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- PDB-5yoz: Solution structure of truncated Rab5a from Leishmania donovani -

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Basic information

Entry
Database: PDB / ID: 5yoz
TitleSolution structure of truncated Rab5a from Leishmania donovani
ComponentsRab5a
KeywordsENDOCYTOSIS / Rab / GTPase / early endocytosis / GTP hydrolysing activity
Function / homology
Function and homology information


GTPase activity / GTP binding
Similarity search - Function
Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 1 / small GTPase Rab1 family profile. / small GTPase Rho family profile. / small GTPase Ras 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 ...Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 1 / small GTPase Rab1 family profile. / small GTPase Rho family profile. / small GTPase Ras 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
Rab5a / Putative ras-related protein rab-5
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodSOLUTION NMR / molecular dynamics
AuthorsMaheshwari, D. / Yadav, R. / Mukhopadhyay, A. / Arora, A.
Funding support India, 1items
OrganizationGrant numberCountry
CSIRBSC0114 India
CitationJournal: Biophys. J. / Year: 2018
Title: Structural and Biophysical Characterization of Rab5a from Leishmania Donovani
Authors: Maheshwari, D. / Yadav, R. / Rastogi, R. / Jain, A. / Tripathi, S. / Mukhopadhyay, A. / Arora, A.
History
DepositionOct 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rab5a


Theoretical massNumber of molelcules
Total (without water)19,3821
Polymers19,3821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10210 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Rab5a /


Mass: 19382.002 Da / Num. of mol.: 1 / Mutation: Q72L, C107S, P58D, P59G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: Rab5a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A109NYM0, UniProt: A4HXY7*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic22D 1H-13C HSQC aliphatic
132isotropic22D 1H-13C HSQC aromatic
142isotropic12D CBHE
152isotropic12D CBHD
162isotropic13D CBCA(CO)NH
1112isotropic13D HN(CA)CB
1102isotropic13D HNCA
192isotropic13D HNCO
182isotropic13D HN(CA)CO
172isotropic13D H(CCO)NH
1152isotropic13D C(CO)NH
1141isotropic23D 1H-15N NOESY
1131isotropic13D 1H-15N TOCSY
1122isotropic13D (H)CCH-TOCSY
1232isotropic23D 1H-13C NOESY aliphatic
1242isotropic23D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM sodium phosphate, 50 mM sodium chloride, 5 mM magnesium chloride, 1 mM GTP, 2 mM DTT, 3 % glycerol, 0.1 % sodium azide, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
solution220 mM sodium phosphate, 50 mM sodium chloride, 5 mM magnesium chloride, 1 mM GTP, 2 mM DTT, 3 % glycerol, 0.1 % sodium azide, 95% H2O/5% D2O13C-15N_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
5 mMmagnesium chloridenatural abundance1
1 mMGTPnatural abundance1
2 mMDTTnatural abundance1
3 %glycerolnatural abundance1
0.1 %sodium azidenatural abundance1
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
5 mMmagnesium chloridenatural abundance2
1 mMGTPnatural abundance2
2 mMDTTnatural abundance2
3 %glycerolnatural abundance2
0.1 %sodium azidenatural abundance2
Sample conditionsIonic strength: 50 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER, ADAMS, CLORE, GROS, NILGES AND READrefinement
CYANAstructure solution
CARAstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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