7WHG

Lokiarchaeota gelsolin (2DGel) bound to two molecules of rabbit actin

PDB DOI: https://doi.org/10.2210/pdb7WHG/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Oryctolagus cuniculus, Candidatus Lokiarchaeota archaeon
Expression System: Oryctolagus cuniculus, Escherichia coli
Mutation(s): No

Deposited: 2021-12-30 Released: 2022-09-21
Deposition Author(s): Robinson, R.C., Akil, C.
Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS), Simons Foundation, Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.232
R-Value Work: 0.175

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural and biochemical evidence for the emergence of a calcium-regulated actin cytoskeleton prior to eukaryogenesis

Akil, C., Tran, L.T., Orhant-Prioux, M., Baskaran, Y., Senju, Y., Takeda, S., Chotchuang, P., Muengsaen, D., Schulte, A., Manser, E., Blanchoin, L., Robinson, R.C.

(2022) Commun Biol 5: 890

DOI: https://doi.org/10.1038/s42003-022-03783-1

Macromolecule Content

Total Structure Weight: 122.98 kDa
Atom Count: 7,607
Modelled Residue Count: 963
Deposited Residue Count: 1,089
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A, B	377	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: ACTA1, ACTA
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135 Go to UniProtKB: P68135
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lokiarchaeota gelsolin (2DGel)	C [auth G]	335	Candidatus Lokiarchaeota archaeon	Mutation(s): 0
UniProt
Find proteins for A0A0F8Y9R4 (Lokiarchaeum sp. (strain GC14_75)) Explore A0A0F8Y9R4 Go to UniProtKB: A0A0F8Y9R4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0F8Y9R4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth G] SDF format, chain J [auth G] SDF format, chain K [auth G] SDF format, chain L [auth G] SDF format, chain M [auth G] SDF format, chain N [auth G] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth G] MOL2 format, chain J [auth G] MOL2 format, chain K [auth G] MOL2 format, chain L [auth G] MOL2 format, chain M [auth G] MOL2 format, chain N [auth G]	E [auth A] F [auth A] H [auth B] I [auth G] J [auth G] E [auth A], F [auth A], H [auth B], I [auth G], J [auth G], K [auth G], L [auth G], M [auth G], N [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A, B	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.232
R-Value Work: 0.175
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.662	α = 90
b = 72.057	β = 92.08
c = 100.385	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-09-21

Deposition Author(s):

Robinson, R.C.

Akil, C.

Funding Organization	Location	Grant Number
Japan Science and Technology		JPMJCR19S5
Japan Society for the Promotion of Science (JSPS)		JP20H00476
Simons Foundation		GBMF9743
Other private		Moore Foundation GBMF9743

Revision History (Full details and data files)

Version 1.0: 2022-09-21
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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Help and Resources

7WHG

Lokiarchaeota gelsolin (2DGel) bound to two molecules of rabbit actin

Structural and biochemical evidence for the emergence of a calcium-regulated actin cytoskeleton prior to eukaryogenesis

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2