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- PDB-5yfg: SOLUTION STRUCTURE OF HUMAN MOG1 -

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Basic information

Entry
Database: PDB / ID: 5yfg
TitleSOLUTION STRUCTURE OF HUMAN MOG1
ComponentsRan guanine nucleotide release factor
KeywordsPROTEIN TRANSPORT / CENTRAL BETA SHEET / ALTERNATIVE SPLICING / CYTOPLASM / GUANINE-NUCLEOTIDE RELEASING FACTOR / NUCLEUS
Function / homology
Function and homology information


: / guanyl-nucleotide exchange factor activity => GO:0005085 / regulation of bundle of His cell action potential / regulation of membrane depolarization during cardiac muscle cell action potential / small GTPase binding => GO:0031267 / regulation of cardiac muscle cell action potential involved in regulation of contraction / protein exit from endoplasmic reticulum / regulation of sodium ion transmembrane transport / regulation of sodium ion transmembrane transporter activity / positive regulation of protein localization to cell surface ...: / guanyl-nucleotide exchange factor activity => GO:0005085 / regulation of bundle of His cell action potential / regulation of membrane depolarization during cardiac muscle cell action potential / small GTPase binding => GO:0031267 / regulation of cardiac muscle cell action potential involved in regulation of contraction / protein exit from endoplasmic reticulum / regulation of sodium ion transmembrane transport / regulation of sodium ion transmembrane transporter activity / positive regulation of protein localization to cell surface / regulation of membrane depolarization / Phase 0 - rapid depolarisation / intercalated disc / sodium channel regulator activity / endoplasmic reticulum to Golgi vesicle-mediated transport / rough endoplasmic reticulum / regulation of heart rate / guanyl-nucleotide exchange factor activity / regulation of membrane potential / caveola / positive regulation of protein localization to plasma membrane / transmembrane transporter binding / perinuclear region of cytoplasm / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ran-interacting Mog1 protein / Ran-interacting Mog1 protein / Mog1/PsbP, alpha/beta/alpha sandwich
Similarity search - Domain/homology
Ran guanine nucleotide release factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, DISTANCE GEOMETRY / torsion angle dynamics
AuthorsHu, Q. / Liu, Y. / Bao, X. / Liu, H.
CitationJournal: J Mol Cell Biol / Year: 2018
Title: Mitosis-specific acetylation tunes Ran effector binding for chromosome segregation
Authors: Bao, X. / Liu, H. / Liu, X. / Ruan, K. / Zhang, Y. / Zhang, Z. / Hu, Q. / Liu, Y. / Akram, S. / Zhang, J. / Gong, Q. / Wang, W. / Yuan, X. / Li, J. / Zhao, L. / Dou, Z. / Tian, R. / Yao, X. / Wu, J. / Shi, Y.
History
DepositionSep 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ran guanine nucleotide release factor


Theoretical massNumber of molelcules
Total (without water)21,5231
Polymers21,5231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11940 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ran guanine nucleotide release factor / RanGNRF / Ran-binding protein MOG1


Mass: 21523.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANGRF, MOG1, RANGNRF, HSPC165, HSPC236, MDS5 / Plasmid: PET22B+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HD47

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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
122isotropic12D 1H-13C HSQC
133isotropic12D 1H-1H TOCSY
143isotropic12D 1H-1H NOESY
153isotropic13D HNCO
163isotropic13D CBCA(CO)NH
173isotropic13D CBCANH
183isotropic13D HNCA
193isotropic13D HN(CO)CA
1103isotropic13D (H)CCH-TOCSY
1113isotropic13D (H)CCH-COSY
1123isotropic13D C(CO)NH-TOCSY
1133isotropic13D HC(CO)NH-TOCSY
1143isotropic13D HBHA(CO)NH
1153isotropic13D 1H-15N NOESY
1163isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.9 mM [U-99% 15N] Mog1, 90% H2O/10% D2O15N90% H2O/10% D2O
solution20.9 mM [U-13C] Mog1, 90% H2O/10% D2O13C90% H2O/10% D2O
solution30.9 mM [U-99% 13C; U-99% 15N] Mog1, 100% D2O13C 15N100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMMog1[U-99% 15N]1
0.9 mMMog1[U-13C]2
0.9 mMMog1[U-99% 13C; U-99% 15N]3
Sample conditionsIonic strength: 150 mM / Label: 1 / pH: 6.8 / Pressure: AMBIENT Pa / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER, ADAMS, CLORE, GROS, NILGES, READrefinement
TALOSCornilescu, Delaglio and Baxdata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
SparkyGoddarddata analysis
Refinement
MethodSoftware ordinal
SIMULATED ANNEALING, DISTANCE GEOMETRY1
torsion angle dynamics7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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