

PRO

GLU

HIS

ILE

LEU

ASP

6

PRO

ARG

LEU

VAL

MET

ALA

TYR

GLU

LYS

7

GLU

ARG

ASP

ARG

ALA

SER

GLY

TYR

ARG

8

LYS

Entity 2, H3K27me2_peptide 16 residues - 1726.093 Da.

1

ALA

PRO

ARG

LYS

GLN

LEU

ALA

THR

LYS

ALA

2

ALA

ARG

MLY

SER

ALA

PRO

Samples:

sample_1: CBX7 chromodomain, [U-100% 15N], 0.5 mM; H3K27me2 peptide 0.75 mM; sodium phosphate 4.3 mM; potassium phosphate 1.4 mM; DTT 5 mM; sodium chloride 137 mM; potassium chloride 3 mM; H2O 90%; D2O 10%

sample_2: CBX7 chromodomain, [U-100% 13C; U-100% 15N], 0.5 mM; H3K27me2 peptide 0.75 mM; sodium phosphate 4.3 mM; potassium phosphate 1.4 mM; DTT 5 mM; sodium chloride 137 mM; potassium chloride 3 mM; H2O 90%; D2O 10%

sample_3: H3K27me2 peptide 0.5 mM; sodium phosphate 4.3 mM; potassium phosphate 1.4 mM; DTT 5 mM; sodium chloride 137 mM; potassium chloride 3 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 140 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1

Software:

ARIA v2.0, Linge, O'Donoghue and Nilges - chemical shift assignment, structure solution

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

TALOS, Cornilescu, Delaglio and Bax - data analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

NMR spectrometers:

Bruker DRX 500 MHz
Bruker Avance 800 MHz
Bruker DRX 600 MHz

BMRB	15674 17072 17079 6997
PDB	2K1B 2KVM 2L12 2L1B 4MN3 1PDQ 2G46 2KVM 3N9P
DBJ	BAI46775 BAM62356
GB	AAH21398 AAH51773 AAH62392 AAR26721 AAX94038 AAY18719 ABB83163 ABL95239 ABL95241 ABN80289
REF	NP_001179547 NP_001247702 NP_659060 NP_783640 NP_954548
SP	O95931 P60889 Q8VDS3
TPG	DAA29144
AlphaFold	O95931 P60889 Q8VDS3