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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 / protein stabilization / cilium / hydrolase activity / GTP binding / nucleoplasm / cytosol / cytoplasm
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: To Be Published
Title: R2TP-like complexes as quaternary chaperones. A comprehensive overview to understand the dynamic R2SP complex
Authors: Chagot, M.E. / Quinternet, M.
History
DepositionDec 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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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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