8EFV

Structure of single homo-hexameric Holliday junction ATP-dependent DNA helicase RuvB motor

PDB DOI: https://doi.org/10.2210/pdb8EFV/pdb
NAKB: 8EFV
EM Map EMD-28101: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-09-09 Released: 2023-05-10
Deposition Author(s): Shen, Z.F., Rish, A.D., Fu, T.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.97 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

Structure of single homo-hexameric Holliday junction ATP-dependent DNA helicase RuvB motor

Shen, Z.F., Rish, A.D., Fu, T.M.

To be published.

Macromolecule Content

Total Structure Weight: 249.93 kDa
Atom Count: 15,295
Modelled Residue Count: 1,863
Deposited Residue Count: 2,044
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Holliday junction ATP-dependent DNA helicase RuvB	A [auth D] B [auth C] C [auth B] D [auth A] E [auth F] A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	324	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: ruvB, TTHA0406 EC: 3.6.4.12
UniProt
Find proteins for Q5SL87 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SL87 Go to UniProtKB: Q5SL87
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SL87
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
49-mer DNA	G	49	Thermus thermophilus HB8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
51-mer DNA	H	51	Thermus thermophilus HB8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain K [auth C] SDF format, chain M [auth B] MOL2 format, chain I [auth D] MOL2 format, chain K [auth C] MOL2 format, chain M [auth B]	I [auth D], K [auth C], M [auth B]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain I [auth D] Focus chain K [auth C] Focus chain M [auth B] Interactions & Density Focus chain I [auth D] Focus chain K [auth C] Focus chain M [auth B]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain R [auth E] SDF format, chain O [auth A] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth E] MOL2 format, chain O [auth A]	O [auth A], Q [auth F], R [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain O [auth A] Focus chain Q [auth F] Focus chain R [auth E] Interactions & Density Focus chain O [auth A] Focus chain Q [auth F] Focus chain R [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain N [auth B] SDF format, chain P [auth A] SDF format, chain L [auth C] MOL2 format, chain J [auth D] MOL2 format, chain N [auth B] MOL2 format, chain P [auth A] MOL2 format, chain L [auth C]	J [auth D], L [auth C], N [auth B], P [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth D] Focus chain L [auth C] Focus chain N [auth B] Focus chain P [auth A] Interactions & Density Focus chain J [auth D] Focus chain L [auth C] Focus chain N [auth B] Focus chain P [auth A]