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- PDB-7eq2: Crystal structure of GDP-bound Rab1a-T75D -

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Basic information

Entry
Database: PDB / ID: 7eq2
TitleCrystal structure of GDP-bound Rab1a-T75D
ComponentsRas-related protein Rab-1A
KeywordsCELL CYCLE / Ras-related protein Rab-1A / small GTPase / protein trafficking / signal transduction / Membrane remolding
Function / homology
Function and homology information


positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic ...positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / transport vesicle membrane / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / COPI-mediated anterograde transport / vesicle-mediated transport / substrate adhesion-dependent cell spreading / small monomeric GTPase / G protein activity / positive regulation of interleukin-8 production / intracellular protein transport / autophagy / endocytosis / melanosome / cell migration / early endosome / defense response to bacterium / cadherin binding / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome / cytosol
Similarity search - Function
ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family 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
CACODYLATE ION / GUANOSINE-5'-DIPHOSPHATE / COBALT HEXAMMINE(III) / Ras-related protein Rab-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55090284637 Å
AuthorsCao, Y.L. / Gu, D.D. / Gao, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Aurora kinase A-mediated phosphorylation triggers structural alteration of Rab1A to enhance ER complexity during mitosis
Authors: Zhang, W. / Zhang, Z. / Xiang, Y. / Gu, D.D. / Chen, J. / Chen, Y. / Zhai, S. / Liu, Y. / Jiang, T. / Liu, C. / He, B. / Yan, M. / Wang, Z. / Xu, J. / Cao, Y.L. / Deng, B. / Zeng, D. / Lei, ...Authors: Zhang, W. / Zhang, Z. / Xiang, Y. / Gu, D.D. / Chen, J. / Chen, Y. / Zhai, S. / Liu, Y. / Jiang, T. / Liu, C. / He, B. / Yan, M. / Wang, Z. / Xu, J. / Cao, Y.L. / Deng, B. / Zeng, D. / Lei, J. / Zhuo, J. / Lei, X. / Long, Z. / Jin, B. / Chen, T. / Li, D. / Shen, Y. / Hu, J. / Gao, S. / Liu, Q.
History
DepositionApr 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-1A
B: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,31614
Polymers42,2262
Non-polymers2,09012
Water6,702372
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A: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0216
Polymers21,1131
Non-polymers9085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-29 kcal/mol
Surface area8630 Å2
MethodPISA
2
B: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2958
Polymers21,1131
Non-polymers1,1827
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-30 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.489, 50.598, 52.626
Angle α, β, γ (deg.)76.945, 84.616, 86.271
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ras-related protein Rab-1A / YPT1-related protein


Mass: 21112.873 Da / Num. of mol.: 2 / Mutation: T75D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1A, RAB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62820, small monomeric GTPase

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Non-polymers , 6 types, 384 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CoH18N6
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 291.15 K / Method: evaporation
Details: 40mM Lithium chloride, 20mM Magnesium chloride hexahydrate, 80mM NaCl, 2mM Hexammine cobalt(III) chloride, 40mM Sodium cacodylate trihydrate pH 5.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97776 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.5509→25.12 Å / Num. obs: 54416 / % possible obs: 95.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.5307915404 Å2 / Rsym value: 0.059 / Net I/σ(I): 42.71
Reflection shellResolution: 1.5509→1.61 Å / Num. unique obs: 5434 / Rsym value: 0.539

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FOL

2fol


Resolution: 1.55090284637→25.1160419845 Å / SU ML: 0.126552402739 / Cross valid method: FREE R-VALUE / σ(F): 1.9676416371 / Phase error: 17.8460324132
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.185187062179 2740 5.06338470636 %
Rwork0.160166333291 51374 -
obs0.161457428126 54114 94.5883586786 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.7969176503 Å2
Refinement stepCycle: LAST / Resolution: 1.55090284637→25.1160419845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 112 372 3259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005576968119163054
X-RAY DIFFRACTIONf_angle_d0.9023730572244196
X-RAY DIFFRACTIONf_chiral_restr0.0557843004204475
X-RAY DIFFRACTIONf_plane_restr0.004119644021507
X-RAY DIFFRACTIONf_dihedral_angle_d10.15161282692456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.550903-1.57760.2172509003531310.1912656660562330X-RAY DIFFRACTION85.4513888889
1.5776-1.60630.2341856378831250.1857783796852504X-RAY DIFFRACTION91.7626527051
1.6063-1.63720.2102711115711250.1844393508482568X-RAY DIFFRACTION94.0621725463
1.6372-1.67060.2072388153971300.171266016552538X-RAY DIFFRACTION94.6434905995
1.6706-1.70690.1758940230111380.1684879646942603X-RAY DIFFRACTION95.2066689823
1.7069-1.74660.189674149711360.1632014135162599X-RAY DIFFRACTION95.3293830603
1.7466-1.79030.2290289304441080.1658384498842618X-RAY DIFFRACTION95.2480782669
1.7903-1.83870.2064817455371480.166755779592585X-RAY DIFFRACTION95.8611013679
1.8387-1.89280.188650977851290.1648043982212624X-RAY DIFFRACTION95.689954814
1.8928-1.95390.177093317321610.1698555384062576X-RAY DIFFRACTION95.665851101
1.9539-2.02370.1881939587441530.161549200392589X-RAY DIFFRACTION96.1430575035
2.0237-2.10470.2000849602431520.164064077052614X-RAY DIFFRACTION96.3091922006
2.1047-2.20040.1878556966311170.1593800675212640X-RAY DIFFRACTION96.1967899512
2.2004-2.31630.1862436635161460.1597890319922583X-RAY DIFFRACTION95.8216292135
2.3163-2.46130.1773429653161300.1617699054092619X-RAY DIFFRACTION95.9176552687
2.4613-2.65120.1991170340831420.1636795812612571X-RAY DIFFRACTION95.1595931252
2.6512-2.91760.1915196345921400.1674468298322463X-RAY DIFFRACTION91.6549295775
2.9176-3.3390.1878877692781360.1489505787872659X-RAY DIFFRACTION97.5907821229
3.339-4.20350.1461624460011570.1342715331622639X-RAY DIFFRACTION97.7622377622
4.2035-25.1160.1871784371971360.1653828411162452X-RAY DIFFRACTION90.4578818595
Refinement TLS params.Method: refined / Origin x: -1.43791920413 Å / Origin y: -10.1777947814 Å / Origin z: 10.4371475876 Å
111213212223313233
T0.072914608776 Å20.00323774110611 Å2-0.00735069896999 Å2-0.11216246854 Å2-0.0307537536667 Å2--0.0915398455756 Å2
L0.136846283309 °2-0.0237670357917 °2-0.0282514827305 °2-0.906674320842 °2-0.524125772921 °2--0.48620614111 °2
S0.00246784433322 Å °0.00296632527745 Å °-0.00552226989832 Å °-0.0224915963937 Å °0.0108228642606 Å °0.00630176532496 Å °0.00213701762767 Å °0.00222659492369 Å °-0.0100759292534 Å °
Refinement TLS groupSelection details: all

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