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Biological Magnetic Resonance Data Bank


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BMRB Entry 15189

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15189
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Title: Solution structure of the N-terminal extracellular domain of the lymphocyte receptor CD5 (CD5 domain 1)   PubMed: 18339402

Deposition date: 2007-03-19 Original release date: 2008-06-27

Authors: Garza-Garcia, Acely; Harris, Richard; Esposito, Diego; Driscoll, Paul

Citation: Garza-Garcia, Acely; Esposito, Diego; Rieping, Wolfgang; Harris, Richard; Briggs, Cherry; Brown, Marion; Driscoll, Paul. "Three-dimensional solution structure and conformational plasticity of the N-terminal scavenger receptor cysteine-rich domain of human CD5"  J. Mol. Biol. 378, 129-144 (2008).

Assembly members:
CD5d1, polymer, 131 residues, 12491.134 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):
CD5d1: MGSSHHHHHHSSGLVPRGSH MRLSWYDPDFQARLTRSNSK CQGQLEVYLKDGWHMVCSQS WGRSSKQWEDPSQASKVCQR LNCGDPLSLGPFLKTYTPQS SIICYGQLGSFSNCSHSRND MCHSLGLTCLE

Data sets:
Data typeCount
13C chemical shifts453
15N chemical shifts105
1H chemical shifts692

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1CD5d11

Entities:

Entity 1, CD5d1 131 residues - 12491.134 Da.

Construct included an N-terminal hexa-histidine tag: MGSSHHHHHHSSGLVPRGSHM

1   METGLYSERSERHISHISHISHISHISHIS
2   SERSERGLYLEUVALPROARGGLYSERHIS
3   METARGLEUSERTRPTYRASPPROASPPHE
4   GLNALAARGLEUTHRARGSERASNSERLYS
5   CYSGLNGLYGLNLEUGLUVALTYRLEULYS
6   ASPGLYTRPHISMETVALCYSSERGLNSER
7   TRPGLYARGSERSERLYSGLNTRPGLUASP
8   PROSERGLNALASERLYSVALCYSGLNARG
9   LEUASNCYSGLYASPPROLEUSERLEUGLY
10   PROPHELEULYSTHRTYRTHRPROGLNSER
11   SERILEILECYSTYRGLYGLNLEUGLYSER
12   PHESERASNCYSSERHISSERARGASNASP
13   METCYSHISSERLEUGLYLEUTHRCYSLEU
14   GLU

Samples:

sample_1: CD5d1, [U-15N], 1 mM; sodium phosphate 50 mM; sodium chloride 200 mM; EDTA 1 mM; H2O 90%; D2O 10%

sample_2: CD5d1, [U-13C; U-15N], 1 mM; EDTA 1 mM; sodium phosphate 50 mM; sodium chloride 200 mM; H2O 90%; D2O 10%

sample_3: CD5d1, [U-13C; U-15N], 1 mM; EDTA 1 mM; sodium phosphate 50 mM; sodium chloride 200 mM; D2O 100%

sample_conditions_1: ionic strength: 0.2 M; pH: 5.0; pressure: 1 atm; temperature: 318 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
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HA(CACO)NHsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1

Software:

NMRPipe v3.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

ANSIG v3.3, Kraulis - data analysis

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

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

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Varian UnityPlus 500 MHz
  • Varian INOVA 800 MHz

Related Database Links:

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