8E9B | pdb_00008e9b

Cryo-EM structure of S. pombe Arp2/3 complex in the branch junction

PDB DOI: https://doi.org/10.2210/pdb8E9B/pdb
EM Map EMD-27962: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Schizosaccharomyces pombe 972h-, Gallus gallus
Mutation(s): No

Deposited: 2022-08-26 Released: 2023-02-01
Deposition Author(s): Chou, S.Z., Pollard, T.P.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Mechanism of actin filament branch formation by Arp2/3 complex revealed by a high-resolution cryo-EM structureof the branch junction.

Chou, S.Z., Chatterjee, M., Pollard, T.D.

(2022) Proc Natl Acad Sci U S A 119: e2206722119-e2206722119

PubMed: 36442092 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2206722119
Primary Citation Related Structures:
8E9B

PubMed Abstract:
We reconstructed the structure of actin filament branch junctions formed by fission yeast Arp2/3 complex at 3.5 Å resolution from images collected by electron cryo-microscopy. During specimen preparation, all of the actin subunits and Arp3 hydrolyzed their bound adenosine triphosphate (ATP) and dissociated the γ-phosphate, but Arp2 retained the γ-phosphate. Binding tightly to the side of the mother filament and nucleating the daughter filament growing as a branch requires Arp2/3 complex to undergo a dramatic conformational change where two blocks of structure rotate relative to each other about 25° to align Arp2 and Arp3 as the first two subunits in the branch. During branch formation, Arp2/3 complex acquires more than 8,000 Å ² of new buried surface, accounting for the stability of the branch. Inactive Arp2/3 complex binds only transiently to the side of an actin filament, because its conformation allows only a subset of the interactions found in the branch junction.

Organizational Affiliation

Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520.

Macromolecule Content

Total Structure Weight: 566.41 kDa
Atom Count: 39,160
Modeled Residue Count: 4,933
Deposited Residue Count: 5,005
Unique protein chains: 8

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 3	A	427	Schizosaccharomyces pombe 972h-	Mutation(s): 0
UniProt
Find proteins for P32390 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P32390 Go to UniProtKB: P32390
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32390
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2	B	390	Schizosaccharomyces pombe 972h-	Mutation(s): 0
UniProt
Find proteins for Q9UUJ1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9UUJ1 Go to UniProtKB: Q9UUJ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UUJ1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 1	C	377	Schizosaccharomyces pombe 972h-	Mutation(s): 0
UniProt
Find proteins for P78774 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P78774 Go to UniProtKB: P78774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78774
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 2	D	317	Schizosaccharomyces pombe 972h-	Mutation(s): 0
UniProt
Find proteins for O14241 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O14241 Go to UniProtKB: O14241
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14241
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 3	E	174	Schizosaccharomyces pombe 972h-	Mutation(s): 0
UniProt
Find proteins for Q9Y7J4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9Y7J4 Go to UniProtKB: Q9Y7J4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y7J4
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 4	F	168	Schizosaccharomyces pombe 972h-	Mutation(s): 0
UniProt
Find proteins for Q92352 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q92352 Go to UniProtKB: Q92352
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92352
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 5	G	152	Schizosaccharomyces pombe 972h-	Mutation(s): 0
UniProt
Find proteins for Q10316 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q10316 Go to UniProtKB: Q10316
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q10316
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	H [auth M] I [auth N] J [auth O] K [auth P] L [auth Q] H [auth M], I [auth N], J [auth O], K [auth P], L [auth Q], M [auth R], N [auth H], O [auth I]	375	Gallus gallus	Mutation(s): 0 EC: 3.6.4
UniProt
Find proteins for P68139 (Gallus gallus) Explore P68139 Go to UniProtKB: P68139
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68139
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain AA [auth P] SDF format, chain CA [auth Q] SDF format, chain EA [auth R] SDF format, chain GA [auth H] SDF format, chain IA [auth I] SDF format, chain Q [auth A] SDF format, chain U [auth M] SDF format, chain W [auth N] SDF format, chain Y [auth O] MOL2 format, chain AA [auth P] MOL2 format, chain CA [auth Q] MOL2 format, chain EA [auth R] MOL2 format, chain GA [auth H] MOL2 format, chain IA [auth I] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth M] MOL2 format, chain W [auth N] MOL2 format, chain Y [auth O] mmCIF format, chain AA [auth P] mmCIF format, chain CA [auth Q] mmCIF format, chain EA [auth R] mmCIF format, chain GA [auth H] mmCIF format, chain IA [auth I] mmCIF format, chain Q [auth A] mmCIF format, chain U [auth M] mmCIF format, chain W [auth N] mmCIF format, chain Y [auth O]	AA [auth P] CA [auth Q] EA [auth R] GA [auth H] IA [auth I] AA [auth P], CA [auth Q], EA [auth R], GA [auth H], IA [auth I], Q [auth A], U [auth M], W [auth N], Y [auth O]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth P] Focus chain CA [auth Q] Focus chain EA [auth R] Focus chain GA [auth H] Focus chain IA [auth I] Focus chain Q [auth A] Focus chain U [auth M] Focus chain W [auth N] Focus chain Y [auth O] Interactions & Density Focus chain AA [auth P] Focus chain CA [auth Q] Focus chain EA [auth R] Focus chain GA [auth H] Focus chain IA [auth I] Focus chain Q [auth A] Focus chain U [auth M] Focus chain W [auth N] Focus chain Y [auth O]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth Q] SDF format, chain DA [auth R] SDF format, chain FA [auth H] SDF format, chain HA [auth I] SDF format, chain P [auth A] SDF format, chain R [auth B] SDF format, chain T [auth M] SDF format, chain V [auth N] SDF format, chain X [auth O] SDF format, chain Z [auth P] MOL2 format, chain BA [auth Q] MOL2 format, chain DA [auth R] MOL2 format, chain FA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth M] MOL2 format, chain V [auth N] MOL2 format, chain X [auth O] MOL2 format, chain Z [auth P] mmCIF format, chain BA [auth Q] mmCIF format, chain DA [auth R] mmCIF format, chain FA [auth H] mmCIF format, chain HA [auth I] mmCIF format, chain P [auth A] mmCIF format, chain R [auth B] mmCIF format, chain T [auth M] mmCIF format, chain V [auth N] mmCIF format, chain X [auth O] mmCIF format, chain Z [auth P]	BA [auth Q] DA [auth R] FA [auth H] HA [auth I] P [auth A] BA [auth Q], DA [auth R], FA [auth H], HA [auth I], P [auth A], R [auth B], T [auth M], V [auth N], X [auth O], Z [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth Q] Focus chain DA [auth R] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain P [auth A] Focus chain R [auth B] Focus chain T [auth M] Focus chain V [auth N] Focus chain X [auth O] Focus chain Z [auth P] Interactions & Density Focus chain BA [auth Q] Focus chain DA [auth R] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain P [auth A] Focus chain R [auth B] Focus chain T [auth M] Focus chain V [auth N] Focus chain X [auth O] Focus chain Z [auth P]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	H [auth M] I [auth N] J [auth O] K [auth P] L [auth Q] H [auth M], I [auth N], J [auth O], K [auth P], L [auth Q], M [auth R], N [auth H], O [auth I]	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-01

Deposition Author(s):

Chou, S.Z.

Pollard, T.P.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM026132
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM026338