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- PDB-7wh3: Solution structure of human stomatin SPFH domain in a phosphate buffer -

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Basic information

Entry
Database: PDB / ID: 7wh3
TitleSolution structure of human stomatin SPFH domain in a phosphate buffer
ComponentsStomatin
KeywordsSTRUCTURAL PROTEIN / erythrocyte / membrane skeleton / actin binding / molecular scaffold / Band 7.2 protein / oligomer/multimer formation
Function / homology
Function and homology information


positive regulation of viral process / positive regulation by host of viral genome replication / regulation of monoatomic ion transmembrane transport / RNA polymerase binding / azurophil granule membrane / RHOB GTPase cycle / ion channel inhibitor activity / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle ...positive regulation of viral process / positive regulation by host of viral genome replication / regulation of monoatomic ion transmembrane transport / RNA polymerase binding / azurophil granule membrane / RHOB GTPase cycle / ion channel inhibitor activity / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / tertiary granule membrane / CDC42 GTPase cycle / RHOH GTPase cycle / positive regulation of protein targeting to membrane / RHOA GTPase cycle / specific granule membrane / Stimuli-sensing channels / melanosome / vesicle / blood microparticle / cytoskeleton / membrane raft / Neutrophil degranulation / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / mitochondrion / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Band-7 stomatin-like / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKataoka, K. / Tenno, T. / Goda, N. / Hibino, E. / Hiroaki, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other private Japan
CitationJournal: Curr Res Struct Biol / Year: 2022
Title: A cryptic phosphate-binding pocket on the SPFH domain of human stomatin that regulates a novel fibril-like self-assembly
Authors: Kataoka, K. / Suzuki, S. / Tenno, T. / Goda, N. / Hibino, E. / Oshima, A. / Hiroaki, H.
History
DepositionDec 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2May 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: Stomatin


Theoretical massNumber of molelcules
Total (without water)12,4781
Polymers12,4781
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Stomatin / Erythrocyte band 7 integral membrane protein / Erythrocyte membrane protein band 7.2 / Protein 7.2b


Mass: 12477.999 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STOM / Plasmid: pGEX-hSTOM(SPFH) / Details (production host): GST fusion protein / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27105

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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
122isotropic23D HN(CA)CB
132isotropic23D CBCA(CO)NH
142isotropic23D 1H-15N NOESY
152isotropic23D HNCO
163isotropic23D (H)CCH-TOCSY
173isotropic23D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1100 uM [U-100% 15N] SPFH domain from stomatin, 95% H2O/5% D2O0.1mM dissolved in 50 mM phosphate buffer (pH 6.4), 100 mM NaCl15N95% H2O/5% D2O
solution2600 uM [U-100% 13C; U-100% 15N] SPFH domain from stomatin, 95% H2O/5% D2OSequential assignment13C15N95% H2O/5% D2O
solution3600 uM [U-100% 13C] SPFH domain from stomatin, 100% D2Osidechain assignment and NOEST13C100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 uMSPFH domain from stomatin[U-100% 15N]1
600 uMSPFH domain from stomatin[U-100% 13C; U-100% 15N]2
600 uMSPFH domain from stomatin[U-100% 13C]3
Sample conditionsDetails: 50 mM phosphate buffer (pH 6.4), 100 mM NaCl / Ionic strength: 200 mM / Label: phosphate buffer / pH: 6.4 pH* / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIBrukerAVANCE II6001@Nagoya University
Bruker AVANCEBrukerAVANCE6002oKobe University

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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