BMRB Entry 11532

Name: solution structure of oxidized human HMGB1 A box
Published: 2014-03-03

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PDB ID: 2rtu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11532
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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 oxidized human HMGB1 A box

Deposition date:

2013-09-12

Original release date:

2014-03-03

Authors:

Jing, Wang; Tochio, Naoya; Tate, Shin-ichi

Citation:

Citation: Jing, Wang; Tochio, Naoya; Tate, Shin-ichi. "Redox-sensitive structural change in the A-domain of HMGB1 and its implication for the binding to cisplatin modified DNA" Biochem. Biophys. Res. Commun. ., .-..
PubMed: 24513216

Assembly members:

Assembly members:
entity, polymer, 87 residues, 10118.729 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: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GSHMGKGDPKKPRGKMSSYA FFVQTCREEHKKKHPDASVN FSEFSKKCSERWKTMSAKEK GKFEDMAKADKARYEREMKT YIPPKGE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	398
15N chemical shifts	87
1H chemical shifts	572

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity	1

Entities:

Entity 1, entity 87 residues - 10118.729 Da.

1

GLY

SER

HIS

MET

GLY

LYS

GLY

ASP

PRO

LYS

2

LYS

PRO

ARG

GLY

LYS

MET

SER

TYR

ALA

3

PHE

VAL

GLN

THR

CYS

ARG

GLU

HIS

4

LYS

HIS

PRO

ASP

ALA

SER

VAL

ASN

5

PHE

SER

GLU

PHE

SER

LYS

CYS

SER

GLU

6

ARG

TRP

LYS

THR

MET

SER

ALA

LYS

GLU

LYS

7

GLY

LYS

PHE

GLU

ASP

MET

ALA

LYS

ALA

ASP

8

LYS

ALA

ARG

TYR

GLU

ARG

GLU

MET

LYS

THR

9

TYR

ILE

PRO

LYS

GLY

GLU

Samples:

sample_1: entity, [U-13C; U-15N], 0.5 – 0.6 mM; potassium phosphate 50 mM; potassium chloride 150 mM; D2O, [U-2H], 10%; H2O 90%

sample_2: entity, [U-13C; U-15N], 0.5 – 0.6 mM; C12E5/n-hexanol 6%; potassium chloride 150 mM; potassium phosphate 50 mM; D2O, [U-2H], 10%; H2O 90%

sample_conditions_1: ionic strength: 200 mM; pH: 6.4; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N IPAP-HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N IPAP-HSQC	sample_2	anisotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

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

MAGRO, Kobayashi N. - data analysis

NMRView, Johnson, One Moon Scientific - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

SPARKY, Goddard - data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

Bruker Avance 700 MHz

BMRB	11147 15148 15149 15502 18709 4079
PDB	1AAB 1CKT 2LY4 2RTU 2YRQ 4QR9
DBJ	BAA09924 BAC29902 BAC34367 BAC34773 BAC38678
EMBL	CAA31110 CAA31284 CAA56631 CAA68441 CAA68526
GB	AAA20508 AAA31050 AAA40729 AAA57042 AAA64970
PIR	S29857
REF	NP_001002937 NP_001004034 NP_001075304 NP_001102843 NP_001162380
SP	A9RA84 B0CM99 B1MTB0 P07156 P09429
TPG	DAA21468 DAA23902
AlphaFold	A9RA84 B0CM99 B1MTB0 P07156 P09429