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- PDB-9ltp: Crystal structure of human RAB43 in GDP-AlF3 transition state com... -

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Basic information

Entry
Database: PDB / ID: 9ltp
TitleCrystal structure of human RAB43 in GDP-AlF3 transition state complex with USP6NL TBC domain
Components
  • Ras-related protein Rab-43
  • USP6 N-terminal-like protein
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 / plasma membrane to endosome transport / cis-Golgi network membrane / phagosome maturation / RAB geranylgeranylation / virion assembly / Golgi organization / positive regulation of GTPase activity ...retrograde transport, plasma membrane to Golgi / regulation of Golgi organization / Retrograde transport at the Trans-Golgi-Network / plasma membrane to endosome transport / cis-Golgi network membrane / phagosome maturation / RAB geranylgeranylation / virion assembly / Golgi organization / positive regulation of GTPase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / autophagosome assembly / phagocytic vesicle / endomembrane system / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / trans-Golgi network membrane / small monomeric GTPase / intracellular protein transport / cellular response to type II interferon / small GTPase binding / phagocytic vesicle membrane / G protein activity / cytoplasmic vesicle / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
: / : / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / : / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...: / : / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / : / 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
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Ras-related protein Rab-43 / USP6 N-terminal-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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

Downloads & links

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Assembly

Deposited unit
A: USP6 N-terminal-like protein
B: Ras-related protein Rab-43
C: USP6 N-terminal-like protein
D: Ras-related protein Rab-43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,81114
Polymers130,2834
Non-polymers1,52710
Water1,982110
1
A: USP6 N-terminal-like protein
B: Ras-related protein Rab-43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7996
Polymers65,1422
Non-polymers6584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-27 kcal/mol
Surface area24690 Å2
MethodPISA
2
C: USP6 N-terminal-like protein
D: Ras-related protein Rab-43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0118
Polymers65,1422
Non-polymers8706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-22 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.669, 65.483, 98.760
Angle α, β, γ (deg.)89.399, 76.734, 67.360
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein USP6 N-terminal-like protein / Related to the N-terminus of tre / RN-tre


Mass: 44076.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP6NL, KIAA0019 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92738
#2: Protein Ras-related protein Rab-43 / Ras-related protein Rab-41


Mass: 21064.801 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

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Non-polymers , 5 types, 120 molecules

#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: 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
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Bis-Tris propane, pH8.5; 20% PEG 3350; 0.02M Na/K phosphate pH7.4
PH range: 8.1-8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979098 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 23, 2024
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979098 Å / Relative weight: 1
ReflectionResolution: 2.49→40 Å / Num. obs: 37977 / % possible obs: 95.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 23.7 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3714 / CC1/2: 0.658 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→35.99 Å / SU ML: 0.3927 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.8421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2982 1901 5 %
Rwork0.2391 36147 -
obs0.2421 37977 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.79 Å2
Refinement stepCycle: LAST / Resolution: 2.49→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8687 0 94 110 8891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00158966
X-RAY DIFFRACTIONf_angle_d0.428412053
X-RAY DIFFRACTIONf_chiral_restr0.03691294
X-RAY DIFFRACTIONf_plane_restr0.00251508
X-RAY DIFFRACTIONf_dihedral_angle_d13.74553370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.560.34821320.27662504X-RAY DIFFRACTION93.34
2.56-2.620.37131400.28412647X-RAY DIFFRACTION97.21
2.62-2.70.34281370.28192609X-RAY DIFFRACTION97.48
2.7-2.790.37821370.28612601X-RAY DIFFRACTION97.86
2.79-2.890.35641390.26922651X-RAY DIFFRACTION98.24
2.89-30.31241380.26142625X-RAY DIFFRACTION97.84
3-3.140.31691410.25322663X-RAY DIFFRACTION98.18
3.14-3.310.30691370.25582606X-RAY DIFFRACTION98.28
3.31-3.510.27581390.24342638X-RAY DIFFRACTION97.85
3.51-3.780.30581360.22372609X-RAY DIFFRACTION96.83
3.78-4.160.25691400.20892657X-RAY DIFFRACTION98.35
4.17-4.770.24431370.19342600X-RAY DIFFRACTION97.23
4.77-60.29361250.24262372X-RAY DIFFRACTION87.86
6-35.990.25441230.20562365X-RAY DIFFRACTION88.07
Refinement TLS params.Method: refined / Origin x: 2.59620785793 Å / Origin y: -3.8742205744 Å / Origin z: 24.1282513342 Å
111213212223313233
T0.113900171179 Å2-0.00285502931617 Å2-0.0686449162929 Å2-0.17309985919 Å20.0399185018433 Å2--0.112584217865 Å2
L0.0385694248625 °2-0.0198692726714 °2-0.0239670147523 °2-0.0858962776872 °2-0.0984577103544 °2--0.900756393065 °2
S0.0424997358933 Å °0.02054375282 Å °-0.0260550608334 Å °0.00183180617191 Å °-0.0185477013673 Å °0.0252257820537 Å °0.0213602963174 Å °-0.0178167093916 Å °-0.0272819879349 Å °
Refinement TLS groupSelection details: all

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