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- PDB-4n3y: Crystal structure of Rabex-5CC and Rabaptin-5C21 complex -

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Basic information

Entry
Database: PDB / ID: 4n3y
TitleCrystal structure of Rabex-5CC 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 / protein localization to ciliary membrane / Kit signaling pathway / negative regulation of mast cell degranulation / negative regulation of mast cell activation / negative regulation of leukocyte migration / negative regulation of receptor-mediated endocytosis ...dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of Fc receptor mediated stimulatory signaling pathway / protein localization to ciliary membrane / Kit signaling pathway / negative regulation of mast cell degranulation / negative regulation of mast cell activation / negative regulation of leukocyte migration / negative regulation of receptor-mediated endocytosis / negative regulation of mast cell cytokine production / Golgi to plasma membrane transport / RAB GEFs exchange GTP for GDP on RABs / negative regulation of Ras protein signal transduction / protein targeting to membrane / TBC/RABGAPs / mast cell degranulation / negative regulation of interleukin-6 production / endocytic vesicle / vesicle-mediated transport / receptor-mediated endocytosis / GTPase activator activity / guanyl-nucleotide exchange factor activity / negative regulation of protein phosphorylation / 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 / 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 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
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: 2.2 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
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: Rab GTPase-binding effector protein 1
C: Rab GTPase-binding effector protein 1


Theoretical massNumber of molelcules
Total (without water)26,6643
Polymers26,6643
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-65 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.007, 28.857, 107.973
Angle α, β, γ (deg.)90.000, 102.240, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 5261.896 Da / Num. of mol.: 1 / Fragment: UNP residues 630-672
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-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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.15M MgAc2, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 13816 / % possible obs: 97.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.4 / Num. unique all: 13816 / % possible all: 85.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X79

1x79


Resolution: 2.2→15.03 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.797 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 691 5 %RANDOM
Rwork0.1929 ---
obs0.195 13815 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.73 Å2 / Biso mean: 58.5336 Å2 / Biso min: 22.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å2-0 Å2-1.54 Å2
2--5.18 Å20 Å2
3----3.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 0 187 1814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191630
X-RAY DIFFRACTIONr_bond_other_d0.0010.021639
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.982173
X-RAY DIFFRACTIONr_angle_other_deg1.20233779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6615198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.8952790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.95515366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0141511
X-RAY DIFFRACTIONr_chiral_restr0.0870.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021843
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02336
X-RAY DIFFRACTIONr_rigid_bond_restr4.75533269
X-RAY DIFFRACTIONr_sphericity_free34.993572
X-RAY DIFFRACTIONr_sphericity_bonded41.07853381
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 53 -
Rwork0.28 816 -
all-869 -
obs--83.24 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6403-2.55982.47213.0486-2.89082.7457-0.02540.1317-0.00810.06440.0063-0.0186-0.05020.01550.01910.32020.0267-0.15610.0536-0.01060.07850.2639-928.7816-60.317
21.1954-0.05322.40130.0292-0.10844.8542-0.0498-0.01070.0628-0.0186-0.03050.0064-0.0126-0.02830.08030.2426-0.0002-0.12810.03440.00160.06895.9162-930.0035-25.2492
30.5018-0.33450.9920.235-0.66492.0207-0.03690.05670.0627-0.0227-0.0528-0.0180.00630.0830.08970.24910.0136-0.12420.0408-0.00560.066512.8565-928.3519-26.9416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A419 - 453
2X-RAY DIFFRACTION1A501 - 524
3X-RAY DIFFRACTION2B552 - 634
4X-RAY DIFFRACTION2B701 - 782
5X-RAY DIFFRACTION3C552 - 634
6X-RAY DIFFRACTION3C701 - 781

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