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- PDB-1bc9: CYTOHESIN-1/B2-1 SEC7 DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1bc9
TitleCYTOHESIN-1/B2-1 SEC7 DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsCYTOHESIN-1
KeywordsEXCHANGE FACTOR / INTEGRIN BINDING PROTEIN
Function / homology
Function and homology information


Intra-Golgi traffic / establishment of epithelial cell polarity / regulation of ARF protein signal transduction / bicellular tight junction / regulation of cell adhesion / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / adherens junction / cytoplasmic side of plasma membrane / Golgi membrane ...Intra-Golgi traffic / establishment of epithelial cell polarity / regulation of ARF protein signal transduction / bicellular tight junction / regulation of cell adhesion / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / adherens junction / cytoplasmic side of plasma membrane / Golgi membrane / lipid binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Annexin V; domain 1 ...Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Annexin V; domain 1 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsBetz, S.F. / Schnuchel, A. / Wang, H. / Olejniczak, E.T. / Meadows, R.P. / Fesik, S.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Solution structure of the cytohesin-1 (B2-1) Sec7 domain and its interaction with the GTPase ADP ribosylation factor 1.
Authors: Betz, S.F. / Schnuchel, A. / Wang, H. / Olejniczak, E.T. / Meadows, R.P. / Lipsky, B.P. / Harris, E.A. / Staunton, D.E. / Fesik, S.W.
History
DepositionMay 6, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOHESIN-1


Theoretical massNumber of molelcules
Total (without water)23,3891
Polymers23,3891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 287MINIMIZED AVERAGE
Representative

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Components

#1: Protein CYTOHESIN-1 / B2-1 / SEC7 HOMOLOG B2-1


Mass: 23388.758 Da / Num. of mol.: 1 / Fragment: SEC7 DOMAIN,
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: B2-1 / Organ: SPLEEN / Plasmid: PET-20B / Species (production host): Escherichia coli / Gene (production host): B2-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q15438

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CO)CA
131HN(CA)CB
141HN (COCA)CB
151HNCO
161HN(CA)CO
171(H)CCH-TOCSY
18113C-NOESY
19115N-NOESY
1101HNHA-J
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED CYTOHESIN-1 SEC7 DOMAIN.

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Sample preparation

DetailsContents: 20 MM NAPI, 150 MM (NH4)2SO4, 3MM DTT, 10% D2O
Sample conditionsIonic strength: 0.47 M / pH: 6.8 / Pressure: 1 atm / Temperature: 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRX500BrukerDRX5005001
Bruker DRX600BrukerDRX6006002
Bruker AMX750BrukerAMX7507503
Bruker DRX800BrukerDRX8008004

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION.
NMR ensembleConformer selection criteria: MINIMIZED AVERAGE / Conformers calculated total number: 287 / Conformers submitted total number: 1

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