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- PDB-9hkr: NMR structure of the C-terminal domain of the human SPAG1 protein -

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Basic information

Entry
Database: PDB / ID: 9hkr
TitleNMR structure of the C-terminal domain of the human SPAG1 protein
ComponentsSperm-associated antigen 1
KeywordsCHAPERONE / R2SP / RUVBL1 / RUVBL2 / cilia
Function / homology
Function and homology information


axonemal dynein complex assembly / dynein axonemal particle / protein folding chaperone complex / single fertilization / sperm principal piece / protein stabilization / cilium / hydrolase activity / GTP binding / nucleoplasm ...axonemal dynein complex assembly / dynein axonemal particle / protein folding chaperone complex / single fertilization / sperm principal piece / protein stabilization / cilium / hydrolase activity / GTP binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
: / RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
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
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Nat Commun / Year: 2026
Title: An integrative structural biology approach reveals the dynamic organization of the R2SP quaternary chaperone complex.
Authors: Paulo E Santo / Marie-Eve Chagot / Hugo Gizardin-Fredon / Marie Ley / Thomas Chenuel / Evolène Deslignière / Laura Plassart / Ana C F Paiva / Pedro M F Sousa / Edouard Bertrand / Bruno ...Authors: Paulo E Santo / Marie-Eve Chagot / Hugo Gizardin-Fredon / Marie Ley / Thomas Chenuel / Evolène Deslignière / Laura Plassart / Ana C F Paiva / Pedro M F Sousa / Edouard Bertrand / Bruno Charpentier / Céline Verheggen / Marc Quinternet / Philippe Meyer / Tiago M Bandeiras / Sarah Cianférani / Célia Plisson-Chastang / Xavier Manival /
Abstract: R2SP belongs to the R2TP-like quaternary chaperone family and consists of RUVBL1/RUVBL2 AAA+ ATPases, which powers the machinery, and SPAG1 and PIH1D2 adapter proteins that engage specific clients to ...R2SP belongs to the R2TP-like quaternary chaperone family and consists of RUVBL1/RUVBL2 AAA+ ATPases, which powers the machinery, and SPAG1 and PIH1D2 adapter proteins that engage specific clients to promote their quaternary assembly. However, little is known about the structure of R2SP and the precise mode of action of these R2TP-like complexes. Here, we combined biochemical (ATPase and fluorescence polarization assays) and structural approaches (NMR, structural mass spectrometry, cryo-EM) to investigate the 3D organization of the R2SP complex, its mode of assembly and ATPase activity. Together with our binding, mutational and kinetic studies, these results led us to propose a model in which SPAG1 and PIH1D2 bind and cooperatively engage RUVBL1/RUVBL2 to produce R2SP. This reveals a 3D structure close to the canonical R2TP complex but also highlights differences in RUVBL1/RUVBL2 ATPase activity, as well as the cooperative binding of SPAG1 and PIH1D2 to this catalytic core that may explain functional difference between the two systems.
History
DepositionDec 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)15,5181
Polymers15,5181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 120structures 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: 15517.994 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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY
121isotropic13D 1H-15N NOESY
131isotropic13D C(CO)NH
141isotropic13D H(CCO)NH
151isotropic13D HBHA(CO)NH
1111isotropic13D HNCA
1101isotropic13D HNCO
191isotropic13D HN(CA)CB
181isotropic13D HN(CO)CA
171isotropic13D HNHA
161isotropic13D (H)CCH-COSY
1121isotropic13D (H)CCH-COSY
1141isotropic12D 1H-15N HSQC
1131isotropic12D 1H-13C HSQC
1151isotropic12D NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] SPAG1, 150 mM sodium chloride, 10 mM sodium phosphate, 95% H2O/5% D2O
Label: 13C15N_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSPAG1[U-100% 13C; U-100% 15N]1
150 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 150 mM / Label: cond1 / pH: 6.4 / Pressure: 1 atm / Temperature: 298 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
CARA1.8.4Keller and Wuthrichchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CARA1.8.4Keller and Wuthrichpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 20

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