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- PDB-9ltq: Crystal structure of human RAB43 in complex with GppNHp -

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Basic information

Entry
Database: PDB / ID: 9ltq
TitleCrystal structure of human RAB43 in complex with GppNHp
ComponentsRas-related protein Rab-43
KeywordsHYDROLASE / Small GTPase / Rab GTPase / P-loop containing nucleotide triphosphate hydrolases
Function / homology
Function and homology information


retrograde transport, plasma membrane to Golgi / regulation of Golgi organization / Retrograde transport at the Trans-Golgi-Network / cis-Golgi network membrane / phagosome maturation / RAB geranylgeranylation / virion assembly / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport ...retrograde transport, plasma membrane to Golgi / regulation of Golgi organization / Retrograde transport at the Trans-Golgi-Network / cis-Golgi network membrane / phagosome maturation / RAB geranylgeranylation / virion assembly / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / phagocytic vesicle / endomembrane system / endoplasmic reticulum-Golgi intermediate compartment membrane / trans-Golgi network membrane / small monomeric GTPase / intracellular protein transport / cellular response to type II interferon / phagocytic vesicle membrane / G protein activity / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / extracellular exosome
Similarity search - Function
: / : / 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-43
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWang, J. / Yan, W.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32101008 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Molecular basis of Rab43 inactivation by RN-Tre in endocytic trafficking unveils a general Rab-GAP recognition mechanism.
Authors: Wang, J. / Liu, T. / Zhang, Z. / Yan, W.
History
DepositionFeb 6, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 14, 2026Provider: 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 Rab-43
B: Ras-related protein Rab-43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8936
Polymers40,8002
Non-polymers1,0934
Water6,287349
1
A: Ras-related protein Rab-43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9473
Polymers20,4001
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9473
Polymers20,4001
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.780, 77.858, 64.064
Angle α, β, γ (deg.)90.000, 128.406, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-391-

HOH

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Components

#1: Protein Ras-related protein Rab-43 / Ras-related protein Rab-41


Mass: 20400.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB43, RAB41 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86YS6
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Imidazole/MES monohydrate, pH6.5; 25% MPD, 25% PEG 1000, 25% PEG 3350; 0.02M DL-Glutamic acid monohydrate, 0.02M DL-Alanine, 0.02M Glycine, 0.02M DL-Lysine monohydrochloride, 0.02M DL-Serine
PH range: 6.2-6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97851 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2022
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 44897 / % possible obs: 97.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.35 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.8
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 4388 / CC1/2: 0.963

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHENIX1.21.1_5286phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→27.48 Å / SU ML: 0.1525 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.7668
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.204 2244 5 %
Rwork0.1664 42637 -
obs0.1682 44881 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.79 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 66 349 3148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612845
X-RAY DIFFRACTIONf_angle_d0.88413856
X-RAY DIFFRACTIONf_chiral_restr0.0582441
X-RAY DIFFRACTIONf_plane_restr0.0074476
X-RAY DIFFRACTIONf_dihedral_angle_d12.86181073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.251360.20672591X-RAY DIFFRACTION95.25
1.63-1.670.25881370.19032598X-RAY DIFFRACTION96.92
1.67-1.710.22131380.17972632X-RAY DIFFRACTION96.92
1.71-1.760.18921400.1662654X-RAY DIFFRACTION97.12
1.76-1.810.20721390.15722642X-RAY DIFFRACTION97.24
1.81-1.870.21211390.16222644X-RAY DIFFRACTION97.31
1.87-1.930.20181400.17112653X-RAY DIFFRACTION97.01
1.93-2.010.18361380.17362620X-RAY DIFFRACTION97.42
2.01-2.10.20351410.16542680X-RAY DIFFRACTION98.16
2.1-2.210.23971410.1642683X-RAY DIFFRACTION97.72
2.21-2.350.22591410.17352674X-RAY DIFFRACTION98.39
2.35-2.530.19751410.18172671X-RAY DIFFRACTION98.29
2.53-2.790.21491420.17592706X-RAY DIFFRACTION98.41
2.79-3.190.21161420.17272700X-RAY DIFFRACTION98.78
3.19-4.020.20981440.15132726X-RAY DIFFRACTION99.07
4.02-27.480.16521450.15532763X-RAY DIFFRACTION99.15
Refinement TLS params.Method: refined / Origin x: 14.5505445038 Å / Origin y: 15.2163178046 Å / Origin z: 13.7220907049 Å
111213212223313233
T0.11843014265 Å2-0.0171455582346 Å20.0151622310604 Å2-0.121805646074 Å20.0141184991488 Å2--0.132465058137 Å2
L0.541376880943 °2-0.471580741333 °2-0.407479155881 °2-0.70137298414 °20.513381858589 °2--0.821208179019 °2
S-0.017068044239 Å °-0.00496258231781 Å °-0.0354579503603 Å °-0.0258248041588 Å °0.0216216995992 Å °0.0209301280423 Å °-0.0195095864119 Å °0.00610018127298 Å °0.00184423250824 Å °
Refinement TLS groupSelection details: all

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