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- PDB-6i57: NMR structure of the third TPR domain of the human SPAG1 protein -

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Basic information

Entry
Database: PDB / ID: 6i57
TitleNMR structure of the third TPR domain of the human SPAG1 protein
ComponentsSperm-associated antigen 1
KeywordsCHAPERONE / HSP70 / HSP90 / ATPase / GTPase / EEVD / MD simulation / RUVBL / R2TP / R2SP / cilia / dynein / assembly factor
Function / homology
Function and homology information


axonemal dynein complex assembly / dynein axonemal particle / protein folding chaperone complex / single fertilization / protein stabilization / hydrolase activity / GTP binding / cytosol / cytoplasm
Similarity search - Function
RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Sperm-associated antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsChagot, M.E. / Quinternet, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-16-CE11-0032-02 France
CitationJournal: Biochem.J. / Year: 2019
Title: Binding properties of the quaternary assembly protein SPAG1.
Authors: Chagot, M.E. / Dos Santos Morais, R. / Dermouche, S. / Lefebvre, D. / Manival, X. / Chipot, C. / Dehez, F. / Quinternet, M.
History
DepositionNov 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 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: Sperm-associated antigen 1


Theoretical massNumber of molelcules
Total (without water)14,3821
Polymers14,3821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7160 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sperm-associated antigen 1 / HSD-3.8 / Infertility-related sperm protein Spag-1


Mass: 14381.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPAG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q07617

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D CBCA(CO)NH
121isotropic13D HNCA
131isotropic13D HN(CA)CB
141isotropic13D HBHA(CO)NH
151isotropic13D H(CCO)NH
191isotropic13D HNCO
181isotropic13D (H)CCH-TOCSY
171isotropic13D HNHA
161isotropic13D 1H-15N NOESY
1151isotropic13D 1H-13C NOESY
1141isotropic12D 1H-15N HSQC
1131isotropic12D 1H-13C HSQC
1121isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] SPAG1-TPR3, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 95% H2O/5% D2O
Label: sample_1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSPAG1-TPR3[U-13C; U-15N]1
150 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
0.5 mMTCEPnatural abundance1
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TALOSCornilescu, Delaglio and Baxstructure calculation
PREDITORBerjanskii MV, Neal S, Wishart DS.structure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 7
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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