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- PDB-4n3z: Crystal structure of Rabex-5delta and Rabaptin-5C21 complex -

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Basic information

Entry
Database: PDB / ID: 4n3z
TitleCrystal structure of Rabex-5delta and Rabaptin-5C21 complex
Components
  • Rab GTPase-binding effector protein 1
  • Rab5 GDP/GTP exchange factor
KeywordsENDOCYTOSIS / Rab5 / Rabex-5 / Rabaptin-5 / GEF activity / early endosome
Function / homology
Function and homology information


dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of mast cell activation / protein localization to ciliary membrane / negative regulation of mast cell degranulation / Kit signaling pathway / presynaptic endosome / negative regulation of leukocyte migration ...dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of mast cell activation / protein localization to ciliary membrane / negative regulation of mast cell degranulation / Kit signaling pathway / presynaptic endosome / negative regulation of leukocyte migration / negative regulation of receptor-mediated endocytosis / Golgi to plasma membrane transport / negative regulation of Ras protein signal transduction / RAB GEFs exchange GTP for GDP on RABs / negative regulation of mast cell cytokine production / TBC/RABGAPs / protein targeting to membrane / mast cell degranulation / regulation of postsynaptic neurotransmitter receptor internalization / negative regulation of interleukin-6 production / endocytic vesicle / vesicle-mediated transport / receptor-mediated endocytosis / GTPase activator activity / guanyl-nucleotide exchange factor activity / growth factor activity / recycling endosome / small GTPase binding / negative regulation of inflammatory response / endocytosis / ubiquitin protein ligase activity / protein transport / early endosome membrane / Ras protein signal transduction / membrane fusion / early endosome / endosome / protein domain specific binding / intracellular membrane-bounded organelle / apoptotic process / dendrite / nucleolus / glutamatergic synapse / protein homodimerization activity / protein-containing complex / DNA binding / zinc ion binding / cytosol
Similarity search - Function
Rabaptin / Rabaptin, GTPase-Rab5 binding domain / Rabaptin coiled-coil domain / Rabaptin / Rabaptin-like protein / VPS9 domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain ...Rabaptin / Rabaptin, GTPase-Rab5 binding domain / Rabaptin coiled-coil domain / Rabaptin / Rabaptin-like protein / VPS9 domain / 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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Rab GTPase-binding effector protein 1 / Rab5 GDP/GTP exchange factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
DepositionOct 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Rab GTPase-binding effector protein 1
C: Rab GTPase-binding effector protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2516
Polymers57,9663
Non-polymers2853
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-83 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.140, 87.140, 168.878
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: 36564.043 Da / Num. of mol.: 1 / Fragment: UNP residues, isoform 2, 132-455 / Mutation: residues 387-408 deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABEX5 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q9UJ41
#2: Protein Rab GTPase-binding effector protein 1 / Rabaptin-5C21 / Rabaptin-4 / Rabaptin-5 / Rabaptin-5alpha / Renal carcinoma antigen NY-REN-17


Mass: 10701.068 Da / Num. of mol.: 2 / Fragment: UNP residues 552-642
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABEP1 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q15276
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
Sequence detailsTHE REFERENCE SEQUENCE OF CHAIN A IS ISOFORM 2 OF Q9UJ41, AND RESIDUES 387-408 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: 3.19 Å3/Da / Density % sol: 61.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0M NaH2PO4/K2HPO4, 0.05% n-octyl-beta-D-galactopyranoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 13730 / % possible obs: 98.1 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.1
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 6 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.4 / Num. unique all: 13730 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TXU

1txu


Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.763 / Occupancy max: 1 / Occupancy min: 1 / SU B: 49.255 / SU ML: 0.406 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.544 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3153 601 5 %RANDOM
Rwork0.264 ---
obs0.2666 12008 85.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 230.81 Å2 / Biso mean: 71.9543 Å2 / Biso min: 14.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å2-0.97 Å20 Å2
2---1.93 Å20 Å2
3---2.9 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3059 0 15 0 3074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193089
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9834153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47325.942138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53815587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5661520
X-RAY DIFFRACTIONr_chiral_restr0.0720.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022239
X-RAY DIFFRACTIONr_rigid_bond_restr2.83533066
X-RAY DIFFRACTIONr_sphericity_bonded53.4753050
LS refinement shellResolution: 3.103→3.184 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 11 -
Rwork0.214 234 -
all-245 -
obs--26.15 %

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