[English] 日本語
Yorodumi
- PDB-4b93: Complex of Vamp7 cytoplasmic domain with 2nd ankyrin repeat domai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b93
TitleComplex of Vamp7 cytoplasmic domain with 2nd ankyrin repeat domain of Varp
Components
  • ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
  • VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
KeywordsEXOCYTOSIS / ENDOCYTOSIS / SNARE
Function / homology
Function and homology information


regulation of protein targeting to vacuolar membrane / positive regulation of histamine secretion by mast cell / chylomicron assembly / neutrophil degranulation / negative regulation of SNARE complex assembly / triglyceride transport / natural killer cell degranulation / tubular endosome / vesicle fusion with Golgi apparatus / endosome to melanosome transport ...regulation of protein targeting to vacuolar membrane / positive regulation of histamine secretion by mast cell / chylomicron assembly / neutrophil degranulation / negative regulation of SNARE complex assembly / triglyceride transport / natural killer cell degranulation / tubular endosome / vesicle fusion with Golgi apparatus / endosome to melanosome transport / eosinophil degranulation / early endosome to late endosome transport / SNARE complex / SNAP receptor activity / platelet alpha granule / calcium-ion regulated exocytosis / vesicle fusion / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / Golgi to plasma membrane protein transport / positive regulation of dendrite morphogenesis / vesicle transport along microtubule / syntaxin binding / azurophil granule membrane / phagocytosis, engulfment / endosome to lysosome transport / SNARE complex assembly / exocytosis / pseudopodium / synaptic vesicle exocytosis / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / neuron projection morphogenesis / phagocytic vesicle / vesicle-mediated transport / GTPase activator activity / guanyl-nucleotide exchange factor activity / secretory granule membrane / secretory granule / cytoplasmic vesicle membrane / hippocampal mossy fiber to CA3 synapse / SNARE binding / filopodium / trans-Golgi network / positive regulation of neuron projection development / small GTPase binding / phagocytic vesicle membrane / apical part of cell / melanosome / late endosome / late endosome membrane / synaptic vesicle membrane / lamellipodium / protein transport / early endosome / lysosome / neuron projection / lysosomal membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / cell surface / Golgi apparatus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / Longin domain / Longin domain profile. / Longin domain ...: / : / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Longin-like domain superfamily / Ankyrin repeat-containing domain / Beta-Lactamase / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Vesicle-associated membrane protein 7 / Ankyrin repeat domain-containing protein 27
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsSchaefer, I.B. / Owen, D.J. / Luzio, J.P. / Evans, P.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: The Binding of Varp to Vamp7 Traps Vamp7 in a Closed, Fusogenically Inactive Conformation.
Authors: Schafer, I.B. / Hesketh, G.G. / Bright, N.A. / Gray, S.R. / Pryor, P.R. / Evans, P.R. / Luzio, J.P. / Owen, D.J.
History
DepositionAug 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Jan 25, 2017Group: Data collection
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
B: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27


Theoretical massNumber of molelcules
Total (without water)51,0132
Polymers51,0132
Non-polymers00
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.570, 122.660, 158.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 / VAMP-7 / SYNAPTOBREVIN-LIKE PROTEIN 1


Mass: 21520.695 Da / Num. of mol.: 1 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 1-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: VAMP7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: P70280
#2: Protein ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27 / VARP / VPS9 DOMAIN-CONTAINING PROTEIN


Mass: 29492.562 Da / Num. of mol.: 1 / Fragment: 2ND ANKYRIN REPEAT DOMAIN, RESIDUES 659-921
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: VARP658-921 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: Q96NW4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.91 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 5 TO 7.5 % (V/V) ISOPROPANOL AND 0.1 M IMIDAZOLE PH 6.5-7.8 IN HANGING AND SITTING DROPS AT 4 DEGREES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2009 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→56 Å / Num. obs: 43692 / % possible obs: 99.7 % / Observed criterion σ(I): 100 / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 0.9 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.7.0018refinement
MOSFLMdata reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2→39.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.895 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 2332 5.1 %RANDOM
Rwork0.21312 ---
obs0.21505 43692 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.152 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å20 Å20 Å2
2--1.07 Å20 Å2
3----3.9 Å2
Refinement stepCycle: LAST / Resolution: 2→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 0 209 2916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192758
X-RAY DIFFRACTIONr_bond_other_d0.0010.022695
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.9513728
X-RAY DIFFRACTIONr_angle_other_deg0.87636169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8845346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26224.58131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70115488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7851517
X-RAY DIFFRACTIONr_chiral_restr0.1070.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023151
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2834.8772758
X-RAY DIFFRACTIONr_mcbond_other1.2364.982695
X-RAY DIFFRACTIONr_mcangle_it6.1897.2233727
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 172 -
Rwork0.391 3184 -
obs--99 %

+
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