[English] 日本語
Yorodumi
- PDB-2vx8: Vamp7 longin domain Hrb peptide complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vx8
TitleVamp7 longin domain Hrb peptide complex
ComponentsNUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
KeywordsENDOCYTOSIS / EXOCYTOSIS / MEMBRANE PROTEIN / SIGNAL-ANCHOR / SNARE / MEMBRANE / ENDOSOME / LYSOSOME / TRANSPORT / CYTOPLASMIC VESICLE / ENDOPLASMIC RETICULUM / PROTEIN TRANSPORT / VESICLE TRANSPORT / TRANSMEMBRANE / GOLGI APPARATUS / CLATHRIN ADAPTOR
Function / homology
Function and homology information


regulation of protein targeting to vacuolar membrane / neutrophil degranulation / spermatid nucleus differentiation / acrosome assembly / intermediate filament organization / eosinophil degranulation / SNARE complex / vesicle fusion / calcium-ion regulated exocytosis / Golgi to plasma membrane protein transport ...regulation of protein targeting to vacuolar membrane / neutrophil degranulation / spermatid nucleus differentiation / acrosome assembly / intermediate filament organization / eosinophil degranulation / SNARE complex / vesicle fusion / calcium-ion regulated exocytosis / Golgi to plasma membrane protein transport / positive regulation of dendrite morphogenesis / SNARE complex assembly / phagocytosis, engulfment / transport vesicle membrane / endosome to lysosome transport / pseudopodium / endoplasmic reticulum to Golgi vesicle-mediated transport / nuclear pore / mRNA export from nucleus / transport vesicle / vesicle-mediated transport / phagocytic vesicle / GTPase activator activity / phagocytic vesicle membrane / late endosome membrane / apical part of cell / Cargo recognition for clathrin-mediated endocytosis / lamellipodium / Clathrin-mediated endocytosis / cytoplasmic vesicle / neuron projection / lysosomal membrane / intracellular membrane-bounded organelle / synapse / endoplasmic reticulum membrane / perinuclear region of cytoplasm / cell surface / Golgi apparatus / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
: / : / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin signature. / Arf GTPase activating protein / ArfGAP domain superfamily ...: / : / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin signature. / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / Synaptobrevin-like / Synaptobrevin / ARFGAP/RecO-like zinc finger / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Longin-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Arf-GAP domain and FG repeat-containing protein 1 / Vesicle-associated membrane protein 7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsEvans, P.R. / Owen, D.J. / Luzio, J.P.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Molecular Basis for the Sorting of the Snare Vamp7 Into Endocytic Clathrin-Coated Vesicles by the Arfgap Hrb.
Authors: Pryor, P.R. / Jackson, L. / Gray, S.R. / Edeling, M.A. / Thompson, A. / Sanderson, C.M. / Evans, P.R. / Owen, D.J. / Luzio, J.P.
History
DepositionJul 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 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: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
B: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
C: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
D: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8307
Polymers74,7244
Non-polymers1063
Water3,063170
1
A: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
B: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4334
Polymers37,3622
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-49.5 kcal/mol
Surface area15940 Å2
MethodPQS
2
A: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7


Theoretical massNumber of molelcules
Total (without water)18,6811
Polymers18,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7523
Polymers18,6811
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7


Theoretical massNumber of molelcules
Total (without water)18,6811
Polymers18,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
D: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7162
Polymers18,6811
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.514, 115.102, 55.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 / HRB / HIV-1 REV-BINDING PROTEIN / REV-INTERACTING PROTEIN / REV/REX ACTIVATION DOMAIN-BINDING ...HRB / HIV-1 REV-BINDING PROTEIN / REV-INTERACTING PROTEIN / REV/REX ACTIVATION DOMAIN-BINDING PROTEIN / VAMP7 / VAMP-7 / SYNAPTOBREVIN-LIKE PROTEIN 1


Mass: 18681.023 Da / Num. of mol.: 4
Fragment: HRB, RESIDUES 136-175, VAMP7 LONGIN DOMAIN, RESIDUES 1-120
Source method: isolated from a genetically manipulated source
Details: CHIMERA OF HUMAN HRB AND MOUSE VAMP7
Source: (gene. exp.) HOMO SAPIENS (human), (gene. exp.) MUS MUSCULUS (house mouse)
Plasmid: PGEX 4T-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P52594, UniProt: P70280
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 44-163 CORRESPOND TO THE LONGIN DOMAIN OF VAMP7 RESIDUES 1-42 ARE FROM HUMAN HRB ...RESIDUES 44-163 CORRESPOND TO THE LONGIN DOMAIN OF VAMP7 RESIDUES 1-42 ARE FROM HUMAN HRB (ACCESSION NUMBER NM_004504) G43 AND THE C-TERMINAL H6 (RESIDUES 163-168) ARE CLONING ARTIFACTS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 54.6 % / Description: A SINGLE HG DERIVATIVE WAS USED
Crystal growpH: 4
Details: 20% PEG 6000, 100MM NA CITRATE PH 4.0, 0.2M LICL, FLASH COOLED IN 22%PEG, 20% GLYCEROL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→78 Å / Num. obs: 34876 / % possible obs: 99.3 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 6.6 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
REFMAC5.5.0035refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.2→57.71 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.892 / SU B: 6.678 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE CRYSTALLISED CHAIN IS A FUSION PROTEIN CORRESPONDING TO RESIDUES 136-176 OF HRB LINKED BY A SINGLE GLYCINE (RESIDUE 43) TO RESIDUES 1- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE CRYSTALLISED CHAIN IS A FUSION PROTEIN CORRESPONDING TO RESIDUES 136-176 OF HRB LINKED BY A SINGLE GLYCINE (RESIDUE 43) TO RESIDUES 1-120 OF VAMP7 THE ASYMMETRIC UNIT CONTAINS 4 MOLECULES. CHAINS C AND D ARE SELF-CONTAINED. CHAINS A & B SWAP THE FIRST 40 RESIDUES OR SO, CORRESPONDING TO THE HRB FRAGMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1747 5 %RANDOM
Rwork0.22 ---
obs0.223 33094 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20 Å2
2---0.13 Å20 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→57.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4245 0 3 170 4418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224338
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9961.9525877
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4415533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.7623.613191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42615722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2771523
X-RAY DIFFRACTIONr_chiral_restr0.1550.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213247
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3031.52686
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.31924318
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.16831652
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0294.51559
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: 2.2→2.25 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 111
Rwork0.258 2305

+
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