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- PDB-7bwt: SopD-Rab8 complex structure -

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Basic information

Entry
Database: PDB / ID: 7bwt
TitleSopD-Rab8 complex structure
Components
  • Ras-related protein Rab-8A
  • SPI-1 type III secretion system effector SopD
KeywordsPROTEIN BINDING / complex
Function / homology
Function and homology information


neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / regulation of protein transport / vesicle-mediated transport in synapse / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / myosin V binding / RAB geranylgeranylation / protein secretion by the type III secretion system / trans-Golgi network transport vesicle ...neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / regulation of protein transport / vesicle-mediated transport in synapse / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / myosin V binding / RAB geranylgeranylation / protein secretion by the type III secretion system / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / protein localization to cilium / endocytic recycling / non-motile cilium / vesicle docking involved in exocytosis / TBC/RABGAPs / host cell cytosol / ciliary membrane / ciliary base / Golgi organization / exocytosis / cilium assembly / protein secretion / host cell membrane / phagocytic vesicle / Anchoring of the basal body to the plasma membrane / centriole / axonogenesis / protein tyrosine kinase binding / ciliary basal body / small monomeric GTPase / trans-Golgi network membrane / regulation of autophagy / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of long-term neuronal synaptic plasticity / cilium / autophagy / small GTPase binding / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / Regulation of PLK1 Activity at G2/M Transition / synaptic vesicle / midbody / dendritic spine / postsynaptic density / endosome membrane / endosome / Golgi membrane / GTPase activity / neuronal cell body / centrosome / glutamatergic synapse / GTP binding / host cell plasma membrane / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Salmonella outer protein D / Salmonella outer protein D / : / 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 ...Salmonella outer protein D / Salmonella outer protein D / : / 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
GUANOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / SPI-1 type III secretion system effector SopD / Secreted effector protein SopD / Ras-related protein Rab-8A
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJiang, K. / Tong, M. / Chen, Z. / Gao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31770143 China
CitationJournal: Nat Microbiol / Year: 2021
Title: The Salmonella effector protein SopD targets Rab8 to positively and negatively modulate the inflammatory response.
Authors: Lian, H. / Jiang, K. / Tong, M. / Chen, Z. / Liu, X. / Galan, J.E. / Gao, X.
History
DepositionApr 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 12, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPI-1 type III secretion system effector SopD
B: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,61315
Polymers59,1042
Non-polymers1,50913
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-22 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.660, 114.660, 107.066
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein SPI-1 type III secretion system effector SopD / Secreted protein in the Sop family transferred to eukaryotic cells


Mass: 38228.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: sopD, SBOV29801, AAK29_13240, AAP89_06495, ABO94_24435, AF480_02445, AF488_02240, AF489_05350, AIC76_09490, AU613_09175, AXR84_08085, AXU58_01945, C2253_22770, CD48_09420, CE87_05150, CET98_ ...Gene: sopD, SBOV29801, AAK29_13240, AAP89_06495, ABO94_24435, AF480_02445, AF488_02240, AF489_05350, AIC76_09490, AU613_09175, AXR84_08085, AXU58_01945, C2253_22770, CD48_09420, CE87_05150, CET98_05145, CQG18_13610, CVR97_12855, D4369_11200, D4380_01675, D4401_11680, D4E62_16310, D6360_15635, D7F20_20305, D7H43_13345, DJ388_17735, DKJ11_15155, DKU57_07540, DLM31_16580, DNV30_17025, DO698_06770, DOJ90_21490, DOQ88_13235, DPJ93_05695, DQ848_11540, DRM14_13800, DSF69_15975, DSR36_07735, DUW48_07630, EBO41_08190, EBP31_13605, EGU67_16485, EHB24_07065, EHC98_13260, EIW53_11070, GW08_01930, JO10_05155, LZ63_05365, NCTC13348_04477, NG18_06005, NU83_05435, QA89_11160, QB40_04780, QD15_03440, RJ78_02245, SAMEA4398682_00981, Y934_05005, YG50_06290, YI33_24045, YR17_16440, ZB89_12730, ZC54_04780
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5K1V7S2, UniProt: P40722*PLUS
#2: Protein Ras-related protein Rab-8A / Oncogene c-mel


Mass: 20875.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: RAB8A, MEL, RAB8 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61006

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Non-polymers , 5 types, 133 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.05M Sodium cacodylate trihydrate pH 6.5, 0.2 M MgCl2, 11.5% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→57.33 Å / Num. obs: 36383 / % possible obs: 99 % / Redundancy: 9 % / Biso Wilson estimate: 68.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.32
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 5694 / CC1/2: 0.566

