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- PDB-4n3x: Crystal structure of Rabex-5 CC domain -

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Basic information

Entry
Database: PDB / ID: 4n3x
TitleCrystal structure of Rabex-5 CC domain
ComponentsRab5 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 / 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 ...dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of Fc receptor mediated stimulatory signaling pathway / 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 / RAB GEFs exchange GTP for GDP on RABs / negative regulation of Ras protein signal transduction / TBC/RABGAPs / protein targeting to membrane / mast cell degranulation / negative regulation of interleukin-6 production / endocytic vesicle / guanyl-nucleotide exchange factor activity / receptor-mediated endocytosis / negative regulation of protein phosphorylation / recycling endosome / small GTPase binding / negative regulation of inflammatory response / ubiquitin protein ligase activity / protein transport / early endosome membrane / Ras protein signal transduction / early endosome / dendrite / nucleolus / DNA binding / zinc ion binding / cytosol
Similarity search - Function
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 ...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
Similarity search - Domain/homology
Rab5 GDP/GTP exchange factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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.name
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: Rab5 GDP/GTP exchange factor
C: Rab5 GDP/GTP exchange factor
D: Rab5 GDP/GTP exchange factor


Theoretical massNumber of molelcules
Total (without water)24,3324
Polymers24,3324
Non-polymers00
Water1,892105
1
A: Rab5 GDP/GTP exchange factor


Theoretical massNumber of molelcules
Total (without water)6,0831
Polymers6,0831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rab5 GDP/GTP exchange factor


Theoretical massNumber of molelcules
Total (without water)6,0831
Polymers6,0831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rab5 GDP/GTP exchange factor


Theoretical massNumber of molelcules
Total (without water)6,0831
Polymers6,0831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Rab5 GDP/GTP exchange factor


Theoretical massNumber of molelcules
Total (without water)6,0831
Polymers6,0831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.757, 40.345, 51.591
Angle α, β, γ (deg.)90.000, 95.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Rab5 GDP/GTP exchange factor / RRabex-5 / AP1 / Rabaptin-5-associated exchange factor for Rab5


Mass: 6082.916 Da / Num. of mol.: 4 / Fragment: Rabex-5 CC domain, UNP residues 626-672
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABEX5 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q9UJ41
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.10M NaAc, 17.5% MPD, 2% PEG4000 , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 12748 / % possible obs: 96.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 23.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 14 / Num. unique all: 12748 / % possible all: 97.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N3Y

4n3y


Resolution: 2→30.51 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.911 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 622 4.9 %RANDOM
Rwork0.1911 ---
obs0.1932 12681 96.3 %-
all-12748 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.16 Å2 / Biso mean: 30.908 Å2 / Biso min: 4.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å20.8 Å2
2---0 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2→30.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1621 0 0 105 1726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191633
X-RAY DIFFRACTIONr_bond_other_d0.0060.021619
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9672180
X-RAY DIFFRACTIONr_angle_other_deg1.00233725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8995191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64326.12993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.76915356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2581512
X-RAY DIFFRACTIONr_chiral_restr0.1720.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021825
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02351
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 39 -
Rwork0.199 891 -
all-930 -
obs--96.07 %
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)
18.42320.2302-2.83910.0153-0.13641.578-0.03960.1409-0.26450.0001-0.00760.01280.03810.10010.04720.00960.01740.00880.0667-0.03060.0957-1.0064-7.7307-17.9882
26.5316-1.0187-4.15580.24260.92213.5952-0.04370.03710.0914-0.00510.07090.0122-0.03550.2411-0.02720.0135-0.00690.0180.120.01120.0634-4.4901-0.3279-21.4323
310.16991.5877-2.85490.2976-0.31641.1455-0.17620.19930.1815-0.03760.06220.09160.0225-0.00310.11390.01320.0002-0.00560.06240.04780.09531.8502-2.2351-9.2092
410.80020.0886-7.42460.0103-0.07745.9597-0.00580.35020.15850.0192-0.01780.0049-0.0608-0.07980.02370.0439-0.02670.01280.0730.04940.0784-0.67465.2282-12.1704
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 49
2X-RAY DIFFRACTION2B1 - 51
3X-RAY DIFFRACTION3C3 - 48
4X-RAY DIFFRACTION4D1 - 49

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