[English] 日本語
Yorodumi
- PDB-4fme: EspG-Rab1-Arf6 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fme
TitleEspG-Rab1-Arf6 complex
Components
  • ADP-ribosylation factor 6
  • EspG protein
  • Ras-related protein Rab-1A
KeywordsPROTEIN BINDING / alpha-beta fold / Rab1-GAP / Arf6 effector / Rab1 / Arf6
Function / homology
Function and homology information


erythrocyte apoptotic process / maintenance of postsynaptic density structure / positive regulation of glycoprotein metabolic process / protein localization to cleavage furrow / growth hormone secretion / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction ...erythrocyte apoptotic process / maintenance of postsynaptic density structure / positive regulation of glycoprotein metabolic process / protein localization to cleavage furrow / growth hormone secretion / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction / COPII-coated vesicle cargo loading / negative regulation of protein localization to cell surface / protein localization to endosome / negative regulation of receptor-mediated endocytosis / ruffle assembly / positive regulation of keratinocyte migration / regulation of filopodium assembly / positive regulation of focal adhesion disassembly / RAB geranylgeranylation / melanosome transport / MET receptor recycling / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / thioesterase binding / Golgi Cisternae Pericentriolar Stack Reorganization / vesicle transport along microtubule / Flemming body / filopodium membrane / protein localization to cell surface / TBC/RABGAPs / COPII-mediated vesicle transport / cortical actin cytoskeleton organization / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / transport vesicle membrane / hepatocyte apoptotic process / positive regulation of actin filament polymerization / Golgi organization / cleavage furrow / autophagosome assembly / endocytic vesicle / synaptic vesicle endocytosis / endoplasmic reticulum to Golgi vesicle-mediated transport / regulation of presynapse assembly / COPI-mediated anterograde transport / vesicle-mediated transport / ruffle / signaling adaptor activity / endomembrane system / substrate adhesion-dependent cell spreading / small monomeric GTPase / positive regulation of protein secretion / positive regulation of interleukin-8 production / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / intracellular protein transport / liver development / positive regulation of neuron projection development / cellular response to nerve growth factor stimulus / autophagy / endocytosis / recycling endosome membrane / GDP binding / melanosome / cell migration / nervous system development / presynapse / Clathrin-mediated endocytosis / G protein activity / early endosome membrane / midbody / cell cortex / early endosome / cell differentiation / postsynapse / cell adhesion / endosome / defense response to bacterium / cadherin binding / Golgi membrane / cell division / cysteine-type endopeptidase activity / focal adhesion / GTPase activity / GTP binding / glutamatergic synapse / endoplasmic reticulum / Golgi apparatus / proteolysis / extracellular exosome / extracellular region / metal ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cysteine protease, VirA/EspG / Cysteine protease, VirA/EspG, N-terminal / EspG protein / ADP-ribosylation factor 6 / : / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family ...Cysteine protease, VirA/EspG / Cysteine protease, VirA/EspG, N-terminal / EspG protein / ADP-ribosylation factor 6 / : / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain 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
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / ADP-ribosylation factor 6 / Ras-related protein Rab-1A / EspG protein / T3SS secreted effector EspG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsShao, F. / Zhu, Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Structurally Distinct Bacterial TBC-like GAPs Link Arf GTPase to Rab1 Inactivation to Counteract Host Defenses.
Authors: Dong, N. / Zhu, Y. / Lu, Q. / Hu, L. / Zheng, Y. / Shao, F.
History
DepositionJun 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EspG protein
B: Ras-related protein Rab-1A
C: ADP-ribosylation factor 6
D: EspG protein
E: Ras-related protein Rab-1A
F: ADP-ribosylation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,87616
Polymers153,6786
Non-polymers2,19810
Water724
1
A: EspG protein
B: Ras-related protein Rab-1A
C: ADP-ribosylation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9388
Polymers76,8393
Non-polymers1,0995
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-51 kcal/mol
Surface area28920 Å2
MethodPISA
2
D: EspG protein
E: Ras-related protein Rab-1A
F: ADP-ribosylation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9388
Polymers76,8393
Non-polymers1,0995
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-50 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.222, 137.222, 126.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

-
Protein , 3 types, 6 molecules ADBECF

#1: Protein EspG protein


Mass: 38903.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157 / Gene: espG / Plasmid: pGEX-6p-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5WMC0, UniProt: Q7DB50*PLUS
#2: Protein Ras-related protein Rab-1A / YPT1-related protein


Mass: 19477.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1, RAB1A / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62820
#3: Protein ADP-ribosylation factor 6


Mass: 18458.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF6 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62330

-
Non-polymers , 5 types, 14 molecules

#4: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF3
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsRESIDUES WERE CONFIRMED BY GENE SEQUENCING

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.26 %
Crystal growTemperature: 298 K / pH: 6.2
Details: 8% PEG8000, 0.1 M NaKPO4 (pH 6.2), and 0.2 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97923
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 4.1→50 Å / Num. obs: 18452 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 5.8
Reflection shellResolution: 4.1→4.25 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.663 / % possible all: 99.6

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1667 9 %RANDOM
Rwork0.208 ---
obs0.208 17134 92.5 %-
all-18489 --
Solvent computationBsol: 81.83 Å2
Displacement parametersBiso mean: 150.5 Å2
Baniso -1Baniso -2Baniso -3
1-19.014 Å2-0 Å20 Å2
2--19.014 Å20 Å2
3----38.028 Å2
Refinement stepCycle: LAST / Resolution: 4.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10774 0 132 4 10910
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it9.16115
X-RAY DIFFRACTIONc_mcangle_it14.20320
X-RAY DIFFRACTIONc_scbond_it13.09420
X-RAY DIFFRACTIONc_scangle_it19.24925
LS refinement shellResolution: 4.1→4.25 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3321 144 -
Rwork0.3181 1332 -
obs--80.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION4CNS_TOPPAR:ION.PARAM
X-RAY DIFFRACTION5CNS_TOPPAR:CARBOHYDRATE.PARAM
X-RAY DIFFRACTION6GAO.PAR
X-RAY DIFFRACTION7GTP.PAR

+
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