[English] 日本語
Yorodumi
- PDB-4fmd: EspG-Rab1 complex structure at 3.05 A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fmd
TitleEspG-Rab1 complex structure at 3.05 A
Components
  • (Ras-related protein Rab- ...) x 2
  • EspG protein
KeywordsPROTEIN BINDING / alpha-beta fold / Rab1-GAP / Rab1
Function / homology
Function and homology information


positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic ...positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / transport vesicle membrane / Golgi organization / virion assembly / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / endomembrane system / G protein activity / small monomeric GTPase / substrate adhesion-dependent cell spreading / vesicle-mediated transport / intracellular protein transport / positive regulation of interleukin-8 production / autophagy / melanosome / endocytosis / cell migration / early endosome / cadherin binding / cysteine-type endopeptidase activity / GTPase activity / Golgi membrane / defense response to bacterium / GTP binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome / extracellular region / metal ion binding / cytosol
Similarity search - Function
EspG protein, N-terminal domain / Cysteine protease, VirA/EspG, N-terminal / Cysteine protease, VirA/EspG / EspG protein / small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Nuclear Transport Factor 2; Chain: A, / Ras family / Small GTPase / Small GTP-binding protein domain ...EspG protein, N-terminal domain / Cysteine protease, VirA/EspG, N-terminal / Cysteine protease, VirA/EspG / EspG protein / small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Nuclear Transport Factor 2; Chain: A, / Ras family / Small GTPase / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ras-related protein Rab-1A / EspG protein / ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / TRIETHYLENE GLYCOL / DI(HYDROXYETHYL)ETHER / T3SS secreted effector EspG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)176,12517
Polymers174,2146
Non-polymers1,91111
Water1448
1
A: EspG protein
B: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9325
Polymers58,3812
Non-polymers5513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-30 kcal/mol
Surface area21480 Å2
MethodPISA
2
C: EspG protein
D: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0826
Polymers58,3812
Non-polymers7024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-30 kcal/mol
Surface area21580 Å2
MethodPISA
3
E: EspG protein
F: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1106
Polymers57,4532
Non-polymers6584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-27 kcal/mol
Surface area21430 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)106.568, 153.221, 230.805
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A48 - 395
2114C48 - 395
3114E48 - 395
1124B8 - 502
2124D8 - 502

NCS ensembles :
ID
1
2

-
Components

-
Protein , 1 types, 3 molecules ACE

#1: Protein EspG protein


Mass: 38903.648 Da / Num. of mol.: 3
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

-
Ras-related protein Rab- ... , 2 types, 3 molecules BDF

#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 Ras-related protein Rab-1A / YPT1-related protein


Mass: 18549.086 Da / Num. of mol.: 1
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 , 6 types, 19 molecules

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


Mass: 83.977 Da / Num. of mol.: 3 / 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.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 298 K / pH: 7
Details: 20% PEG3350, 0.1 M trisodium citrate, pH 7.0, 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: 3.05→50 Å / Num. obs: 36189 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.2
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.781 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 1 / SU B: 51.765 / SU ML: 0.412 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1807 5 %RANDOM
Rwork0.212 ---
obs0.214 36032 99 %-
all-36414 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.82 Å2
Baniso -1Baniso -2Baniso -3
1--5.62 Å20 Å20 Å2
2---1.05 Å20 Å2
3---6.67 Å2
Refinement stepCycle: LAST / Resolution: 3.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12024 0 114 8 12146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02212349
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.97716764
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.11851535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.77624.575553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.441152152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.811581
X-RAY DIFFRACTIONr_chiral_restr0.0760.21936
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219183
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4531.57701
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.856212493
X-RAY DIFFRACTIONr_scbond_it0.91934648
X-RAY DIFFRACTIONr_scangle_it1.6434.54271
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2696medium positional0.420.5
12C2696medium positional0.360.5
13E2696medium positional0.370.5
21B1387medium positional0.220.5
11A2696medium thermal0.42
12C2696medium thermal0.32
13E2696medium thermal0.322
21B1387medium thermal0.432
LS refinement shellResolution: 3.05→3.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 137 -
Rwork0.289 2513 -
obs--99.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.18411.0568-0.97551.8312-0.79221.3144-0.00350.0712-0.2741-0.00090.0589-0.1089-0.08990.0975-0.05540.0940.0174-0.05510.1205-0.08120.3494-32.6679-59.110155.2994
25.14161.019-0.37012.9780.48622.12380.05750.0167-0.0516-0.0530.21940.2597-0.35710.2022-0.27690.1623-0.16630.1020.2362-0.0980.1287-13.8221-32.773748.7227
32.32210.2126-0.17282.9034-0.1681.4399-0.23120.58520.0697-0.5730.50750.4120.1484-0.2372-0.27630.3733-0.191-0.16710.520.20980.3258-51.6717-49.556322.9004
44.03121.187-0.5215.1692-0.94043.00480.00160.52651.07830.07040.51370.407-0.6312-0.1-0.51530.44110.00490.1090.19680.27760.699-42.2915-18.518130.1933
55.7102-2.03871.7843.47450.3583.73340.3894-0.18350.2487-0.0667-0.2731-0.17690.369-0.3512-0.11640.3011-0.0586-0.01310.52520.02290.2905-16.8327-25.1628-10.0808
63.12231.05151.29857.51032.71193.75960.8320.4992-1.32320.5209-0.3386-0.3751.58950.0227-0.49341.25770.1065-0.57940.5794-0.31911.0335-8.4048-55.963-17.5539
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A47 - 397
2X-RAY DIFFRACTION2B6 - 176
3X-RAY DIFFRACTION2B202 - 203
4X-RAY DIFFRACTION2B301 - 302
5X-RAY DIFFRACTION3C47 - 397
6X-RAY DIFFRACTION4D6 - 176
7X-RAY DIFFRACTION4D202 - 203
8X-RAY DIFFRACTION4D301 - 302
9X-RAY DIFFRACTION5E47 - 396
10X-RAY DIFFRACTION6F13 - 176
11X-RAY DIFFRACTION6F202 - 203
12X-RAY DIFFRACTION6F301

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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