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CPC,4LHW

5cpc

4lhw


Resolution: 2.3→57.33 Å / SU ML: 0.3308 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3886
RfactorNum. reflection% reflection
Rfree0.2147 3836 5.54 %
Rwork0.1883 --
obs0.1898 36321 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 85.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→57.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 0 97 120 3932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263871
X-RAY DIFFRACTIONf_angle_d0.58645193
X-RAY DIFFRACTIONf_chiral_restr0.0437566
X-RAY DIFFRACTIONf_plane_restr0.0032653
X-RAY DIFFRACTIONf_dihedral_angle_d17.8667519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.35511200.3791993X-RAY DIFFRACTION81.55
2.33-2.360.42491390.3592338X-RAY DIFFRACTION97.14
2.36-2.390.38361420.34372425X-RAY DIFFRACTION98.73
2.39-2.430.32851440.31832445X-RAY DIFFRACTION99.85
2.43-2.460.30771420.31652345X-RAY DIFFRACTION97.53
2.46-2.50.34331400.31592459X-RAY DIFFRACTION99.24
2.5-2.540.30591480.28352469X-RAY DIFFRACTION99.96
2.54-2.590.32491380.25212430X-RAY DIFFRACTION100
2.59-2.630.24861400.24072417X-RAY DIFFRACTION100
2.63-2.680.25181410.23072470X-RAY DIFFRACTION100
2.68-2.740.26031400.21872442X-RAY DIFFRACTION100
2.74-2.80.25211480.21972484X-RAY DIFFRACTION100
2.8-2.860.26961380.23432435X-RAY DIFFRACTION100
2.86-2.940.24731480.23052415X-RAY DIFFRACTION100
2.94-3.010.29061440.23622472X-RAY DIFFRACTION100
3.01-3.10.27461410.22272422X-RAY DIFFRACTION100
3.1-3.20.25171460.22012477X-RAY DIFFRACTION100
3.2-3.320.22211400.21642429X-RAY DIFFRACTION100
3.32-3.450.25141370.19952412X-RAY DIFFRACTION100
3.45-3.610.23081440.19122470X-RAY DIFFRACTION100
3.61-3.80.18831500.1872423X-RAY DIFFRACTION100
3.8-4.040.18471480.16682451X-RAY DIFFRACTION100
4.04-4.350.18891480.15362450X-RAY DIFFRACTION100
4.35-4.780.15381340.14272452X-RAY DIFFRACTION99.96
4.79-5.470.17611420.15822438X-RAY DIFFRACTION99.96
5.48-6.890.2321420.19272444X-RAY DIFFRACTION99.88
6.9-57.330.19131520.15562446X-RAY DIFFRACTION99.62
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)
14.97730571378-2.077221855890.5223996560314.10454937011-0.2829122609145.57151524275-0.0133585184750.5568098623270.374524529362-0.4210243876990.3515578780060.715075612369-0.313022323734-0.661293101611-0.3429773481050.764365095007-0.06584490236640.04128831817741.025830992440.2809528249221.135172409171.36797518183-15.464916185210.1719995313
25.81741031329-2.23086190672-1.591107218981.838879905930.006881338306195.639435504930.110290772696-0.1462987071160.2953057540150.32534364593-0.02724035695650.299727104594-0.0906401317897-0.123640673274-0.05480233074750.704260725046-0.141563499750.04921591393060.4680910868150.02097471585740.65398609739425.1441578223-15.874346445412.6741908347
32.37376125130.639169750691-1.875117377182.3761646553-1.068481380263.25974804753-0.06920815802910.278550100112-0.280278338328-0.3022942285760.02852409201570.1100285080150.323986660981-0.4581860424140.05123572579160.609989833173-0.107429943033-0.07411595022670.4195616281640.02357047203280.48574981354335.7536449676-17.5245711512-8.98885282921
43.454913556690.1784923069950.2496383185976.984417168122.5735827343.374305264530.1196106050450.0412499150850.0545541015105-0.447727314238-0.00301835130318-0.149757778199-0.6282161100680.170059591177-0.1305153091960.593006270991-0.1326353765740.01466333681210.5256524856850.01355126880290.53656954152255.2643202770.55520680199-2.11746977942
56.15590095493.108766922162.517753512772.847192731992.058055029691.513936093380.0134475346006-0.03558410503122.528240194260.309727852342-0.148902669931.02221464927-1.04773979227-0.5205717016620.1391556473551.08442857167-0.1005754055560.1692468698430.9011880635060.02776515699091.3232530759649.0817989812.4092677854-2.61057907469
62.00524973723-2.56576902418-1.691706824196.228817002011.242929089474.359469813210.2423692019120.460221228495-0.00011617969394-0.750046549198-0.119037893829-0.533711672325-0.674044983810.656525879345-0.1009498042120.653365184002-0.1589864993370.03511727024550.580729861770.02354108518110.4950214451257.9869998333-3.4710854502-8.49572255475
74.285559241490.722045591757-0.9570144118064.63159006986-1.494345255843.92412709297-0.0409761725529-1.468469230180.0583235088972.163070389340.1982183062662.135481583610.00899666865953-1.86828921781-0.1400555229261.24325044787-0.1638970827020.1647603791581.208476234820.03621672825631.2212609687744.5287909485-1.6067248263510.5963754392
85.205420953662.786997420430.6303554859875.62920866730.7915867440674.658173318920.51508846525-1.2240405106-0.248497442531.26501245738-0.4726264880680.116231682050.114056735724-0.040517678-0.05088967965710.803641059914-0.241510927748-0.02144970713990.8178121064320.0714873734670.52305843391855.8105015577-3.5154689790211.9876176605
95.22415955446-0.54793048715-0.5765483845154.359475518660.4308475859143.81821307420.227356763389-0.932292689968-0.1447626518120.929410087818-0.00817593133369-0.683002646164-0.08339720722710.434394940481-0.1807325677120.696518194909-0.22988080725-0.07568883007490.7550386203630.04655561453680.60896977455165.44348099620.02784309465156.61294979528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 160 )
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 317 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 30 )
5X-RAY DIFFRACTION5chain 'B' and (resid 31 through 44 )
6X-RAY DIFFRACTION6chain 'B' and (resid 45 through 62 )
7X-RAY DIFFRACTION7chain 'B' and (resid 63 through 74 )
8X-RAY DIFFRACTION8chain 'B' and (resid 75 through 121 )
9X-RAY DIFFRACTION9chain 'B' and (resid 122 through 180 )

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