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- PDB-9lgo: Cryo-EM structure of the SPATA5-SPATA5L1-CINP-C1orf109 complex -

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Basic information

Entry
Database: PDB / ID: 9lgo
TitleCryo-EM structure of the SPATA5-SPATA5L1-CINP-C1orf109 complex
Components
  • (ATPase family gene 2 protein homolog ...) x 2
  • Cyclin-dependent kinase 2-interacting protein
  • cDNA FLJ55172
KeywordsCYTOSOLIC PROTEIN / ribosomal biogenesis / SPATA5 / ATPase complex
Function / homology
Function and homology information


preribosome binding / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / retrograde protein transport, ER to cytosol / non-chaperonin molecular chaperone ATPase / polyubiquitin modification-dependent protein binding / autophagosome maturation / ribosomal large subunit biogenesis / brain development / spindle ...preribosome binding / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / retrograde protein transport, ER to cytosol / non-chaperonin molecular chaperone ATPase / polyubiquitin modification-dependent protein binding / autophagosome maturation / ribosomal large subunit biogenesis / brain development / spindle / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / DNA replication / cell division / DNA repair / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ribosome biogenesis protein C1orf109-like / Ribosome biogenesis protein C1orf109-like / Cyclin-dependent kinase 2-interacting protein / : / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) ...Ribosome biogenesis protein C1orf109-like / Ribosome biogenesis protein C1orf109-like / Cyclin-dependent kinase 2-interacting protein / : / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / cDNA FLJ55172 / ATPase family gene 2 protein homolog A / ATPase family gene 2 protein homolog B / Cyclin-dependent kinase 2-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsDai, Y. / Zhang, Y. / Gao, N.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32230051 China
CitationJournal: To Be Published
Title: cryo-EM structure of the SPATA5-SPATA5L1-CINP-C1orf109 complex
Authors: Dai, Y. / Zhang, Y. / Gao, N.
History
DepositionJan 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATPase family gene 2 protein homolog A
J: Cyclin-dependent kinase 2-interacting protein
I: Cyclin-dependent kinase 2-interacting protein
H: cDNA FLJ55172
G: cDNA FLJ55172
F: ATPase family gene 2 protein homolog B
E: ATPase family gene 2 protein homolog A
D: ATPase family gene 2 protein homolog A
C: ATPase family gene 2 protein homolog B
B: ATPase family gene 2 protein homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)672,03419
Polymers667,95210
Non-polymers4,0829
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATPase family gene 2 protein homolog ... , 2 types, 6 molecules AEDBFC

#1: Protein
ATPase family gene 2 protein homolog A / AFG2 AAA ATPase homolog A / Ribosome biogenesis protein SPATA5 / Spermatogenesis-associated factor ...AFG2 AAA ATPase homolog A / Ribosome biogenesis protein SPATA5 / Spermatogenesis-associated factor protein / Spermatogenesis-associated protein 5


Mass: 97276.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AFG2A, SPAF, SPATA5 / Production host: Homo sapiens (human)
References: UniProt: Q8NB90, non-chaperonin molecular chaperone ATPase
#4: Protein ATPase family gene 2 protein homolog B / AFG2 AAA ATPase homolog B / Ribosome biogenesis protein SPATA5L1 / Spermatogenesis-associated ...AFG2 AAA ATPase homolog B / Ribosome biogenesis protein SPATA5L1 / Spermatogenesis-associated protein 5-like protein 1


Mass: 80409.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AFG2B, SPATA5L1 / Production host: Homo sapiens (human)
References: UniProt: Q9BVQ7, non-chaperonin molecular chaperone ATPase

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Protein , 2 types, 4 molecules JIHG

#2: Protein Cyclin-dependent kinase 2-interacting protein / CDK2-interacting protein


Mass: 27421.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CINP / Production host: Homo sapiens (human) / References: UniProt: Q9BW66
#3: Protein cDNA FLJ55172 / C1orf109(Long isoform)


Mass: 31592.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: B4DRQ5

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Non-polymers , 2 types, 9 molecules

#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The SPATA5 complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194789 / Symmetry type: POINT
RefinementHighest resolution: 3.51 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00739257
ELECTRON MICROSCOPYf_angle_d1.24553223
ELECTRON MICROSCOPYf_dihedral_angle_d7.4345362
ELECTRON MICROSCOPYf_chiral_restr0.0636182
ELECTRON MICROSCOPYf_plane_restr0.0116850

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