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- PDB-4q9u: Crystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex -

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Basic information

Entry
Database: PDB / ID: 4q9u
TitleCrystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex
Components
  • Rab GTPase-binding effector protein 1
  • Rab5 GDP/GTP exchange factor
  • Ras-related protein Rab-5A
KeywordsENDOCYTOSIS / Rab5 / Rabex-5 / Rabaptin-5 / GEF activity / early endosomes / VPS9 / coiled-coil / GEF / effector / small GTPases
Function / homology
Function and homology information


dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of endosome size / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of mast cell activation / cytoplasmic side of early endosome membrane / protein localization to ciliary membrane / Kit signaling pathway / negative regulation of mast cell degranulation ...dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of endosome size / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of mast cell activation / cytoplasmic side of early endosome membrane / protein localization to ciliary membrane / Kit signaling pathway / negative regulation of mast cell degranulation / synaptic vesicle recycling / amyloid-beta clearance by transcytosis / presynaptic endosome / negative regulation of leukocyte migration / negative regulation of receptor-mediated endocytosis / host-mediated perturbation of viral process / early endosome to late endosome transport / regulation of filopodium assembly / Golgi to plasma membrane transport / RAB geranylgeranylation / regulation of autophagosome assembly / RAB GEFs exchange GTP for GDP on RABs / negative regulation of Ras protein signal transduction / early phagosome / negative regulation of mast cell cytokine production / TBC/RABGAPs / protein targeting to membrane / mast cell degranulation / regulation of postsynaptic neurotransmitter receptor internalization / regulation of synaptic vesicle exocytosis / Synthesis of PIPs at the plasma membrane / negative regulation of interleukin-6 production / Respiratory syncytial virus (RSV) attachment and entry / positive regulation of exocytosis / endocytic vesicle / canonical Wnt signaling pathway / Prevention of phagosomal-lysosomal fusion / phagocytosis / vesicle-mediated transport / phagocytic vesicle / ruffle / axon terminus / somatodendritic compartment / endomembrane system / GTPase activator activity / receptor-mediated endocytosis / guanyl-nucleotide exchange factor activity / small monomeric GTPase / intracellular protein transport / growth factor activity / clathrin-coated endocytic vesicle membrane / regulation of long-term neuronal synaptic plasticity / recycling endosome / receptor internalization / small GTPase binding / negative regulation of inflammatory response / phagocytic vesicle membrane / endocytosis / terminal bouton / synaptic vesicle / GDP binding / synaptic vesicle membrane / ubiquitin protein ligase activity / Clathrin-mediated endocytosis / melanosome / protein transport / actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / G protein activity / early endosome membrane / Ras protein signal transduction / membrane fusion / early endosome / endosome membrane / endosome / membrane raft / axon / protein domain specific binding / neuronal cell body / intracellular membrane-bounded organelle / GTPase activity / apoptotic process / dendrite / GTP binding / nucleolus / glutamatergic synapse / protein homodimerization activity / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rabaptin / Rabaptin, GTPase-Rab5 binding domain / Rabaptin coiled-coil domain / Rabaptin / Rabaptin-like protein / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily ...Rabaptin / Rabaptin, GTPase-Rab5 binding domain / Rabaptin coiled-coil domain / Rabaptin / Rabaptin-like protein / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / 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
Ras-related protein Rab-5A / Rab GTPase-binding effector protein 1 / Rab5 GDP/GTP exchange factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.618 Å
AuthorsZhang, Z. / Zhang, T. / Ding, J.
CitationJournal: Elife / Year: 2014
Title: Molecular mechanism for Rabex-5 GEF activation by Rabaptin-5
Authors: Zhang, Z. / Zhang, T. / Wang, S. / Gong, Z. / Tang, C. / Chen, J. / Ding, J.
History
DepositionMay 1, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rab5 GDP/GTP exchange factor
B: Ras-related protein Rab-5A
C: Rab GTPase-binding effector protein 1
D: Rab GTPase-binding effector protein 1
E: Rab5 GDP/GTP exchange factor
F: Ras-related protein Rab-5A
G: Rab GTPase-binding effector protein 1
H: Rab GTPase-binding effector protein 1


Theoretical massNumber of molelcules
Total (without water)155,5958
Polymers155,5958
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.821, 174.821, 148.995
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Rab5 GDP/GTP exchange factor / Rabex-5delta / RAP1 / Rabaptin-5-associated exchange factor for Rab5 / Rabex-5


Mass: 37320.891 Da / Num. of mol.: 2 / Fragment: UNP residues 132-455 / Mutation: 393-407 deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABGEF1, RABEX5 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q9UJ41
#2: Protein Ras-related protein Rab-5A / Rabaptin-5C21


Mass: 19074.648 Da / Num. of mol.: 2 / Fragment: UNP residues 15-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB5A, RAB5 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: P20339
#3: Protein
Rab GTPase-binding effector protein 1 / Rab5 / Rabaptin-4 / Rabaptin-5 / Rabaptin-5alpha / Renal carcinoma antigen NY-REN-17


Mass: 10701.068 Da / Num. of mol.: 4 / Fragment: UNP residues 552-642
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABEP1, RAB5EP, RABPT5, RABPT5A / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q15276
Sequence detailsTHE REFERENCE SEQUENCE OF CHAIN A, E IS ISOFORM 2 OF Q9UJ41, AND RESIDUES 393-407 HAVE BEEN DELETED.

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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: 3.66 Å3/Da / Density % sol: 66.38 % / Mosaicity: 1.181 °
Crystal growTemperature: 289 K / Method: hanging drop / pH: 5
Details: 1.0M NaH2PO4/K2HPO4, pH 5.0, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 4.6→50 Å / Num. obs: 12699 / % possible obs: 97.6 % / Redundancy: 9.8 % / Biso Wilson estimate: 172.68 Å2 / Rmerge(I) obs: 0.117 / Χ2: 1.181 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
4.6-4.7690.94312091.07395.8
4.76-4.959.30.57812271.20595.9
4.95-5.189.40.50812161.12296.1
5.18-5.459.70.7412231.03395.9
5.45-5.799.60.63812340.99396.6
5.79-6.249.60.49912651.00498.4
6.24-6.879.60.25212911.03399.4
6.87-7.869.80.11713021.28999.6
7.86-9.8911.10.0613361.62599.9
9.89-5010.60.04813961.27798.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OT3

2ot3


Resolution: 4.618→40.781 Å / FOM work R set: 0.5655 / SU ML: 0.78 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 45.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3427 631 5 %random
Rwork0.2513 ---
obs0.2561 12613 95.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 501.19 Å2 / Biso mean: 187.29 Å2 / Biso min: 33.68 Å2
Refinement stepCycle: LAST / Resolution: 4.618→40.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9679 0 0 0 9679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0159797
X-RAY DIFFRACTIONf_angle_d1.87313145
X-RAY DIFFRACTIONf_chiral_restr0.1091483
X-RAY DIFFRACTIONf_plane_restr0.0081699
X-RAY DIFFRACTIONf_dihedral_angle_d21.8713829
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.6182-4.97420.40161030.29012164226788
4.9742-5.47370.38451130.29672338245195
5.4737-6.26330.47081170.34612399251697
6.2633-7.88170.37031370.3052489262699
7.8817-40.78270.29241610.19542592275399

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