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- PDB-4fme: EspG-Rab1-Arf6 complex -

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Basic information

Entry
Database: PDB / ID: 4fme
TitleEspG-Rab1-Arf6 complex
Components
  • ADP-ribosylation factor 6ARF6
  • EspG protein
  • Ras-related protein Rab-1A
KeywordsPROTEIN BINDING / alpha-beta fold / Rab1-GAP / Arf6 effector / Rab1 / Arf6
Function / homology
Function and homology information


positive regulation of glycoprotein metabolic process / erythrocyte apoptotic process / growth hormone secretion / maintenance of postsynaptic density structure / regulation of dendritic spine development / melanosome transport / COPII-coated vesicle cargo loading / establishment of epithelial cell polarity / negative regulation of receptor-mediated endocytosis / protein localization to endosome ...positive regulation of glycoprotein metabolic process / erythrocyte apoptotic process / growth hormone secretion / maintenance of postsynaptic density structure / regulation of dendritic spine development / melanosome transport / COPII-coated vesicle cargo loading / establishment of epithelial cell polarity / negative regulation of receptor-mediated endocytosis / protein localization to endosome / negative regulation of dendrite development / ruffle assembly / negative regulation of protein localization to cell surface / regulation of Rac protein signal transduction / vesicle transport along microtubule / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / thioesterase binding / MET receptor recycling / filopodium membrane / Golgi Cisternae Pericentriolar Stack Reorganization / protein localization to cell surface / Flemming body / TBC/RABGAPs / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / transport vesicle membrane / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / Golgi organization / cleavage furrow / autophagosome assembly / regulation of presynapse assembly / synaptic vesicle endocytosis / endocytic vesicle / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / signaling adaptor activity / COPI-mediated anterograde transport / vesicle-mediated transport / ruffle / substrate adhesion-dependent cell spreading / cellular response to nerve growth factor stimulus / small monomeric GTPase / G protein activity / liver development / positive regulation of interleukin-8 production / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / intracellular protein transport / positive regulation of neuron projection development / autophagy / endocytosis / recycling endosome membrane / GDP binding / melanosome / cell migration / presynapse / Clathrin-mediated endocytosis / nervous system development / cell cortex / early endosome membrane / postsynapse / cell differentiation / early endosome / cell adhesion / endosome / defense response to bacterium / cadherin binding / cell cycle / cell division / cysteine-type endopeptidase activity / Golgi membrane / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / endoplasmic reticulum / proteolysis / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Cysteine protease, VirA/EspG / Cysteine protease, VirA/EspG, N-terminal / EspG protein / ADP-ribosylation factor 6 / small GTPase Arf family 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 Rab1 family profile. ...Cysteine protease, VirA/EspG / Cysteine protease, VirA/EspG, N-terminal / EspG protein / ADP-ribosylation factor 6 / small GTPase Arf family 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 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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 / ARF6


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

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Non-polymers , 5 types, 14 molecules

#4: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


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


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

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Details

Sequence detailsRESIDUES WERE CONFIRMED BY GENE SEQUENCING

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Experimental details

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Experiment

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

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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

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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

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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

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