[English] 日本語
Yorodumi
- PDB-2rr3: Solution structure of the complex between human VAP-A MSP domain ... -

+
Open data


ID or keywords:

Loading...

-
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 / intracellular cholesterol transport / ceramide transport / sterol binding / COPII-coated vesicle budding / positive regulation by host of viral genome replication ...positive regulation of secretory granule organization / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / sterol transfer activity / sphingomyelin biosynthetic process / intracellular cholesterol transport / ceramide transport / sterol binding / COPII-coated vesicle budding / positive regulation by host of viral genome replication / negative regulation by host of viral genome replication / sterol transport / perinuclear endoplasmic reticulum / bile acid biosynthetic process / protein localization to endoplasmic reticulum / Sphingolipid de novo biosynthesis / phospholipid transport / oxysterol binding / cholesterol transport / phosphatidylinositol-4-phosphate binding / azurophil granule membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / viral release from host cell / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Synthesis of bile acids and bile salts / bicellular tight junction / endoplasmic reticulum to Golgi vesicle-mediated transport / protein-membrane adaptor activity / trans-Golgi network / neuron projection development / cell junction / microtubule cytoskeleton / microtubule binding / nuclear membrane / vesicle / positive regulation of canonical NF-kappaB signal transduction / membrane fusion / cadherin binding / protein domain specific binding / protein heterodimerization activity / Golgi membrane / Neutrophil degranulation / endoplasmic reticulum membrane / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
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 / Immunoglobulin-like fold / Immunoglobulins / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more