BMRB Entry 11323

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PDB ID: 2d8q
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11323
MolProbity Validation Chart

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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 structure of the MYND domain of the human zinc finger MYND domain-containing protein 10

Deposition date:

2010-08-10

Original release date:

2011-08-19

Authors:

Miyamoto, K.; Kigawa, T.; Tomizawa, T.; Tochio, N.; Sasagawa, A.; Koshiba, S.; Inoue, M.; Yokoyama, S.

Citation:

Citation: Miyamoto, K.; Kigawa, T.; Tomizawa, T.; Tochio, N.; Sasagawa, A.; Koshiba, S.; Inoue, M.; Yokoyama, S.. "Solution structure of the MYND domain of the human zinc finger MYND domain-containing protein 10" .

Assembly members:

Assembly members:
zf-MYND, polymer, 70 residues, Formula weight is not available
ZN, 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: cell free synthesis Host organism: E. coli - cell free Vector: P040816-10

Entity Sequences (FASTA):

Entity Sequences (FASTA):
zf-MYND: GSSGSSGLEAVAPERPRCAY CSAEASKRCSRCQNEWYCCR ECQVKHWEKHGKTCVLAAQG DRAKSGPSSG

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	262
15N chemical shifts	63
1H chemical shifts	395

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	zf-MYND	1
2	ZINC ION no.1	2
3	ZINC ION no.2	2

Entities:

Entity 1, zf-MYND 70 residues - Formula weight is not available

1	GLY	SER	SER	GLY	SER	SER	GLY	LEU	GLU	ALA
2	VAL	ALA	PRO	GLU	ARG	PRO	ARG	CYS	ALA	TYR
3	CYS	SER	ALA	GLU	ALA	SER	LYS	ARG	CYS	SER
4	ARG	CYS	GLN	ASN	GLU	TRP	TYR	CYS	CYS	ARG
5	GLU	CYS	GLN	VAL	LYS	HIS	TRP	GLU	LYS	HIS
6	GLY	LYS	THR	CYS	VAL	LEU	ALA	ALA	GLN	GLY
7	ASP	ARG	ALA	LYS	SER	GLY	PRO	SER	SER	GLY

Entity 2, ZINC ION no.1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: zf-MYND, [U-13C; U-15N], 0.3 mM; d-Tris-HCl 20 mM; NaCl 100 mM; d-DTT 1 mM; NaN3 0.02%; ZnCl2 0.1 mM; H2O 90%; D2O 10%

condition_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 15N-separated NOESY	sample_1	isotropic	condition_1
3D 13C-separated NOESY	sample_1	isotropic	condition_1

Software:

xwinnmr v2.6, Bruker - collection

NMRPipe v20031121, Delaglio, F. - processing

NMRView v5.0.4, Johnson, B. A. - data analysis

Kujira v0.9321, Kobayashi, N. - data analysis

CYANA v2.0.17, Guntert, P. - refinement, structure solution

NMR spectrometers:

Bruker AVANCE 800 MHz

PDB	2D8Q
DBJ	BAD97063 BAG53316 BAG73936 BAK63946
EMBL	CAD38688 CAL37695 CAL38065
GB	AAC24726 AAC24728 AAH33732 AIC56440 EAW65104
REF	NP_001233432 NP_001295308 NP_056980 XP_001090964 XP_003257157
SP	O75800
AlphaFold	O75800

1	GLY	SER	SER	GLY	SER	SER	GLY	LEU	GLU	ALA
2	VAL	ALA	PRO	GLU	ARG	PRO	ARG	CYS	ALA	TYR
3	CYS	SER	ALA	GLU	ALA	SER	LYS	ARG	CYS	SER
4	ARG	CYS	GLN	ASN	GLU	TRP	TYR	CYS	CYS	ARG
5	GLU	CYS	GLN	VAL	LYS	HIS	TRP	GLU	LYS	HIS
6	GLY	LYS	THR	CYS	VAL	LEU	ALA	ALA	GLN	GLY
7	ASP	ARG	ALA	LYS	SER	GLY	PRO	SER	SER	GLY

1	GLY	SER	SER	GLY	SER	SER	GLY	LEU	GLU	ALA
2	VAL	ALA	PRO	GLU	ARG	PRO	ARG	CYS	ALA	TYR
3	CYS	SER	ALA	GLU	ALA	SER	LYS	ARG	CYS	SER
4	ARG	CYS	GLN	ASN	GLU	TRP	TYR	CYS	CYS	ARG
5	GLU	CYS	GLN	VAL	LYS	HIS	TRP	GLU	LYS	HIS
6	GLY	LYS	THR	CYS	VAL	LEU	ALA	ALA	GLN	GLY
7	ASP	ARG	ALA	LYS	SER	GLY	PRO	SER	SER	GLY