[English] 日本語
Yorodumi
- PDB-7bwt: SopD-Rab8 complex structure -

+
Open data


ID or keywords:

Loading...

-
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 / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / vesicle-mediated transport in synapse / protein secretion by the type III secretion system / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle ...neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / regulation of protein transport / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / vesicle-mediated transport in synapse / protein secretion by the type III secretion system / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / non-motile cilium / vesicle docking involved in exocytosis / TBC/RABGAPs / host cell cytosol / ciliary membrane / ciliary base / Golgi organization / exocytosis / host cell membrane / cilium assembly / phagocytic vesicle / centriole / axonogenesis / Anchoring of the basal body to the plasma membrane / protein tyrosine kinase binding / trans-Golgi network membrane / small monomeric GTPase / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of long-term neuronal synaptic plasticity / small GTPase binding / autophagy / centriolar satellite / phagocytic vesicle membrane / recycling endosome membrane / cellular response to insulin stimulus / synaptic vesicle / GDP binding / Regulation of PLK1 Activity at G2/M Transition / actin cytoskeleton / midbody / lysosome / endosome membrane / endosome / regulation of autophagy / cilium / ciliary basal body / Golgi membrane / neuronal cell body / GTPase activity / dendrite / centrosome / GTP binding / nucleolus / host cell plasma membrane / glutamatergic synapse / Golgi apparatus / extracellular exosome / extracellular region / nucleoplasm / 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 Rab domain 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 Rab domain 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 )

+
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