BMRB Entry 26060

Name: Solution NMR structures of AF9 yeats domain in complex with histone H3 crotonylation at K18
Published: 2016-09-01

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PDB ID: 2ndg
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR26060
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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:

Solution NMR structures of AF9 yeats domain in complex with histone H3 crotonylation at K18

Deposition date:

2016-05-19

Original release date:

2016-09-01

Authors:

Zeng, Lei; ZHOU, MING-MING

Citation:

Citation: Zhang, Qiang; Zeng, Lei; Zhao, Chengcheng; Ju, Ying; Konuma, Tsuyoshi; ZHOU, MING-MING. "Structural Insights into Histone Crotonyl-Lysine Recognition by the AF9 YEATS Domain" Structure 24, 1606-1612 (2016).
PubMed: 27545619

Assembly members:

Assembly members:
entity_1, polymer, 141 residues, 16611.314 Da.
entity_2, polymer, 13 residues, 1181.408 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: BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSHMASSCAVQVKLELGHRA QVRKKPTVEGFTHDWMVFVR GPEHSNIQHFVEKVVFHLHE SFPRPKRVCKDPPYKVEESG YAGFILPIEVYFKNKEEPRK VRFDYDLFLHLEGHPPVNHL RCEKLTFNNPTEDFRRKLLK A
entity_2: GGKAPRXQLATKA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	665
15N chemical shifts	123
1H chemical shifts	1007

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_1 141 residues - 16611.314 Da.

1

GLY

SER

HIS

MET

ALA

SER

CYS

ALA

VAL

2

GLN

VAL

LYS

LEU

GLU

LEU

GLY

HIS

ARG

ALA

3

GLN

VAL

ARG

LYS

PRO

THR

VAL

GLU

GLY

4

PHE

THR

HIS

ASP

TRP

MET

VAL

PHE

VAL

ARG

5

GLY

PRO

GLU

HIS

SER

ASN

ILE

GLN

HIS

PHE

6

VAL

GLU

LYS

VAL

PHE

HIS

LEU

HIS

GLU

7

SER

PHE

PRO

ARG

PRO

LYS

ARG

VAL

CYS

LYS

8

ASP

PRO

TYR

LYS

VAL

GLU

SER

GLY

9

TYR

ALA

GLY

PHE

ILE

LEU

PRO

ILE

GLU

VAL

10

TYR

PHE

LYS

ASN

LYS

GLU

PRO

ARG

LYS

11

VAL

ARG

PHE

ASP

TYR

ASP

LEU

PHE

LEU

HIS

12

LEU

GLU

GLY

HIS

PRO

VAL

ASN

HIS

LEU

13

ARG

CYS

GLU

LYS

LEU

THR

PHE

ASN

PRO

14

THR

GLU

ASP

PHE

ARG

LYS

LEU

LYS

15

ALA

Entity 2, entity_2 13 residues - 1181.408 Da.

1

GLY

LYS

ALA

PRO

ARG

KCR

GLN

LEU

ALA

2

THR

LYS

ALA

Samples:

sample_1: sodium phosphate 10 mM; sodium chloride 500 mM; EDTA 2 mM; DTT, [U-100% 2H], 2 mM; H20 90%; D2O 10%; entity_1, 13C/15N-labelled, 0.5 mM; entity_2, 13C/15N-labelled, 0.25 mM

sample_2: sodium phosphate 10 mM; sodium chloride 500 mM; EDTA 2 mM; DTT, [U-100% 2H], 2 mM; D2O 100%; entity_1, 13C/15N-labelled, 0.5 mM; entity_2, 13C/15N-labelled, 0.25 mM

sample_conditions_1: ionic strength: 500 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
3D HNCACB	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 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	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 filtered 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D filtered 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1

Software:

ARIA v2.3, Linge, O'Donoghue and Nilges - refinement

NMRPipe v7.1, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift calculation, processing

NMRView v5.04 C-version, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

TALOS vtalosn, talosplus, Cornilescu, Delaglio and Bax - refinement

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - geometry optimization, refinement, structure solution

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 900 MHz
Bruker Avance 600 MHz
Bruker Avance 500 MHz

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