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BMRB Entry 17704

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17704
MolProbity Validation Chart

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Title: RAGEC2-S100A13 tetrameric complex

Deposition date: 2011-06-14 Original release date: 2015-06-26

Authors: Rani, Sandhya; Mohan, Sepuru; Yu, Chin

Citation: Rani, Sandhya; Mohan, Sepuru; Yu, Chin. "Interaction of S100A13 with Receptor for Advanced Glycation End products (RAGE) C2 domain"  .

Assembly members:
entity_1, polymer, 93 residues, 9645.887 Da.
entity_2, polymer, 97 residues, 11359.112 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   Vector: pET28a

Entity Sequences (FASTA):
entity_1: LEEVQLVVEPEGGAVAPGGT VTLTCEVPAQPSPQIHWMKD GVPLPLPPSPVLILPEIGPQ DQGTYSCVATHSSHGPQESR AVSISIIEPGEEG
entity_2: AAEPLTELEESIETVVTTFF TFARQEGRKDSLSVNEFKEL VTQQLPHLLKDVGSLDEKMK SLDVNQDSELKFNEYWRLIG ELAKEIRKKKDLKIRKK

Data sets:
Data typeCount
13C chemical shifts349
15N chemical shifts74
1H chemical shifts568

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1_11
2entity_1_21
3entity_2_12
4entity_2_22

Entities:

Entity 1, entity_1_1 93 residues - 9645.887 Da.

1   LEUGLUGLUVALGLNLEUVALVALGLUPRO
2   GLUGLYGLYALAVALALAPROGLYGLYTHR
3   VALTHRLEUTHRCYSGLUVALPROALAGLN
4   PROSERPROGLNILEHISTRPMETLYSASP
5   GLYVALPROLEUPROLEUPROPROSERPRO
6   VALLEUILELEUPROGLUILEGLYPROGLN
7   ASPGLNGLYTHRTYRSERCYSVALALATHR
8   HISSERSERHISGLYPROGLNGLUSERARG
9   ALAVALSERILESERILEILEGLUPROGLY
10   GLUGLUGLY

Entity 2, entity_2_1 97 residues - 11359.112 Da.

1   ALAALAGLUPROLEUTHRGLULEUGLUGLU
2   SERILEGLUTHRVALVALTHRTHRPHEPHE
3   THRPHEALAARGGLNGLUGLYARGLYSASP
4   SERLEUSERVALASNGLUPHELYSGLULEU
5   VALTHRGLNGLNLEUPROHISLEULEULYS
6   ASPVALGLYSERLEUASPGLULYSMETLYS
7   SERLEUASPVALASNGLNASPSERGLULEU
8   LYSPHEASNGLUTYRTRPARGLEUILEGLY
9   GLULEUALALYSGLUILEARGLYSLYSLYS
10   ASPLEULYSILEARGLYSLYS

Samples:

sample_1: entity_1, [U-100% 13C; U-100% 15N], 1.1 mM; entity_2 1.1 mM; sodium phosphate 25 mM; sodium chloride 100 mM; DTT 1 mM; sodium azide 0.02 mM; H2O 90%; D2O 10%

sample_2: entity_1 1.2 mM; entity_2, [U-100% 13C; U-100% 15N], 1.2 mM; sodium phosphate 25 mM; sodium chloride 100 mM; DTT 1 mM; sodium azide 0.02 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 13C-Filter NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
13C Filter NOESYsample_2isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1

Software:

ARIA v1.2 & 2.2, Linge, O'Donoghue and Nilges - refinement, structure solution

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

HADDOCK v2.0, Alexandre Bonvin - complex structure

SPARKY, Goddard - chemical shift assignment, chemical shift calculation, peak picking

VNMR, Varian - collection, processing

TALOS, Cornilescu, Delaglio and Bax - dihedral angles

NMR spectrometers:

  • Varian INOVA 700 MHz

Related Database Links:

PDB
DBJ BAA05958 BAA89369 BAC65465 BAC65466 BAG35995
GB AAA03574 AAB47491 AAH20669 AAQ10686 AAX07272
REF NP_001127 NP_001193858 NP_001193861 NP_001193863 NP_001193869
SP Q15109
AlphaFold Q6FGF8 Q15109

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