BMRB Entry 10011

Name: SOLUTION STRUCTURE OF THE SWIRM DOMAIN OF HUMAN LSD1
Published: 2006-11-14

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PDB ID: 2com
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR10011
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 SWIRM DOMAIN OF HUMAN LSD1

Deposition date:

2005-11-07

Original release date:

2006-11-14

Authors:

Tochio, N.; Umehara, T.; Koshiba, S.; Inoue, M.; TANAKA, A.; Kigawa, T.; Yokoyama, S.

Citation:

Citation: Tochio, N.; Umehara, T.; Koshiba, S.; Inoue, M.; Yabuki, T.; Aoki, M.; Seki, E.; Watanabe, S.; Tomo, Y.; Hanada, M.; Ikari, M.; Sato, M.; Terada, T.; Nagase, T.; Ohara, O.; Shirouzu, M.; Tanaka, A.; Kigawa, T.; Yokoyama, S.. "Solution structure of the SWIRM domain of human histone demethylase LSD1" Structure 14, 457-468 (2006).
PubMed: 16531230

Assembly members:

Assembly members:
SWIRM domain, polymer, 124 residues, 13710.63 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 Vector: P040401-21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SWIRM domain: GSSGSSGEEPSGVEGAAFQS RLPHDRMTSQEAACFPDIIS GPQQTQKVFLFIRNRTLQLW LDNPKIQLTFEATLQQLEAP YNSDTVLVHRVHSYLERHGL INFGIYKRIKPLPTKKTGSG PSSG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shift_1

Data type	Count
13C chemical shifts	525
15N chemical shifts	119
1H chemical shifts	828

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SWIRM domain	1

Entities:

Entity 1, SWIRM domain 124 residues - 13710.63 Da.

1

GLY

SER

GLY

SER

GLY

GLU

PRO

2

SER

GLY

VAL

GLU

GLY

ALA

PHE

GLN

SER

3

ARG

LEU

PRO

HIS

ASP

ARG

MET

THR

SER

GLN

4

GLU

ALA

CYS

PHE

PRO

ASP

ILE

SER

5

GLY

PRO

GLN

THR

GLN

LYS

VAL

PHE

LEU

6

PHE

ILE

ARG

ASN

ARG

THR

LEU

GLN

LEU

TRP

7

LEU

ASP

ASN

PRO

LYS

ILE

GLN

LEU

THR

PHE

8

GLU

ALA

THR

LEU

GLN

LEU

GLU

ALA

PRO

9

TYR

ASN

SER

ASP

THR

VAL

LEU

VAL

HIS

ARG

10

VAL

HIS

SER

TYR

LEU

GLU

ARG

HIS

GLY

LEU

11

ILE

ASN

PHE

GLY

ILE

TYR

LYS

ARG

ILE

LYS

12

PRO

LEU

PRO

THR

LYS

THR

GLY

SER

GLY

13

PRO

SER

GLY

Samples:

sample_1: SWIRM domain, [U-13C, U-15N], 1.2 mM; D-Tris 20 mM; NaCl 100 mM; d-DTT 1 mM; NaN3 0.02%; D2O 10%; H2O 90%

condition_1: ionic strength: 0.12 M; pH: 7.0; pressure: 1 atm; temperature: 296 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D_13C-separated_NOESY	sample_1	not available	condition_1
3D_15N-separated_NOESY	sample_1	not available	condition_1

Software:

xwinnmr v2.6, Bruker - collection

NMRPipe v20031121 - processing

NMRView v5.0.4 - data analysis

Kujira v0.8994 - data analysis

CYANA v2.0.17 - refinement, structure solution

NMR spectrometers:

Bruker AVANCE 800 MHz

BMRB	17171
PDB	2COM 2DW4 2EJR 2H94 2HKO 2IW5 2L3D 2UXN 2UXX 2V1D 2X0L 2XAF 2XAG 2XAH 2XAJ 2XAQ 2XAS 2Y48 2Z3Y 2Z5U 3ABT 3ABU 4BAY 4KUM 4UXN
DBJ	BAA25527 BAC97980 BAF83017 BAG09773
EMBL	CAH90077
GB	AAH16639 AAH48134 AAI51757 ABX10191 AIC62107
REF	NP_055828 NP_598633 XP_002685763 XP_003271633 XP_003415419
SP	O60341 Q6ZQ88
TPG	DAA32188
AlphaFold	O60341 Q6ZQ88