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- PDB-8yim: Crystal Structure of Human Rab23 in complex with GMPPNP (1.35 Ang... -

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Basic information

Entry
Database: PDB / ID: 8yim
TitleCrystal Structure of Human Rab23 in complex with GMPPNP (1.35 Angstroms Resolution)
ComponentsRas-related protein Rab-23
KeywordsHYDROLASE / Small GTPase Rossmann Fold
Function / homology
Function and homology information


craniofacial suture morphogenesis / RAB geranylgeranylation / GTP metabolic process / negative regulation of protein import into nucleus / cilium assembly / autophagosome assembly / cellular defense response / phagocytic vesicle / endomembrane system / autophagosome ...craniofacial suture morphogenesis / RAB geranylgeranylation / GTP metabolic process / negative regulation of protein import into nucleus / cilium assembly / autophagosome assembly / cellular defense response / phagocytic vesicle / endomembrane system / autophagosome / small monomeric GTPase / intracellular protein transport / phagocytic vesicle membrane / cell junction / endosome membrane / ciliary basal body / cilium / GTPase activity / centrosome / GTP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ras-related protein Rab-23 / : / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsChau, Y.Y. / Liang, H. / Aik, W.S.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Other privateHKBU Faculty of Science Seed Money Hong Kong
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural basis for Rab23 activation and a loss-of-function mutation in Carpenter syndrome.
Authors: Chau, Y.Y. / Liang, H. / Tung, W.L. / Hor, C.H.H. / Aik, W.S.
History
DepositionFeb 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 8, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6363
Polymers19,0901
Non-polymers5472
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-14 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.523, 60.523, 93.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

21A-492-

HOH

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Components

#1: Protein Ras-related protein Rab-23


Mass: 19089.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Truncated to residues 7-172 / Source: (gene. exp.) Homo sapiens (human) / Gene: RAB23, HSPC137 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULC3
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Imidazole pH 8.0, 0.2M NaCl, 0.4M sodium phosphate monobasic/1.6M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.35→22.88 Å / Num. obs: 44414 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 9.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.046 / Rrim(I) all: 0.141 / Χ2: 1.37 / Net I/σ(I): 24.5
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.087 / Num. unique obs: 2185 / CC1/2: 0.724 / Rpim(I) all: 0.862 / Rrim(I) all: 2.26 / Χ2: 0.52

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
CrysalisProdata scaling
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→22.88 Å / SU ML: 0.111 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.5251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1794 2354 5.31 %
Rwork0.1496 42015 -
obs0.1513 44369 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.58 Å2
Refinement stepCycle: LAST / Resolution: 1.35→22.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1242 0 33 193 1468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271348
X-RAY DIFFRACTIONf_angle_d0.68051831
X-RAY DIFFRACTIONf_chiral_restr0.0648212
X-RAY DIFFRACTIONf_plane_restr0.0025229
X-RAY DIFFRACTIONf_dihedral_angle_d14.2101516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.23481610.18982438X-RAY DIFFRACTION100
1.38-1.410.19611520.17432424X-RAY DIFFRACTION100
1.41-1.440.20091320.15672434X-RAY DIFFRACTION100
1.44-1.480.20091300.14232438X-RAY DIFFRACTION100
1.48-1.520.20451230.13462451X-RAY DIFFRACTION100
1.52-1.560.1625950.132476X-RAY DIFFRACTION100
1.56-1.610.17271410.12662417X-RAY DIFFRACTION100
1.61-1.670.16111180.12812492X-RAY DIFFRACTION100
1.67-1.740.18251440.12752453X-RAY DIFFRACTION100
1.74-1.810.17841230.1352459X-RAY DIFFRACTION100
1.81-1.910.16931460.13912447X-RAY DIFFRACTION100
1.91-2.030.16371320.13532500X-RAY DIFFRACTION100
2.03-2.190.16251410.13752468X-RAY DIFFRACTION100
2.19-2.410.16841220.14772490X-RAY DIFFRACTION100
2.41-2.750.19471650.1642487X-RAY DIFFRACTION100
2.75-3.470.1821400.16532523X-RAY DIFFRACTION100
3.47-22.880.17531890.15922618X-RAY DIFFRACTION99.96

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