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- PDB-4fmc: EspG-Rab1 complex -

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Basic information

Entry
Database: PDB / ID: 4fmc
TitleEspG-Rab1 complex
Components
  • (Ras-related protein Rab- ...) x 2
  • ROrf2
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 / virion assembly / transport vesicle membrane / Golgi organization / autophagosome assembly / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / vesicle-mediated transport / substrate adhesion-dependent cell spreading / small monomeric GTPase / positive regulation of interleukin-8 production / intracellular protein transport / G protein activity / autophagy / endocytosis / melanosome / cell migration / early endosome / defense response to bacterium / cadherin binding / Golgi membrane / cysteine-type endopeptidase activity / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / 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 Rab1 family 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 Rab1 family 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 / TRIETHYLENE GLYCOL / ROrf2 / Ras-related protein Rab-1A / T3SS secreted effector EspG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ROrf2
B: Ras-related protein Rab-1A
C: ROrf2
D: Ras-related protein Rab-1A
E: ROrf2
F: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,79516
Polymers168,9906
Non-polymers1,80510
Water905
1
A: ROrf2
B: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0946
Polymers58,3932
Non-polymers7024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-29 kcal/mol
Surface area21810 Å2
MethodPISA
2
C: ROrf2
D: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9445
Polymers58,3932
Non-polymers5513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-29 kcal/mol
Surface area21760 Å2
MethodPISA
3
E: ROrf2
F: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7565
Polymers52,2052
Non-polymers5513
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-29 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.566, 152.707, 226.706
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 - 501
2124D8 - 501

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 3 molecules ACE

#1: Protein ROrf2


Mass: 38915.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157 / Gene: EspG, rorf2 / Plasmid: pGEX-6p-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O52121, UniProt: Q7DB50*PLUS

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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: 13288.965 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

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Non-polymers , 5 types, 15 molecules

#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: AlF3
#6: 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
#7: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 298 K / pH: 7
Details: 20% PEG3350 and 0.1 M potassium sodium tartrate, pH 7.0, 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: 0.97921
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: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 47307 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.625 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 1 / SU B: 43.137 / SU ML: 0.375 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2335 5.1 %RANDOM
Rwork0.225 ---
obs0.227 45891 99 %-
all-46331 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 104.77 Å2
Baniso -1Baniso -2Baniso -3
1--4.05 Å20 Å20 Å2
2---2.09 Å20 Å2
3---6.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11375 0 90 5 11470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211671
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.97515829
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91451452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.66424.504524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.862152023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0911580
X-RAY DIFFRACTIONr_chiral_restr0.0830.21830
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218681
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_it0.5491.57312
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05211841
X-RAY DIFFRACTIONr_scbond_it1.3534359
X-RAY DIFFRACTIONr_scangle_it2.334.53988
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 181 -
Rwork0.315 3226 -
obs--99.79 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.56921.31011.14981.78790.8770.7786-0.04430.03020.2737-0.05880.04290.33010.019-0.02340.00130.11070.00640.04250.04130.05590.3001-20.670558.839454.7046
24.43150.83840.49223.3326-0.54092.22580.0140.0672-0.1142-0.04920.08130.02250.2553-0.0547-0.09530.1556-0.1302-0.04170.13520.06610.1346-39.712732.625547.8677
32.43271.0980.4853.50560.2351.5069-0.50770.6848-0.1964-1.16880.8308-0.3859-0.30650.4112-0.32310.6571-0.37220.27450.545-0.26590.1923-1.669649.203822.2403
43.94141.65171.29166.92621.29753.1525-0.01170.4398-1.1911-0.33680.6181-0.41940.63240.1456-0.60640.5146-0.0367-0.02890.2644-0.25390.6636-11.080118.287429.5783
516.5678-2.8289-7.11582.17420.20967.07590.5918-0.9454-0.9827-0.055-0.49130.137-0.67280.3975-0.10050.2519-0.0831-0.02050.47320.06460.2277-36.639125.1919-9.8151
61.06340.85930.76373.0712-1.8876-0.55880.87840.47972.15621.0813-0.63660.4433-0.9790.0615-0.24192.34940.84542.21711.1171.02933.3638-44.392150.9587-14.8409
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 DIFFRACTION3C48 - 397
6X-RAY DIFFRACTION4D6 - 176
7X-RAY DIFFRACTION4D202 - 203
8X-RAY DIFFRACTION4C401
9X-RAY DIFFRACTION4D301
10X-RAY DIFFRACTION5E47 - 396
11X-RAY DIFFRACTION6F14 - 130
12X-RAY DIFFRACTION6F202 - 203

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