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
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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. PubMed: 20223219
Deposition date: 2009-12-18 Original release date: 2010-05-05
Authors: Beglova, Natalia
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).
Assembly members:
beta2GPI, polymer, 85 residues, 9366.987 Da.
LDLR, polymer, 40 residues, 4181.480 Da.
CA, non-polymer, 40.078 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):
beta2GPI: GSCKLPVKKATVVYQGERVK
IQEKFKNGMLHGDKVSFFCK
NKEKKCSYTEDAQCIDGTIE
VPKCFKEHSSLAFWKTDASD
VKPCA
LDLR: TCGPASFQCNSSTCIPQLWA
CDNDPDCEDGSDEWPQRCRG
- assigned_chemical_shifts
- heteronucl_T1_relaxation
- heteronucl_T2_relaxation
| Data type | Count |
| 15N chemical shifts | 104 |
| 1H chemical shifts | 104 |
| T1 relaxation values | 95 |
| T2 relaxation values | 95 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | beta2GPI | 1 |
| 2 | LDLR | 2 |
| 3 | Calcium ion | 3 |
Entities:
Entity 1, beta2GPI 85 residues - 9366.987 Da.
| 1 | GLY | SER | CYS | LYS | LEU | PRO | VAL | LYS | LYS | ALA | ||||
| 2 | THR | VAL | VAL | TYR | GLN | GLY | GLU | ARG | VAL | LYS | ||||
| 3 | ILE | GLN | GLU | LYS | PHE | LYS | ASN | GLY | MET | LEU | ||||
| 4 | HIS | GLY | ASP | LYS | VAL | SER | PHE | PHE | CYS | LYS | ||||
| 5 | ASN | LYS | GLU | LYS | LYS | CYS | SER | TYR | THR | GLU | ||||
| 6 | ASP | ALA | GLN | CYS | ILE | ASP | GLY | THR | ILE | GLU | ||||
| 7 | VAL | PRO | LYS | CYS | PHE | LYS | GLU | HIS | SER | SER | ||||
| 8 | LEU | ALA | PHE | TRP | LYS | THR | ASP | ALA | SER | ASP | ||||
| 9 | VAL | LYS | PRO | CYS | ALA |
Entity 2, LDLR 40 residues - 4181.480 Da.
| 1 | THR | CYS | GLY | PRO | ALA | SER | PHE | GLN | CYS | ASN | |
| 2 | SER | SER | THR | CYS | ILE | PRO | GLN | LEU | TRP | ALA | |
| 3 | CYS | ASP | ASN | ASP | PRO | ASP | CYS | GLU | ASP | GLY | |
| 4 | SER | ASP | GLU | TRP | PRO | GLN | ARG | CYS | ARG | GLY |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_2 | isotropic | sample_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
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts