8EFY

Structure of double homo-hexameric AAA+ ATPase RuvB motors

PDB DOI: https://doi.org/10.2210/pdb8EFY/pdb
NAKB: 8EFY
EM Map EMD-28107: EMDB EMDataResource

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

Deposited: 2022-09-10 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: 3.16 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 double homo-hexameric AAA+ ATPase RuvB motor binding with DNA substrate

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

To be published.

Macromolecule Content

Total Structure Weight: 499.87 kDa
Atom Count: 31,274
Modelled Residue Count: 3,801
Deposited Residue Count: 4,088
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, B, C, D, E A, B, C, D, E, F, I, J, K, L, M, N	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
ssDNA	G, O	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
ssDNA	H, P	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 CA [auth J] SDF format, chain EA [auth K] SDF format, chain GA [auth L] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain W [auth D] MOL2 format, chain CA [auth J] MOL2 format, chain EA [auth K] MOL2 format, chain GA [auth L] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain W [auth D]	CA [auth J] EA [auth K] GA [auth L] S [auth B] U [auth B] CA [auth J], EA [auth K], GA [auth L], S [auth B], U [auth B], W [auth D]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain CA [auth J] Focus chain EA [auth K] Focus chain GA [auth L] Focus chain S [auth B] Focus chain U [auth B] Focus chain W [auth D] Interactions & Density Focus chain CA [auth J] Focus chain EA [auth K] Focus chain GA [auth L] Focus chain S [auth B] Focus chain U [auth B] Focus chain W [auth D]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain IA [auth M] SDF format, chain JA [auth N] SDF format, chain Q [auth A] SDF format, chain Y [auth E] SDF format, chain Z [auth F] MOL2 format, chain AA [auth I] MOL2 format, chain IA [auth M] MOL2 format, chain JA [auth N] MOL2 format, chain Q [auth A] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth F]	AA [auth I] IA [auth M] JA [auth N] Q [auth A] Y [auth E] AA [auth I], IA [auth M], JA [auth N], Q [auth A], Y [auth E], Z [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth I] Focus chain IA [auth M] Focus chain JA [auth N] Focus chain Q [auth A] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth I] Focus chain IA [auth M] Focus chain JA [auth N] Focus chain Q [auth A] Focus chain Y [auth E] Focus chain Z [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain DA [auth J] SDF format, chain FA [auth K] SDF format, chain HA [auth L] SDF format, chain R [auth A] SDF format, chain T [auth B] SDF format, chain V [auth C] SDF format, chain X [auth D] MOL2 format, chain BA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain FA [auth K] MOL2 format, chain HA [auth L] MOL2 format, chain R [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D]	BA [auth I] DA [auth J] FA [auth K] HA [auth L] R [auth A] BA [auth I], DA [auth J], FA [auth K], HA [auth L], R [auth A], T [auth B], V [auth C], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D]