9LGO | pdb_00009lgo

Cryo-EM structure of the SPATA5-SPATA5L1-CINP-C1orf109 complex

PDB DOI: https://doi.org/10.2210/pdb9LGO/pdb
EM Map EMD-63069: EMDB EMDataResource

Classification: CYTOSOLIC PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-01-10 Released: 2025-04-23
Deposition Author(s): Dai, Y., Zhang, Y., Gao, N.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.51 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

cryo-EM structure of the SPATA5-SPATA5L1-CINP-C1orf109 complex

Dai, Y., Zhang, Y., Gao, N.

To be published.

Macromolecule Content

Total Structure Weight: 672.03 kDa
Atom Count: 38,406
Modeled Residue Count: 4,935
Deposited Residue Count: 6,076
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase family gene 2 protein homolog A	A, G [auth E], H [auth D], J [auth B]	886	Homo sapiens	Mutation(s): 0 Gene Names: AFG2A, SPAF, SPATA5 EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NB90 (Homo sapiens) Explore Q8NB90 Go to UniProtKB: Q8NB90
PHAROS: Q8NB90 GTEx: ENSG00000145375
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NB90
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2-interacting protein	B [auth J], C [auth I]	242	Homo sapiens	Mutation(s): 0 Gene Names: CINP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BW66 (Homo sapiens) Explore Q9BW66 Go to UniProtKB: Q9BW66
PHAROS: Q9BW66 GTEx: ENSG00000100865
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BW66
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
cDNA FLJ55172	D [auth H], E [auth G]	275	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for B4DRQ5 (Homo sapiens) Explore B4DRQ5 Go to UniProtKB: B4DRQ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4DRQ5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase family gene 2 protein homolog B	F, I [auth C]	749	Homo sapiens	Mutation(s): 0 Gene Names: AFG2B, SPATA5L1 EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVQ7 (Homo sapiens) Explore Q9BVQ7 Go to UniProtKB: Q9BVQ7
PHAROS: Q9BVQ7 GTEx: ENSG00000171763
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BVQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth F] SDF format, chain M [auth F] SDF format, chain N [auth E] SDF format, chain O [auth D] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth F] MOL2 format, chain M [auth F] MOL2 format, chain N [auth E] MOL2 format, chain O [auth D] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth F] mmCIF format, chain M [auth F] mmCIF format, chain N [auth E] mmCIF format, chain O [auth D] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth B]	K [auth A] L [auth F] M [auth F] N [auth E] O [auth D] K [auth A], L [auth F], M [auth F], N [auth E], O [auth D], P [auth C], Q [auth C], S [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain K [auth A] Focus chain L [auth F] Focus chain M [auth F] Focus chain N [auth E] Focus chain O [auth D] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth F] Focus chain M [auth F] Focus chain N [auth E] Focus chain O [auth D] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]