[English] 日本語
Yorodumi
- PDB-4fmb: VirA-Rab1 complex structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fmb
TitleVirA-Rab1 complex structure
Components
  • Cysteine protease-like virA
  • Ras-related protein Rab-1A
KeywordsPROTEIN BINDING / alpha-beta fold / Rab1-GAP complex / Rab1
Function / homology
Function and homology information


positive regulation of glycoprotein metabolic process / growth hormone secretion / COPII-coated vesicle cargo loading / RAB geranylgeranylation / melanosome transport / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / vesicle transport along microtubule / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic ...positive regulation of glycoprotein metabolic process / growth hormone secretion / COPII-coated vesicle cargo loading / RAB geranylgeranylation / melanosome transport / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / vesicle transport along microtubule / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / transport vesicle membrane / virion assembly / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / vesicle-mediated transport / endomembrane system / substrate adhesion-dependent cell spreading / small monomeric GTPase / positive regulation of interleukin-8 production / intracellular protein transport / autophagy / endocytosis / melanosome / cell migration / G protein activity / early endosome / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / defense response to bacterium / cadherin binding / Golgi membrane / cysteine-type endopeptidase activity / GTPase activity / GTP binding / endoplasmic reticulum / Golgi apparatus / proteolysis / extracellular exosome / extracellular region / cytosol
Similarity search - Function
EspG protein, N-terminal domain / Cysteine protease, VirA/EspG / Cysteine protease, VirA/EspG, N-terminal / EspG protein / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Nuclear Transport Factor 2; Chain: A, / Rho (Ras homology) subfamily of Ras-like small GTPases ...EspG protein, N-terminal domain / Cysteine protease, VirA/EspG / Cysteine protease, VirA/EspG, N-terminal / EspG protein / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Nuclear Transport Factor 2; Chain: A, / 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 nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-1A / Cysteine protease-like VirA
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_ref_seq_dif.details / _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: Cysteine protease-like virA
B: Ras-related protein Rab-1A
C: Cysteine protease-like virA
D: Ras-related protein Rab-1A
E: Cysteine protease-like virA
F: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,23015
Polymers178,5766
Non-polymers1,6549
Water1629
1
A: Cysteine protease-like virA
B: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0775
Polymers59,5252
Non-polymers5513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-27 kcal/mol
Surface area23200 Å2
MethodPISA
2
C: Cysteine protease-like virA
D: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0775
Polymers59,5252
Non-polymers5513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-27 kcal/mol
Surface area23180 Å2
MethodPISA
3
E: Cysteine protease-like virA
F: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0775
Polymers59,5252
Non-polymers5513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-28 kcal/mol
Surface area23170 Å2
MethodPISA
4
A: Cysteine protease-like virA
B: Ras-related protein Rab-1A
C: Cysteine protease-like virA
D: Ras-related protein Rab-1A
E: Cysteine protease-like virA
F: Ras-related protein Rab-1A
hetero molecules

A: Cysteine protease-like virA
B: Ras-related protein Rab-1A
C: Cysteine protease-like virA
D: Ras-related protein Rab-1A
E: Cysteine protease-like virA
F: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,46030
Polymers357,15112
Non-polymers3,30918
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area38290 Å2
ΔGint-246 kcal/mol
Surface area126990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.118, 127.311, 107.325
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 6 molecules ACEBDF

#1: Protein Cysteine protease-like virA / Effector protein virA


Mass: 40140.234 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 301 / Gene: CP0181, pWR501_0191, virA / Plasmid: pGEX-6p-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7BU69, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Ras-related protein Rab-1A / YPT1-related protein


Mass: 19384.988 Da / Num. of mol.: 3
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

-
Non-polymers , 4 types, 18 molecules

#3: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: AlF3
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsRESIDUES WERE CONFIRMED BY GENE SEQUENCING

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.35 %
Crystal growTemperature: 298 K / pH: 7.6
Details: 0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 40511 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 4

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1886 4.6 %RANDOM
Rwork0.228 ---
obs0.228 37746 93.2 %-
all-40511 --
Solvent computationBsol: 55.06 Å2
Displacement parametersBiso mean: 105.24 Å2
Baniso -1Baniso -2Baniso -3
1--16.368 Å2-0 Å232.263 Å2
2--24.747 Å20 Å2
3----8.379 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12327 0 99 9 12435
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_it4.6031.5
X-RAY DIFFRACTIONc_mcangle_it5.2842
X-RAY DIFFRACTIONc_scbond_it7.4262
X-RAY DIFFRACTIONc_scangle_it8.8252.5
LS refinement shellResolution: 3.2→3.31 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3884 142 -
Rwork0.4134 2594 -
obs--66.6 %
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 DIFFRACTION6GDP.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