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- PDB-8kb8: Structure of the WDR91 WD40 domain complexed with Rab7 -

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Basic information

Entry
Database: PDB / ID: 8kb8
TitleStructure of the WDR91 WD40 domain complexed with Rab7
Components
  • Ras-related protein Rab-7a
  • WD repeat-containing protein 91
KeywordsENDOCYTOSIS / GTPase / Effector / WD40 / complex
Function / homology
Function and homology information


phosphatidylinositol 3-kinase inhibitor activity / lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / epidermal growth factor catabolic process / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / Suppression of autophagy ...phosphatidylinositol 3-kinase inhibitor activity / lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / epidermal growth factor catabolic process / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / Suppression of autophagy / phagosome-lysosome fusion / phagosome maturation / establishment of vesicle localization / retromer complex binding / endosome to plasma membrane protein transport / melanosome membrane / phosphatidylinositol 3-kinase regulator activity / RAB geranylgeranylation / protein targeting to lysosome / phagophore assembly site membrane / early endosome to late endosome transport / positive regulation of exosomal secretion / RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / RHOD GTPase cycle / retrograde transport, endosome to Golgi / TBC/RABGAPs / endosome to lysosome transport / regulation of protein catabolic process / RHOJ GTPase cycle / RHOQ GTPase cycle / autophagosome membrane / CDC42 GTPase cycle / RHOH GTPase cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / viral release from host cell / RHOG GTPase cycle / autophagosome assembly / intracellular transport / RAC2 GTPase cycle / RAC3 GTPase cycle / bone resorption / lipid catabolic process / Prevention of phagosomal-lysosomal fusion / phagocytic vesicle / RAC1 GTPase cycle / MHC class II antigen presentation / lipid droplet / small monomeric GTPase / secretory granule membrane / G protein activity / mitochondrial membrane / response to bacterium / small GTPase binding / synaptic vesicle membrane / endocytosis / positive regulation of protein catabolic process / phagocytic vesicle membrane / GDP binding / protein transport / late endosome / late endosome membrane / early endosome membrane / lysosome / endosome membrane / lysosomal membrane / GTPase activity / Neutrophil degranulation / GTP binding / Golgi apparatus / mitochondrion / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
WD repeat-containing protein 91 / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / 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 ...WD repeat-containing protein 91 / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / 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 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / WD repeat-containing protein 91 / Ras-related protein Rab-7a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsLi, J. / Ma, X.L. / Banerjee, S. / Dong, Z.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of the WDR91 WD40 domain complexed with Rab7
Authors: Li, J. / Ma, X.L. / Banerjee, S. / Dong, Z.G.
History
DepositionAug 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 91
B: WD repeat-containing protein 91
C: Ras-related protein Rab-7a
D: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,5648
Polymers120,4694
Non-polymers1,0954
Water48627
1
C: Ras-related protein Rab-7a
hetero molecules

A: WD repeat-containing protein 91


Theoretical massNumber of molelcules
Total (without water)60,7824
Polymers60,2352
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,y-1/2,-z1
2
D: Ras-related protein Rab-7a
hetero molecules

B: WD repeat-containing protein 91


Theoretical massNumber of molelcules
Total (without water)60,7824
Polymers60,2352
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Unit cell
Length a, b, c (Å)55.452, 81.077, 116.404
Angle α, β, γ (deg.)90.000, 94.406, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein WD repeat-containing protein 91


Mass: 39824.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR91 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A4D1P6
#2: Protein Ras-related protein Rab-7a


Mass: 20410.355 Da / Num. of mol.: 2 / Mutation: Q67L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB7A / Production host: Escherichia coli (E. coli) / References: UniProt: P51149
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 5% Tacsimate pH 7.0, 0.1 M HEPES pH 7.0, 10% Polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.49→48.49 Å / Num. obs: 35731 / % possible obs: 98.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 64.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.5
Reflection shellResolution: 2.49→2.59 Å / Rmerge(I) obs: 0.63 / Num. unique obs: 3982 / CC1/2: 0.684

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→48.49 Å / SU ML: 0.3538 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.0235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2612 1811 5.07 %
Rwork0.1974 33898 -
obs0.2007 35709 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.92 Å2
Refinement stepCycle: LAST / Resolution: 2.49→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7892 0 66 27 7985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00998119
X-RAY DIFFRACTIONf_angle_d1.303811008
X-RAY DIFFRACTIONf_chiral_restr0.07191233
X-RAY DIFFRACTIONf_plane_restr0.00791399
X-RAY DIFFRACTIONf_dihedral_angle_d18.96781112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.560.3611410.2842533X-RAY DIFFRACTION96.67
2.56-2.630.3281470.27572617X-RAY DIFFRACTION99.71
2.63-2.720.33131410.26512616X-RAY DIFFRACTION99.64
2.72-2.810.32371240.25012636X-RAY DIFFRACTION99.64
2.81-2.930.30961290.2542627X-RAY DIFFRACTION99.42
2.93-3.060.3481270.24952626X-RAY DIFFRACTION99.49
3.06-3.220.30531410.23672634X-RAY DIFFRACTION99.61
3.22-3.420.25291270.21342621X-RAY DIFFRACTION98.99
3.42-3.690.2631220.20332547X-RAY DIFFRACTION95.83
3.69-4.060.2411620.19782575X-RAY DIFFRACTION98.67
4.06-4.650.25881500.16052613X-RAY DIFFRACTION98.4
4.65-5.850.21921460.17242600X-RAY DIFFRACTION98.49
5.85-48.490.24421540.17412653X-RAY DIFFRACTION97.53

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