23FD | pdb_000023fd

Cryo-EM structure of human ATR-ATRIP complex with ATPgammaS, Chk1 and TopBp1

PDB DOI: https://doi.org/10.2210/pdb23FD/pdb
EM Map EMD-68920: EMDB EMDataResource

Classification: NUCLEAR PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens, Spodoptera frugiperda
Mutation(s): No

Deposited: 2026-02-04 Released: 2026-08-26
Deposition Author(s): Wang, L., Wang, M., Zhao, L., Rao, Q., Wu, H., Ma, B., Wang, J., Zheng, J., Li, Y., Xu, Y., Guo, J., Cheng, J., Qiao, S.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 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

Mechanistic insights into phosphorylation-driven activation and therapeutic inhibition of human ATR-ATRIP

Wang, L., Wang, M., Zhao, L., Rao, Q., Wu, H., Ma, B., Wang, J., Zheng, J., Li, Y., Xu, Y., Guo, J., Cheng, J., Qiao, S.

To be published.

Macromolecule Content

Total Structure Weight: 901.97 kDa
Atom Count: 46,339
Modeled Residue Count: 5,823
Deposited Residue Count: 7,988
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase ATR	A, B	2,644	Homo sapiens	Mutation(s): 0 Gene Names: ATR, FRP1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13535 (Homo sapiens) Explore Q13535 Go to UniProtKB: Q13535
GTEx: ENSG00000175054
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13535
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATR-interacting protein	C, D	791	Homo sapiens	Mutation(s): 0 Gene Names: ATRIP, AGS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WXE1 (Homo sapiens) Explore Q8WXE1 Go to UniProtKB: Q8WXE1
GTEx: ENSG00000164053
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WXE1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	E, F	14	Homo sapiens	Mutation(s): 0 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens) Explore O14757 Go to UniProtKB: O14757
GTEx: ENSG00000149554
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14757
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2-binding protein 1	G, H	545	Homo sapiens	Mutation(s): 0 Gene Names: TOPBP1, KIAA0259
UniProt & NIH Common Fund Data Resources
Find proteins for Q92547 (Homo sapiens) Explore Q92547 Go to UniProtKB: Q92547
GTEx: ENSG00000163781
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92547
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A], L [auth B]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C]	O [auth C], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Focus chain P [auth D] Interactions & Density Focus chain O [auth C] Focus chain P [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], M [auth B], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B]