BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 7413

Title: Mapping intramolecular interactions between domains in HMGB1 using a tail-truncation approach   PubMed: 17988686

Deposition date: 2007-10-02 Original release date: 2008-02-11

Authors: Watson, Matthew; Stott, Katherine; Thomas, Jean

Citation: Watson, Matthew; Stott, Katherine; Thomas, Jean. "Mapping intramolecular interactions between domains in HMGB1 using a tail-truncation approach"  J. Mol. Biol. 374, 1286-1297 (2007).

Assembly members:
HMGB1-delta25, polymer, 189 residues, Formula weight is not available

Natural source:   Common Name: Rat   Taxonomy ID: 10116   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Rattus norvegicus

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pBAT4

Entity Sequences (FASTA):
HMGB1-delta25: GKGDPKKPRGKMSSYAFFVQ TCREEHKKKHPDASVNFSEF SKKCSERWKTMSAKEKGKFE DMAKADKARYEREMKTYIPP KGETKKKFKDPNAPKRPPSA FFLFCSEYRPKIKGEHPGLS IGDVAKKLGEMWNNTAADDK QPYEKKAAKLKEKYEKDIAA YRAKGKPDAAKKGVVKAEKS KKKKEEEDD

Data sets:
Data typeCount
15N chemical shifts175
1H chemical shifts181

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1HMGB1, delta251

Entities:

Entity 1, HMGB1, delta25 189 residues - Formula weight is not available

1   GLYLYSGLYASPPROLYSLYSPROARGGLY
2   LYSMETSERSERTYRALAPHEPHEVALGLN
3   THRCYSARGGLUGLUHISLYSLYSLYSHIS
4   PROASPALASERVALASNPHESERGLUPHE
5   SERLYSLYSCYSSERGLUARGTRPLYSTHR
6   METSERALALYSGLULYSGLYLYSPHEGLU
7   ASPMETALALYSALAASPLYSALAARGTYR
8   GLUARGGLUMETLYSTHRTYRILEPROPRO
9   LYSGLYGLUTHRLYSLYSLYSPHELYSASP
10   PROASNALAPROLYSARGPROPROSERALA
11   PHEPHELEUPHECYSSERGLUTYRARGPRO
12   LYSILELYSGLYGLUHISPROGLYLEUSER
13   ILEGLYASPVALALALYSLYSLEUGLYGLU
14   METTRPASNASNTHRALAALAASPASPLYS
15   GLNPROTYRGLULYSLYSALAALALYSLEU
16   LYSGLULYSTYRGLULYSASPILEALAALA
17   TYRARGALALYSGLYLYSPROASPALAALA
18   LYSLYSGLYVALVALLYSALAGLULYSSER
19   LYSLYSLYSLYSGLUGLUGLUASPASP

Samples:

sample_1: HMGB1, delta25, [U-98% 15N], 0.3-1.4 mM

sample_conditions_1: ionic strength: 0.001 M; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1

Software:

Analysis, CCPN - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Bruker DRX 800 MHz

Related Database Links:

BMRB 11147 15148 15149 15502 7408 7409 7410 7411 7412
PDB
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 P09429 A9RA84 B0CM99 B1MTB0 P07156

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