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- PDB-9vlb: Crystal Structure of a GDP-bound Bombyx mori RabX6 -

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Basic information

Entry
Database: PDB / ID: 9vlb
TitleCrystal Structure of a GDP-bound Bombyx mori RabX6
ComponentsRas-related protein Rab7
KeywordsPROTEIN BINDING / Rab / ras-related protein
Function / homology
Function and homology information


GTPase activity / GTP binding
Similarity search - Function
: / Small GTPase Rab domain profile. / Small GTPase Ras domain profile. / 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 / Ras-related protein Rab7
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsUrushihara, R. / Umemoto, Y. / Liu, J. / Nishimoto, E. / Teramoto, T. / Kakuta, Y. / Uno, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Biochem. / Year: 2025
Title: Crystal Structure of a GDP-bound Bombyx mori RabX6.
Authors: Urushihara, R. / Umemoto, Y. / Liu, J. / Nishimoto, E. / Teramoto, T. / Kakuta, Y. / Uno, T.
History
DepositionJun 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab7
B: Ras-related protein Rab7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0859
Polymers40,0782
Non-polymers1,0087
Water18010
1
A: Ras-related protein Rab7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5555
Polymers20,0391
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5314
Polymers20,0391
Non-polymers4923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.593, 109.735, 40.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ras-related protein Rab7


Mass: 20038.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: NP_001040271 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2F5M5
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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 Å3/Da / Density % sol: 38.39 %
Crystal growTemperature: 293.4 K / Method: vapor diffusion, hanging drop
Details: 0.2 M MgCl2, 0.1 M Tris-HCl pH8.5 ,25% PEG 3350, 4% Polypropylene glycol P400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→44.8 Å / Num. obs: 6694 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Net I/σ(I): 12.75
Reflection shellResolution: 3.1→3.15 Å / Num. unique obs: 669 / CC1/2: 0.651

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z0A

1z0a


Resolution: 3.1→44.8 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2912 324 4.84 %
Rwork0.2359 --
obs0.2387 6694 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 61 10 2607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022637
X-RAY DIFFRACTIONf_angle_d0.5473570
X-RAY DIFFRACTIONf_dihedral_angle_d12.521933
X-RAY DIFFRACTIONf_chiral_restr0.04410
X-RAY DIFFRACTIONf_plane_restr0.005442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.910.31641600.24833101X-RAY DIFFRACTION99
3.91-44.80.27511640.22843269X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 33.1414 Å / Origin y: 41.071 Å / Origin z: 28.2262 Å
111213212223313233
T0.3436 Å20.0581 Å20.1217 Å2-0.2394 Å2-0.0151 Å2--0.3278 Å2
L3.2593 °2-1.1906 °22.5525 °2-1.7169 °2-1.2585 °2--3.3119 °2
S0.0298 Å °0.0089 Å °-0.0202 Å °0.0154 Å °0.0488 Å °0.319 Å °-0.2195 Å °-0.2213 Å °-0.0736 Å °
Refinement TLS groupSelection details: all

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