7T5Q

Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation

PDB DOI: https://doi.org/10.2210/pdb7T5Q/pdb
EM Map EMD-25707: EMDB EMDataResource

Classification: CONTRACTILE PROTEIN
Organism(s): Bos taurus, Oryctolagus cuniculus, Homo sapiens, Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-12-13 Released: 2023-06-14
Deposition Author(s): Rebowski, G., van Eeuwen, T., Boczkowska, M., Dominguez, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of an Arp2/3 complex mini-branch capped by capping protein (CapZ)

Rebowski, G., van Eeuwen, T., Dominguez, R., Boczkowska, M.

To be published.

Macromolecule Content

Total Structure Weight: 345.23 kDa
Atom Count: 21,671
Modelled Residue Count: 2,703
Deposited Residue Count: 3,033
Unique protein chains: 10

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 3	A	418	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P61157 (Bos taurus) Explore P61157 Go to UniProtKB: P61157
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61157
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2	B	394	Bos taurus	Mutation(s): 0
UniProt
Find proteins for A7MB62 (Bos taurus) Explore A7MB62 Go to UniProtKB: A7MB62
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7MB62
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 1A	C	370	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q1JP79 (Bos taurus) Explore Q1JP79 Go to UniProtKB: Q1JP79
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1JP79
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 2	D	300	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q3MHR7 (Bos taurus) Explore Q3MHR7 Go to UniProtKB: Q3MHR7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3MHR7
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 3	E	178	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q3T035 (Bos taurus) Explore Q3T035 Go to UniProtKB: Q3T035
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3T035
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 4	F	168	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q148J6 (Bos taurus) Explore Q148J6 Go to UniProtKB: Q148J6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q148J6
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 5	G	151	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q3SYX9 (Bos taurus) Explore Q3SYX9 Go to UniProtKB: Q3SYX9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3SYX9
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	H	375	Oryctolagus cuniculus	Mutation(s): 0
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
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
F-actin-capping protein subunit alpha-1/Actin nucleation-promoting factor WASL chimera	I	346	Homo sapiens, Mus musculus This entity is chimeric	Mutation(s): 0 Gene Names: CAPZA1, Wasl
UniProt & NIH Common Fund Data Resources
Find proteins for P52907 (Homo sapiens) Explore P52907 Go to UniProtKB: P52907
PHAROS: P52907 GTEx: ENSG00000116489
Find proteins for Q91YD9 (Mus musculus) Explore Q91YD9 Go to UniProtKB: Q91YD9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q91YD9P52907
Sequence Annotations Expand
Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
F-actin-capping protein subunit beta/Actin nucleation-promoting factor WASL chimera	J	333	Homo sapiens, Mus musculus This entity is chimeric	Mutation(s): 0 Gene Names: CAPZB, Wasl
UniProt & NIH Common Fund Data Resources
Find proteins for Q91YD9 (Mus musculus) Explore Q91YD9 Go to UniProtKB: Q91YD9
Find proteins for P47756 (Homo sapiens) Explore P47756 Go to UniProtKB: P47756
PHAROS: P47756 GTEx: ENSG00000077549
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q91YD9P47756
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B]	L [auth A], N [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain L [auth A] Focus chain N [auth B] Interactions & Density Focus chain L [auth A] Focus chain N [auth B]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain O [auth H] MOL2 format, chain O [auth H]	O [auth H]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain O [auth H] Interactions & Density Focus chain O [auth H]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain P [auth H] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth H]	K [auth A], M [auth B], P [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth H] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth H]

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.0

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM07391
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32-GM008275
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	F31-HL146077

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 1.1: 2023-08-02
Changes: Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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Help and Resources

7T5Q

Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation

Cryo-EM structure of an Arp2/3 complex mini-branch capped by capping protein (CapZ)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)