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- PDB-2ot3: Crystal structure of rabex-5 VPS9 domain in complex with nucleoti... -

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Basic information

Entry
Database: PDB / ID: 2ot3
TitleCrystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21
Components
  • Rab5 GDP/GTP exchange factor
  • Ras-related protein Rab-21
KeywordsPROTEIN TRANSPORT / Rabex-5 / Vps9 Domain / Rab21 / vesicular traffic
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 / cytoplasmic side of early endosome membrane / Kit signaling pathway / negative regulation of mast cell degranulation / Rab protein signal transduction / positive regulation of early endosome to late endosome transport / negative regulation of mast cell activation ...dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of Fc receptor mediated stimulatory signaling pathway / cytoplasmic side of early endosome membrane / Kit signaling pathway / negative regulation of mast cell degranulation / Rab protein signal transduction / positive regulation of early endosome to late endosome transport / negative regulation of mast cell activation / negative regulation of leukocyte migration / negative regulation of receptor-mediated endocytosis / negative regulation of mast cell cytokine production / regulation of exocytosis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / anterograde axonal transport / negative regulation of Ras protein signal transduction / positive regulation of dendrite morphogenesis / protein targeting to membrane / vesicle membrane / TBC/RABGAPs / regulation of axon extension / Golgi cisterna membrane / mast cell degranulation / cleavage furrow / negative regulation of interleukin-6 production / endocytic vesicle / endomembrane system / axon cytoplasm / receptor-mediated endocytosis / negative regulation of protein phosphorylation / guanyl-nucleotide exchange factor activity / intracellular protein transport / trans-Golgi network / recycling endosome / negative regulation of inflammatory response / positive regulation of receptor-mediated endocytosis / small GTPase binding / cytoplasmic side of plasma membrane / GDP binding / ubiquitin protein ligase activity / protein transport / early endosome membrane / Ras protein signal transduction / early endosome / protein stabilization / endosome / Golgi membrane / focal adhesion / GTPase activity / dendrite / synapse / endoplasmic reticulum membrane / nucleolus / GTP binding / DNA binding / extracellular exosome / zinc ion binding / cytosol
Similarity search - Function
Rab21 / Serum Albumin; Chain A, Domain 1 - #120 / 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. ...Rab21 / Serum Albumin; Chain A, Domain 1 - #120 / 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 / Serum Albumin; Chain A, Domain 1 / small GTPase Rab1 family profile. / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Rab5 GDP/GTP exchange factor / Ras-related protein Rab-21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDelprato, A. / Lambright, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structural basis for Rab GTPase activation by VPS9 domain exchange factors.
Authors: Delprato, A. / Lambright, D.G.
History
DepositionFeb 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Data collection
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE The protein sequence matches to isoform 2 of the UNP reference

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rab5 GDP/GTP exchange factor
B: Ras-related protein Rab-21


Theoretical massNumber of molelcules
Total (without water)51,4182
Polymers51,4182
Non-polymers00
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-19 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.897, 113.400, 60.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 32082.791 Da / Num. of mol.: 1 / Fragment: residues 132-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABGEF1, RABEX5 / Plasmid: PET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: Q9UJ41
#2: Protein Ras-related protein Rab-21


Mass: 19335.209 Da / Num. of mol.: 1 / Fragment: residues 16-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB21, KIAA0118 / Plasmid: PGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: Q9UL25
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% PEG 6000, 0.2M MgCl2, 0.05 NaMES Microseeded, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
Details: Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator
RadiationMonochromator: SI(11) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 40412 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rsym value: 7.5 / Net I/σ(I): 22
Reflection shellResolution: 2.1→2.154 Å / Redundancy: 1 % / Mean I/σ(I) obs: 4 / Num. unique all: 40412 / Rsym value: 38.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z0I, 1TXU

1z0i

1txu


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.642 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24272 1500 5.1 %RANDOM
Rwork0.18821 ---
obs0.19099 28020 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.088 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20 Å2
2---0.33 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 0 463 3642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223234
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9654372
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.245407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85624.412136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6215572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8291517
X-RAY DIFFRACTIONr_chiral_restr0.080.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022392
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21761
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22274
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2432
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8581.52105
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48623277
X-RAY DIFFRACTIONr_scbond_it1.99431285
X-RAY DIFFRACTIONr_scangle_it3.2114.51095
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 93 -
Rwork0.208 2022 -
obs--100 %

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