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- PDB-2kri: Structure of a complex between domain V of beta2-glycoprotein I a... -

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Basic information

Entry
Database: PDB / ID: 2kri
TitleStructure of a complex between domain V of beta2-glycoprotein I and the fourth ligand-binding module from LDLR determined with Haddock
Components
  • Beta-2-glycoprotein 1
  • Low-density lipoprotein receptor
KeywordsPROTEIN BINDING/ENDOCYTOSIS / Antiphospholipid syndrome / Thrombosis / LDLR / Receptor / Disulfide bond / Glycoprotein / Heparin-binding / Sushi / PROTEIN BINDING-ENDOCYTOSIS complex
Function / homology
Function and homology information


triglyceride transport / lipoprotein lipase activator activity / platelet dense granule lumen / receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / negative regulation of microglial cell activation / very-low-density lipoprotein particle receptor activity ...triglyceride transport / lipoprotein lipase activator activity / platelet dense granule lumen / receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / negative regulation of microglial cell activation / very-low-density lipoprotein particle receptor activity / PCSK9-LDLR complex / cholesterol import / positive regulation of lipoprotein lipase activity / low-density lipoprotein particle clearance / clathrin heavy chain binding / negative regulation of receptor recycling / positive regulation of triglyceride biosynthetic process / intestinal cholesterol absorption / blood coagulation, intrinsic pathway / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle receptor activity / response to caloric restriction / Chylomicron clearance / low-density lipoprotein particle binding / amyloid-beta clearance by cellular catabolic process / LDL clearance / negative regulation of myeloid cell apoptotic process / high-density lipoprotein particle clearance / regulation of fibrinolysis / chylomicron / regulation of protein metabolic process / lipoprotein catabolic process / phospholipid transport / low-density lipoprotein particle / cholesterol transport / high-density lipoprotein particle / very-low-density lipoprotein particle / endolysosome membrane / negative regulation of amyloid fibril formation / negative regulation of endothelial cell migration / regulation of cholesterol metabolic process / negative regulation of protein metabolic process / artery morphogenesis / cellular response to fatty acid / triglyceride metabolic process / plasminogen activation / sorting endosome / negative regulation of endothelial cell proliferation / negative regulation of smooth muscle cell apoptotic process / amyloid-beta clearance / lipoprotein particle binding / cellular response to low-density lipoprotein particle stimulus / negative regulation of blood coagulation / positive regulation of blood coagulation / long-term memory / negative regulation of fibrinolysis / phagocytosis / retinoid metabolic process / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / receptor-mediated endocytosis / cholesterol metabolic process / negative regulation of angiogenesis / cholesterol homeostasis / clathrin-coated endocytic vesicle membrane / phospholipid binding / lipid metabolic process / positive regulation of inflammatory response / endocytosis / apical part of cell / late endosome / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / heparin binding / Clathrin-mediated endocytosis / amyloid-beta binding / virus receptor activity / protease binding / : / basolateral plasma membrane / molecular adaptor activity / early endosome / lysosome / receptor complex / endosome membrane / external side of plasma membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / lipid binding / calcium ion binding / positive regulation of gene expression / cell surface / Golgi apparatus / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Beta-2-glycoprotein-1 fifth domain / Beta-2-glycoprotein-1 fifth domain / : / Complement Module, domain 1 / Complement Module; domain 1 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A ...Beta-2-glycoprotein-1 fifth domain / Beta-2-glycoprotein-1 fifth domain / : / Complement Module, domain 1 / Complement Module; domain 1 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / : / Calcium-binding EGF domain / LDL-receptor class A (LDLRA) domain profile. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
Low-density lipoprotein receptor / Beta-2-glycoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest haddock score, model 1
AuthorsBeglova, N.
CitationJournal: Structure / Year: 2010
Title: Mode of interaction between beta2GPI and lipoprotein receptors suggests mutually exclusive binding of beta2GPI to the receptors and anionic phospholipids.
Authors: Lee, C.J. / De Biasio, A. / Beglova, N.
History
DepositionDec 18, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: pdbx_database_related / pdbx_nmr_sample_details ...pdbx_database_related / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_related.db_id / _pdbx_nmr_sample_details.contents ..._pdbx_database_related.db_id / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2-glycoprotein 1
B: Low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0183
Polymers13,9782
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area920 Å2
ΔGint-3 kcal/mol
Surface area7650 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 200lowest haddock score
RepresentativeModel #1lowest haddock score

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Components

#1: Protein Beta-2-glycoprotein 1 / Beta-2-glycoprotein I / Beta(2)GPI / B2GPI / Apolipoprotein H / Apo-H / Activated protein C-binding ...Beta-2-glycoprotein I / Beta(2)GPI / B2GPI / Apolipoprotein H / Apo-H / Activated protein C-binding protein / APC inhibitor / Anticardiolipin cofactor


Mass: 9582.129 Da / Num. of mol.: 1 / Fragment: Sushi-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOH, B2G1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02749
#2: Protein/peptide Low-density lipoprotein receptor / LDL receptor


Mass: 4395.716 Da / Num. of mol.: 1 / Fragment: LDL-receptor class A 4 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDLR / Production host: Escherichia coli (E. coli) / References: UniProt: P01130
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-15N HSQC
1323D HNCA
1423D HN(CA)CB
1523D HN(CO)CA
1613D HNCA
1713D CBCA(CO)NH
1813D HN(CO)CA

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] entity_2-1, 100 uM [U-100% 15N] entity_2-2, 300 uM [U-100% 15N] entity_2-3, 90% H2O/10% D2O90% H2O/10% D2O
2600 uM [U-100% 13C; U-100% 15N] entity_1-4, 300 uM [U-100% 15N] entity_1-5, 515 uM [U-100% 15N] entity_1-6, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_2-1[U-100% 13C; U-100% 15N]1
100 uMentity_2-2[U-100% 15N]1
300 uMentity_2-3[U-100% 15N]1
600 uMentity_1-4[U-100% 13C; U-100% 15N]2
300 uMentity_1-5[U-100% 15N]2
515 uMentity_1-6[U-100% 15N]2
Sample conditionsIonic strength: 25 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Gifa4.3Delsucprocessing
Gifa4.3Delsucdata analysis
VNMRVariancollection
HADDOCK2Bonvinstructure solution
xcrvfit4.0.12Robert Boyko, Brian Sykesdata analysis
HADDOCK2Bonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest haddock score
NMR ensembleConformer selection criteria: lowest haddock score / Conformers calculated total number: 200 / Conformers submitted total number: 1

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