BMRB Entry 11606

Name: Solution structure of the chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide
Published: 2021-07-16

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PDB ID: 2rvn
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR11606
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: Solution structure of the chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide PubMed: 26934956

Deposition date: 2015-12-18 Original release date: 2021-07-16

Authors: Kawaguchi, Ayumi; Nishimura, Yoshifumi

Citation: Shimojo, Hideaki; Kawaguchi, Ayumi; Oda, Takashi; Hashiguchi, Nobuto; Omori, Satoshi; Moritsugu, Kei; Kidera, Akinori; Hiragami-Hamada, Kyoko; Nakayama, Jun-Ichi; Sato, Mamoru; Nishimura, Yoshifumi. "Extended string-like binding of the phosphorylated HP1? N-terminal tail to the lysine 9-methylated histone H3 tail" Sci. Rep. 6, 22527-22527 (2016).

Assembly members:
entity_1, polymer, 83 residues, 10169.125 Da.
entity_2, polymer, 18 residues, 2025.379 Da.

Natural source: Common Name: Mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

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

Entity Sequences (FASTA):
entity_1: GSHMGKKTKRTADXXXXEDE EEYVVEKVLDRRMVKGQVEY LLKWKGFSEEHNTWEPEKNL DCPELISEFMKKYKKMKEGE NNK
entity_2: ARTKQTARXSTGGKAPRY

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	372
15N chemical shifts	88
1H chemical shifts	651

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	entity_2	2

Entities:

Entity 1, entity_1 83 residues - 10169.125 Da.

1

GLY

SER

HIS

MET

GLY

LYS

THR

LYS

ARG

2

THR

ALA

ASP

SEP

GLU

ASP

GLU

3

GLU

TYR

VAL

GLU

LYS

VAL

LEU

ASP

4

ARG

MET

VAL

LYS

GLY

GLN

VAL

GLU

TYR

5

LEU

LYS

TRP

LYS

GLY

PHE

SER

GLU

6

HIS

ASN

THR

TRP

GLU

PRO

GLU

LYS

ASN

LEU

7

ASP

CYS

PRO

GLU

LEU

ILE

SER

GLU

PHE

MET

8

LYS

TYR

LYS

MET

LYS

GLU

GLY

GLU

9

ASN

LYS

Entity 2, entity_2 18 residues - 2025.379 Da.

1

ALA

ARG

THR

LYS

GLN

THR

ALA

ARG

M3L

SER

2

THR

GLY

LYS

ALA

PRO

ARG

TYR

Samples:

sample_1: HP1alpha, [U-99% 13C; U-99% 15N], mM; H3K9me3, [U-99% 13C; U-99% 15N], mM; potassium phosphate 20 mM; sodium chloride 10 mM; DTT 5 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: HP1alpha, [U-99% 13C; U-99% 15N], mM; H3K9me3, [U-99% 13C; U-99% 15N], mM; potassium phosphate, "natural abundance, 20 mM; sodium chloride 10 mM; DTT 5 mM; D2O, [U-2H], 100%

sample_conditions_1: pH: 6.8; 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 aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	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 HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	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

Software:

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

Olivia, Yokochi, M., Sekiguchi, S. and Inagaki, F. - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 700 MHz
Bruker Avance 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts