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- PDB-2rr3: Solution structure of the complex between human VAP-A MSP domain ... -

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Basic information

Entry
Database: PDB / ID: 2rr3
TitleSolution structure of the complex between human VAP-A MSP domain and human OSBP FFAT motif
Components
  • Oxysterol-binding protein 1
  • Vesicle-associated membrane protein-associated protein A
Keywordsmembrane protein/transport protein / Lipid transport / Transport / PROTEIN-PEPTIDE COMPLEX / major sperm protein domain / protein binding / endoplasmic reticulum / lipid binding / membrane protein-transport protein complex
Function / homology
Function and homology information


positive regulation of secretory granule organization / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / sterol transfer activity / sphingomyelin biosynthetic process / sterol transport / : / ceramide transport / sterol binding / intracellular cholesterol transport ...positive regulation of secretory granule organization / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / sterol transfer activity / sphingomyelin biosynthetic process / sterol transport / : / ceramide transport / sterol binding / intracellular cholesterol transport / COPII-coated vesicle budding / negative regulation by host of viral genome replication / positive regulation by host of viral genome replication / perinuclear endoplasmic reticulum / protein localization to endoplasmic reticulum / Sphingolipid de novo biosynthesis / bile acid biosynthetic process / phospholipid transport / oxysterol binding / cholesterol transport / phosphatidylinositol-4-phosphate binding / azurophil granule membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of insulin secretion involved in cellular response to glucose stimulus / viral release from host cell / Synthesis of bile acids and bile salts / bicellular tight junction / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of tyrosine phosphorylation of STAT protein / trans-Golgi network / neuron projection development / microtubule cytoskeleton / cell junction / microtubule binding / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / vesicle / membrane fusion / cadherin binding / protein heterodimerization activity / protein domain specific binding / Golgi membrane / Neutrophil degranulation / endoplasmic reticulum membrane / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Vesicle-associated membrane-protein-associated protein / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / PapD-like superfamily ...Vesicle-associated membrane-protein-associated protein / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / PapD-like superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Oxysterol-binding protein 1 / Vesicle-associated membrane protein-associated protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsFuruita, K. / Jee, J. / Fukada, H. / Mishima, M. / Kojima, C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Electrostatic interaction between oxysterol-binding protein and VAMP-associated protein A revealed by NMR and mutagenesis studies
Authors: Furuita, K. / Jee, J. / Fukada, H. / Mishima, M. / Kojima, C.
History
DepositionMar 9, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vesicle-associated membrane protein-associated protein A
B: Oxysterol-binding protein 1


Theoretical massNumber of molelcules
Total (without water)20,1852
Polymers20,1852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1484.8 Å2
ΔGint-10.8 kcal/mol
Surface area12542.7 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Vesicle-associated membrane protein-associated protein A / VAMP-A / VAMP-associated protein A / VAP-A / 33 kDa VAMP-associated protein / VAP-33


Mass: 14774.982 Da / Num. of mol.: 1 / Fragment: MSP domain, UNP residues 11-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P0L0
#2: Protein/peptide Oxysterol-binding protein 1 / OSBP


Mass: 5409.747 Da / Num. of mol.: 1 / Fragment: FFAT motif, residues 346-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P22059

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HN(CA)CO
1313D HN(CA)CB
1413D HN(COCA)CB
1513D C(CO)NH
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1814D HC(CO)NH
1932D 1H-1H NOESY
11033D 1H-15N TOCSY
11123D HNCO
11223D HN(CA)CO
11323D HN(CA)CB
11423D HN(COCA)CB
11523D C(CO)NH
11623D H(CCO)NH
11723D (H)CCH-TOCSY
11824D HC(CO)NH
11933D 1H-15N NOESY
12043D 1H-13C NOESY
12113D 13C-edited/13C-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-13C; U-15N] VAP-A MSP domain; 1mM OSBP FFAT motif; 50mM potassium phosphate; 100mM potassium chloride; 1mM DTT; 0.1mM EDTA; 93% H2O/7% D2O93% H2O/7% D2O
21mM VAP-A MSP domain; 1mM [U-13C; U-15N] OSBP FFAT motif; 50mM potassium phosphate; 100mM potassium chloride; 1mM DTT; 0.1mM EDTA; 93% H2O/7% D2O93% H2O/7% D2O
31mM [U-15N] VAP-A MSP domain; 1mM [U-15N] OSBP FFAT motif; 50mM potassium phosphate; 100mM potassium chloride; 1mM DTT; 0.1mM EDTA; 93% H2O/7% D2O93% H2O/7% D2O
41mM [U-13C; U-15N] VAP-A MSP domain; 1mM [U-13C; U-15N] OSBP FFAT motif; 50mM potassium phosphate; 100mM potassium chloride; 1mM DTT; 0.1mM EDTA; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMVAP-A MSP domain-1[U-13C; U-15N]1
1 mMOSBP FFAT motif-2[U-13C; U-15N]1
50 mMpotassium phosphate-31
100 mMpotassium chloride-41
1 mMDTT-51
0.1 mMEDTA-61
1 mMVAP-A MSP domain-7[U-13C; U-15N]2
1 mMOSBP FFAT motif-82
50 mMpotassium phosphate-92
100 mMpotassium chloride-102
1 mMDTT-112
0.1 mMEDTA-122
1 mMVAP-A MSP domain-133
1 mMOSBP FFAT motif-14[U-13C; U-15N]3
50 mMpotassium phosphate-153
100 mMpotassium chloride-163
1 mMDTT-173
0.1 mMEDTA-183
1 mMVAP-A MSP domain-19[U-15N]4
1 mMOSBP FFAT motif-20[U-15N]4
50 mMpotassium phosphate-214
100 mMpotassium chloride-224
1 mMDTT-234
0.1 mMEDTA-244
1 mMVAP-A MSP domain-25[U-13C; U-15N]5
1 mMOSBP FFAT motif-26[U-13C; U-15N]5
50 mMpotassium phosphate-275
100 mMpotassium chloride-285
1 mMDTT-295
0.1 mMEDTA-305
Sample conditionspH: 6.9 / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20 / Representative conformer: 1

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