[English] 日本語
Yorodumi
- PDB-8vyb: Cryo-EM structure of human core Rab3GAP1/2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vyb
TitleCryo-EM structure of human core Rab3GAP1/2 complex
Components
  • Isoform 2 of Rab3 GTPase-activating protein catalytic subunit
  • Rab3 GTPase-activating protein non-catalytic subunit
KeywordsCYTOSOLIC PROTEIN / Complex / GAP / GEF / Rab3GAP / Lipid droplet / ER / Rab regulator / membrane trafficking
Function / homology
Function and homology information


positive regulation of glutamate neurotransmitter secretion in response to membrane depolarization / positive regulation of endoplasmic reticulum tubular network organization / establishment of protein localization to endoplasmic reticulum membrane / regulation of calcium ion-dependent exocytosis of neurotransmitter / synaptic signaling / endoplasmic reticulum tubular network / positive regulation of protein lipidation / positive regulation of autophagosome assembly / lipid droplet organization / RAB GEFs exchange GTP for GDP on RABs ...positive regulation of glutamate neurotransmitter secretion in response to membrane depolarization / positive regulation of endoplasmic reticulum tubular network organization / establishment of protein localization to endoplasmic reticulum membrane / regulation of calcium ion-dependent exocytosis of neurotransmitter / synaptic signaling / endoplasmic reticulum tubular network / positive regulation of protein lipidation / positive regulation of autophagosome assembly / lipid droplet organization / RAB GEFs exchange GTP for GDP on RABs / cis-Golgi network / camera-type eye development / regulation of short-term neuronal synaptic plasticity / COPI-independent Golgi-to-ER retrograde traffic / face morphogenesis / regulation of GTPase activity / hypothalamus development / enzyme regulator activity / lipid droplet / positive regulation of GTPase activity / GTPase activator activity / autophagosome / enzyme activator activity / guanyl-nucleotide exchange factor activity / excitatory postsynaptic potential / intracellular protein transport / macroautophagy / brain development / small GTPase binding / presynaptic membrane / postsynapse / endoplasmic reticulum membrane / Golgi apparatus / protein-containing complex / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Rab3GAP regulatory subunit / Rab3GAP catalytic subunit, conserved domain / Rab3GAP regulatory subunit, C-terminal / Rab3-GAP regulatory subunit, N-terminal / Rab3GAP catalytic subunit, C-terminal / Rab3GAP catalytic subunit / Rab3 GTPase-activating protein catalytic subunit / Rab3 GTPase-activating protein regulatory subunit N-terminus / Rab3 GTPase-activating protein regulatory subunit C-terminus / Rab3 GTPase-activating protein catalytic subunit C-terminal
Similarity search - Domain/homology
Rab3 GTPase-activating protein catalytic subunit / Rab3 GTPase-activating protein non-catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsNguyen, K.M. / Yip, C.K.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-168907 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-03951 Canada
CitationJournal: Nat Commun / Year: 2025
Title: Biochemical and structural characterization of Rab3GAP reveals insights into Rab18 nucleotide exchange activity.
Authors: Gage M J Fairlie / Kha M Nguyen / Sung-Eun Nam / Alexandria L Shaw / Matthew A H Parson / Hannah R Shariati / Xinyin Wang / Meredith L Jenkins / Michael Gong / John E Burke / Calvin K Yip /
Abstract: The heterodimeric Rab3GAP complex is a guanine nucleotide exchange factor (GEF) for the Rab18 GTPase that regulates lipid droplet metabolism, ER-to-Golgi trafficking, secretion, and autophagy. Why ...The heterodimeric Rab3GAP complex is a guanine nucleotide exchange factor (GEF) for the Rab18 GTPase that regulates lipid droplet metabolism, ER-to-Golgi trafficking, secretion, and autophagy. Why both subunits of Rab3GAP are required for Rab18 GEF activity and the molecular basis of how Rab3GAP engages and activates its cognate substrate are unknown. Here we show that human Rab3GAP is conformationally flexible and potentially autoinhibited by the C-terminal domain of its Rab3GAP2 subunit. Our high-resolution structure of the catalytic core of Rab3GAP, determined by cryo-EM, shows that the Rab3GAP2 N-terminal domain binds Rab3GAP1 via an extensive interface. AlphaFold3 modelling analysis together with targeted mutagenesis and in vitro activity assay reveal that Rab3GAP likely engages its substrate Rab18 through an interface away from the switch and interswitch regions. Lastly, we find that three Warburg Micro Syndrome-associated missense mutations do not affect the overall architecture of Rab3GAP but instead likely interfere with substrate binding.
History
DepositionFeb 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform 2 of Rab3 GTPase-activating protein catalytic subunit
B: Rab3 GTPase-activating protein non-catalytic subunit


Theoretical massNumber of molelcules
Total (without water)181,8692
Polymers181,8692
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Isoform 2 of Rab3 GTPase-activating protein catalytic subunit / RAB3 GTPase-activating protein 130 kDa subunit / Rab3-GAP p130 / Rab3-GAP


Mass: 116747.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3GAP1, KIAA0066, RAB3GAP / Plasmid: pBIG1A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15042
#2: Protein Rab3 GTPase-activating protein non-catalytic subunit / RGAP-iso / Rab3 GTPase-activating protein 150 kDa subunit / Rab3-GAP p150 / Rab3-GAP150 / Rab3-GAP ...RGAP-iso / Rab3 GTPase-activating protein 150 kDa subunit / Rab3-GAP p150 / Rab3-GAP150 / Rab3-GAP regulatory subunit


Mass: 65121.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3GAP2, KIAA0839 / Plasmid: pBIG1A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H2M9
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Core Rab3GAP1/2 complexCOMPLEXall0RECOMBINANT
2Rab3GAP1COMPLEX#11RECOMBINANT
3Rab3GAP2COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDPlasmid
21Spodoptera frugiperda (fall armyworm)7108pBIG1A
32Spodoptera frugiperda (fall armyworm)7108pBIG1A
43Spodoptera frugiperda (fall armyworm)7108pBIG1A
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMSodium chlorideNaCl1
31 mMTCEPC9H15O6P1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 2s blot time, 5s blot force

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 215000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
4cryoSPARC4.2.1CTF correction
7PHENIX1.20.1-4487model fitting
9Coot0.9.8.8model refinement
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARC4.2.1final Euler assignment
12cryoSPARC4.2.1classification
13cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 12427326
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170636 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

+
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