[English] 日本語
Yorodumi
- PDB-4q9u: Crystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q9u
TitleCrystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex
Components
  • Rab GTPase-binding effector protein 1
  • Rab5 GDP/GTP exchange factor
  • Ras-related protein Rab-5A
KeywordsENDOCYTOSIS / Rab5 / Rabex-5 / Rabaptin-5 / GEF activity / early endosomes / VPS9 / coiled-coil / GEF / effector / small GTPases
Function / homology
Function and homology information


dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of endosome size / postsynaptic early endosome / regulation of Fc receptor mediated stimulatory signaling pathway / cytoplasmic side of early endosome membrane / protein localization to ciliary membrane / Kit signaling pathway / negative regulation of mast cell degranulation ...dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of endosome size / postsynaptic early endosome / regulation of Fc receptor mediated stimulatory signaling pathway / cytoplasmic side of early endosome membrane / protein localization to ciliary membrane / Kit signaling pathway / negative regulation of mast cell degranulation / synaptic vesicle recycling / negative regulation of mast cell activation / amyloid-beta clearance by transcytosis / negative regulation of leukocyte migration / modulation by host of viral process / negative regulation of receptor-mediated endocytosis / regulation of autophagosome assembly / negative regulation of mast cell cytokine production / regulation of filopodium assembly / Golgi to plasma membrane transport / RAB geranylgeranylation / early endosome to late endosome transport / negative regulation of Ras protein signal transduction / RAB GEFs exchange GTP for GDP on RABs / early phagosome / TBC/RABGAPs / protein targeting to membrane / regulation of synaptic vesicle exocytosis / mast cell degranulation / positive regulation of exocytosis / Synthesis of PIPs at the plasma membrane / negative regulation of interleukin-6 production / endocytic vesicle / canonical Wnt signaling pathway / endomembrane system / phagocytic vesicle / axon terminus / phagocytosis / vesicle-mediated transport / somatodendritic compartment / Prevention of phagosomal-lysosomal fusion / ruffle / receptor-mediated endocytosis / GTPase activator activity / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / negative regulation of protein phosphorylation / clathrin-coated endocytic vesicle membrane / regulation of long-term neuronal synaptic plasticity / intracellular protein transport / growth factor activity / terminal bouton / receptor internalization / recycling endosome / small GTPase binding / negative regulation of inflammatory response / endocytosis / phagocytic vesicle membrane / GDP binding / ubiquitin protein ligase activity / melanosome / synaptic vesicle / actin cytoskeleton / protein transport / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production / early endosome membrane / Ras protein signal transduction / membrane fusion / early endosome / endosome membrane / endosome / membrane raft / axon / protein domain specific binding / intracellular membrane-bounded organelle / GTPase activity / dendrite / neuronal cell body / apoptotic process / GTP binding / nucleolus / protein homodimerization activity / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rabaptin / Rabaptin, GTPase-Rab5 binding domain / Rabaptin coiled-coil domain / Rabaptin / Rabaptin-like protein / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily ...Rabaptin / Rabaptin, GTPase-Rab5 binding domain / Rabaptin coiled-coil domain / Rabaptin / Rabaptin-like protein / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ras-related protein Rab-5A / Rab GTPase-binding effector protein 1 / Rab5 GDP/GTP exchange factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.618 Å
AuthorsZhang, Z. / Zhang, T. / Ding, J.
CitationJournal: Elife / Year: 2014
Title: Molecular mechanism for Rabex-5 GEF activation by Rabaptin-5
Authors: Zhang, Z. / Zhang, T. / Wang, S. / Gong, Z. / Tang, C. / Chen, J. / Ding, J.
History
DepositionMay 1, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rab5 GDP/GTP exchange factor
B: Ras-related protein Rab-5A
C: Rab GTPase-binding effector protein 1
D: Rab GTPase-binding effector protein 1
E: Rab5 GDP/GTP exchange factor
F: Ras-related protein Rab-5A
G: Rab GTPase-binding effector protein 1
H: Rab GTPase-binding effector protein 1


Theoretical massNumber of molelcules
Total (without water)155,5958
Polymers155,5958
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.821, 174.821, 148.995
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Rab5 GDP/GTP exchange factor / Rabex-5delta / RAP1 / Rabaptin-5-associated exchange factor for Rab5 / Rabex-5


Mass: 37320.891 Da / Num. of mol.: 2 / Fragment: UNP residues 132-455 / Mutation: 393-407 deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABGEF1, RABEX5 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q9UJ41
#2: Protein Ras-related protein Rab-5A / Rabaptin-5C21


Mass: 19074.648 Da / Num. of mol.: 2 / Fragment: UNP residues 15-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB5A, RAB5 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: P20339
#3: Protein
Rab GTPase-binding effector protein 1 / Rab5 / Rabaptin-4 / Rabaptin-5 / Rabaptin-5alpha / Renal carcinoma antigen NY-REN-17


Mass: 10701.068 Da / Num. of mol.: 4 / Fragment: UNP residues 552-642
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABEP1, RAB5EP, RABPT5, RABPT5A / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q15276
Sequence detailsTHE REFERENCE SEQUENCE OF CHAIN A, E IS ISOFORM 2 OF Q9UJ41, AND RESIDUES 393-407 HAVE BEEN DELETED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.38 % / Mosaicity: 1.181 °
Crystal growTemperature: 289 K / Method: hanging drop / pH: 5
Details: 1.0M NaH2PO4/K2HPO4, pH 5.0, hanging drop, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 4.6→50 Å / Num. obs: 12699 / % possible obs: 97.6 % / Redundancy: 9.8 % / Biso Wilson estimate: 172.68 Å2 / Rmerge(I) obs: 0.117 / Χ2: 1.181 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
4.6-4.7690.94312091.07395.8
4.76-4.959.30.57812271.20595.9
4.95-5.189.40.50812161.12296.1
5.18-5.459.70.7412231.03395.9
5.45-5.799.60.63812340.99396.6
5.79-6.249.60.49912651.00498.4
6.24-6.879.60.25212911.03399.4
6.87-7.869.80.11713021.28999.6
7.86-9.8911.10.0613361.62599.9
9.89-5010.60.04813961.27798.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OT3

2ot3


Resolution: 4.618→40.781 Å / FOM work R set: 0.5655 / SU ML: 0.78 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 45.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3427 631 5 %random
Rwork0.2513 ---
obs0.2561 12613 95.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 501.19 Å2 / Biso mean: 187.29 Å2 / Biso min: 33.68 Å2
Refinement stepCycle: LAST / Resolution: 4.618→40.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9679 0 0 0 9679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0159797
X-RAY DIFFRACTIONf_angle_d1.87313145
X-RAY DIFFRACTIONf_chiral_restr0.1091483
X-RAY DIFFRACTIONf_plane_restr0.0081699
X-RAY DIFFRACTIONf_dihedral_angle_d21.8713829
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.6182-4.97420.40161030.29012164226788
4.9742-5.47370.38451130.29672338245195
5.4737-6.26330.47081170.34612399251697
6.2633-7.88170.37031370.3052489262699
7.8817-40.78270.29241610.19542592275399

+
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