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BMRB Entry 25694

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25694
MolProbity Validation Chart

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Title: Structure of constitutively monomeric CXCL12 in complex with the CXCR4 N-terminus   PubMed: 27058821

Deposition date: 2015-07-07 Original release date: 2016-04-25

Authors: Ziarek, Joshua; Peterson, Francis; Volkman, Brian

Citation: Smith, Emmanuel; Nevins, Amanda; Qiao, Zhen; Liu, Yan; Getschman, Anthony; Vankayala, Sai; Kemp, M. Trent; Peterson, Francis; Li, Rongshi; Volkman, Brian; Chen, Yu. "Structure-Based Identification of Novel Ligands Targeting Multiple Sites within a Chemokine-G-Protein-Coupled-Receptor Interface"  J. Med. Chem. 59, 4342-4351 (2016).

Assembly members:
entity_1, polymer, 70 residues, 8146.729 Da.
entity_2, polymer, 40 residues, 4518.798 Da.

Natural source:   Common Name: human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

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

Entity Sequences (FASTA):
entity_1: GMKPVSLSYRCPCRFFESHV ARANVKHLKILNTPNCALQI VARLKNNNRQVCIDPKCKWC QEYLEKALNK
entity_2: GSMEGISIYTSDNYTEEMGS GDYDSMKEPAFREENANFNK

Data sets:
Data typeCount
13C chemical shifts452
15N chemical shifts110
1H chemical shifts753

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1CXCL121
2CXCR42

Entities:

Entity 1, CXCL12 70 residues - 8146.729 Da.

The N-terminal GM dipeptide is a cloning artifact.

1   GLYMETLYSPROVALSERLEUSERTYRARG
2   CYSPROCYSARGPHEPHEGLUSERHISVAL
3   ALAARGALAASNVALLYSHISLEULYSILE
4   LEUASNTHRPROASNCYSALALEUGLNILE
5   VALALAARGLEULYSASNASNASNARGGLN
6   VALCYSILEASPPROLYSCYSLYSTRPCYS
7   GLNGLUTYRLEUGLULYSALALEUASNLYS

Entity 2, CXCR4 40 residues - 4518.798 Da.

The N-terminal GS dipeptide is a cloning artifact.

1   GLYSERMETGLUGLYILESERILETYRTHR
2   SERASPASNTYRTHRGLUGLUMETGLYSER
3   GLYASPTYRASPSERMETLYSGLUPROALA
4   PHEARGGLUGLUASNALAASNPHEASNLYS

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 2 mM; MES, [U-2H], 25 mM; D2O, [U-99% 2H], 10%; sodium azide 0.02%; entity_2 2 mM; H2O 90%

sample_2: entity_2, [U-99% 13C; U-99% 15N], 1 mM; MES, [U-2H], 25 mM; sodium azide 0.02%; D2O, [U-99% 2H], 10%; entity_1 2 mM; H2O, [U-99% 2H], 90%

sample_conditions_1: ionic strength: 0.02 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
3D F1-13C filtered/F3-13C edited NOESY aliphaticsample_1isotropicsample_conditions_1
3D F1-13C filtered/F3-13C edited NOESY aliphaticsample_2isotropicsample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

XEASY, Bartels et al. - chemical shift assignment

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

GARANT, Bartels, Guntert, Billeter and Wuthrich - chemical shift assignment

TOPSPIN, Bruker Biospin - collection

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization

TALOS, Cornilescu, Delaglio and Bax - data analysis

NMR spectrometers:

  • Bruker DRX 600 MHz

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