BMRB Entry 16639

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16639
MolProbity Validation Chart

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Title:
Structure of a complex between domain V of beta2-glycoprotein I and the fourth ligand-binding module from LDLR determined with Haddock.
Deposition date:
2009-12-18
Original release date:
2010-05-05
Authors:
Beglova, Natalia
Citation:

Citation: Lee, Chang-Jin; De Biasio, Alfredo; Beglova, Natalia. "Mode of interaction between beta2GPI and lipoprotein receptors suggests mutually exclusive binding of beta2GPI to the receptors and anionic phospholipids."  Structure (Cambridge, MA, U. S.) 18, 366-376 (2010).
PubMed: 20223219

Assembly members:

Assembly members:
beta2GPI, polymer, 85 residues, 9366.987 Da.
LDLR, polymer, 40 residues, 4181.480 Da.
CA, non-polymer, 40.078 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: pET 15

Entity Sequences (FASTA):

Entity Sequences (FASTA):
beta2GPI: GSCKLPVKKATVVYQGERVK IQEKFKNGMLHGDKVSFFCK NKEKKCSYTEDAQCIDGTIE VPKCFKEHSSLAFWKTDASD VKPCA
LDLR: TCGPASFQCNSSTCIPQLWA CDNDPDCEDGSDEWPQRCRG

Data sets:
Data typeCount
15N chemical shifts104
1H chemical shifts104
T1 relaxation values95
T2 relaxation values95

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1beta2GPI1
2LDLR2
3Calcium ion3

Entities:

Entity 1, beta2GPI 85 residues - 9366.987 Da.

1   GLYSERCYSLYSLEUPROVALLYSLYSALA
2   THRVALVALTYRGLNGLYGLUARGVALLYS
3   ILEGLNGLULYSPHELYSASNGLYMETLEU
4   HISGLYASPLYSVALSERPHEPHECYSLYS
5   ASNLYSGLULYSLYSCYSSERTYRTHRGLU
6   ASPALAGLNCYSILEASPGLYTHRILEGLU
7   VALPROLYSCYSPHELYSGLUHISSERSER
8   LEUALAPHETRPLYSTHRASPALASERASP
9   VALLYSPROCYSALA

Entity 2, LDLR 40 residues - 4181.480 Da.

1   THRCYSGLYPROALASERPHEGLNCYSASN
2   SERSERTHRCYSILEPROGLNLEUTRPALA
3   CYSASPASNASPPROASPCYSGLUASPGLY
4   SERASPGLUTRPPROGLNARGCYSARGGLY

Entity 3, Calcium ion - Ca - 40.078 Da.

1   CA

Samples:

sample_1: entity_1, [U-100% 13C; U-100% 15N], 600 uM; entity_2, [U-100% 13C; U-100% 15N], 1 mM; CaCl2 10 mM; bis-Tris 10 mM

sample_2: entity_1, [U-100% 15N], 300 uM; entity_2, [U-100% 15N], 100 uM; CaCl2 10 mM; bis-Tris 10 mM

sample_3: entity_1, [U-100% 15N], 515 uM; entity_2, [U-100% 15N], 300 uM; CaCl2 10 mM; bis-Tris 10 mM

sample_conditions_1: ionic strength: 25 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1

Software:

GIFA v4.3, Delsuc - data analysis, processing

VNMR, Varian - collection

HADDOCK v2.0, Bonvin - structure solution

xcrvfit v4.0.12, Robert Boyko, Brian Sykes - data analysis

NMR spectrometers:

  • Varian Unity 500 MHz

Related Database Links:

UNP P02749 P01130
AlphaFold Q9UCN7 Q9UDH7

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