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- EMDB-25707: Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-25707

Title

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

Map data

Main map post processed with deepEMhancer

Sample

Complex: bovine Arp2/3 complex and Actin, CapZ
- Complex: bovine Arp2/3
  - Protein or peptide: x 7 types
- Complex: Actin skeletal muscle
  - Protein or peptide: x 1 types
- Complex: F-actin-capping protein
  - Protein or peptide: x 2 types
Ligand: x 3 types

Keywords

actin /

ATPase / actin related protein / arp /

cytoskeleton / Arp2-3 complex / actin nucleation / actin branching /

CONTRACTILE PROTEIN /

CapZ

Function / homology

Function and homology information

negative regulation of membrane tubulation / muscle cell projection membrane / spindle localization / membrane invagination / positive regulation of clathrin-dependent endocytosis / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / plasma membrane tubulation /

Arp2/3 protein complex ...negative regulation of membrane tubulation / muscle cell projection membrane / spindle localization / membrane invagination / positive regulation of clathrin-dependent endocytosis / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / plasma membrane tubulation /

Arp2/3 protein complex / negative regulation of lymphocyte migration / Arp2/3 complex-mediated actin nucleation / actin nucleation / WASH complex / postsynapse organization / sperm connecting piece / F-actin capping protein complex / negative regulation of filopodium assembly / regulation of cell projection assembly / actin cap / vesicle organization / postsynaptic actin cytoskeleton organization / positive regulation of chemotaxis / vesicle budding from membrane / regulation of actin filament polymerization /

Clathrin-mediated endocytosis / COPI-independent Golgi-to-ER retrograde traffic /

cell junction assembly / barbed-end actin filament capping / vesicle transport along actin filament / actin polymerization or depolymerization / dendritic spine morphogenesis / protein-containing complex localization / RHOF GTPase cycle / RHOD GTPase cycle / regulation of cell morphogenesis /

regulation of lamellipodium assembly / Sensory processing of sound by inner hair cells of the cochlea / regulation of postsynapse organization / Neutrophil degranulation /

lamellipodium assembly / positive regulation of filopodium assembly / cytoskeletal motor activator activity /

tropomyosin binding / cortical cytoskeleton /

myosin heavy chain binding / positive regulation of double-strand break repair via homologous recombination / mesenchyme migration /

troponin I binding / actin filament bundle / cell leading edge / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly /

brush border / striated muscle thin filament / Advanced glycosylation endproduct receptor signaling / skeletal muscle myofibril /

cilium assembly / actin monomer binding / skeletal muscle fiber development / COPI-mediated anterograde transport / positive regulation of lamellipodium assembly /

stress fiber / cytoskeleton organization /

titin binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / hippocampal mossy fiber to CA3 synapse / MHC class II antigen presentation / actin filament polymerization / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation /

cytoskeletal protein binding /

sarcomere /

filopodium / cell projection /

actin filament / response to bacterium /

Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / cell morphogenesis / structural constituent of cytoskeleton / calcium-dependent protein binding /

regulation of protein localization /

actin filament binding /

cell migration /

actin cytoskeleton /

lamellipodium / site of double-strand break /

cell body /

actin binding / Factors involved in megakaryocyte development and platelet production / cytoplasmic vesicle / actin cytoskeleton organization / postsynapse / protein-containing complex assembly /

postsynaptic density /

cytoskeleton /

hydrolase activity / neuron projection /

cadherin binding
Similarity search - Function

Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 /

Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily ...Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 /

Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily /

Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit / ARP2/3 complex 16 kDa subunit (p16-Arc) / ARP2/3 complex 20 kDa subunit (ARPC4) / WH2 motif / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / Wiskott Aldrich syndrome homology region 2 / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / WH2 domain / WH2 domain profile. / WH1/EVH1 domain /

WH1 domain / WH1 domain profile. / WASP homology region 1 / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Actins signature 1. /

Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. /

Actin /

Actin family /

Actin /

ATPase, nucleotide binding domain / PH-like domain superfamily /

WD domain, G-beta repeat /

WD40 repeats /

WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology

Biological species

Bos taurus (cattle) /

Oryctolagus cuniculus (rabbit) /

Homo sapiens (human) /

cattle (cattle) /

rabbit (rabbit) /

Mus musculus (house mouse)

Method

single particle reconstruction /

cryo EM / Resolution: 3.4 Å

Authors

Rebowski G / van Eeuwen T / Boczkowska M / Dominguez R

Funding support

United States, 3 items

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

Citation

Journal: To Be Published
Title: Cryo-EM structure of an Arp2/3 complex mini-branch capped by capping protein (CapZ)
Authors: Rebowski G / van Eeuwen T / Dominguez R / Boczkowska M

History

Deposition	Dec 13, 2021	-
Header (metadata) release	Jun 14, 2023	-
Map release	Jun 14, 2023	-
Update	Aug 2, 2023	-
Current status	Aug 2, 2023	Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images	emd_25707.png

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Downloads & links

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EMDB archive

Map data	emd_25707.map.gz	146.5 MB		EMDB map data format
Header (meta data)	emd-25707-v30.xml emd-25707.xml	37.8 KB 37.8 KB	Display Display	EMDB header
FSC (resolution estimation)	emd_25707_fsc.xml	11.6 KB	Display	FSC data file
Images	emd_25707.png	90.7 KB
Others	emd_25707_additional_1.map.gz emd_25707_additional_2.map.gz emd_25707_half_map_1.map.gz emd_25707_half_map_2.map.gz	157.1 MB 83.1 MB 154.7 MB 154.7 MB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-25707 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25707	HTTPS FTP

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Related structure data

Related structure data	7t5qMC M: atomic model generated by this map C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

EMDB pages	EMDB (EBI/PDBe) / EMDataResource
Related items in Molecule of the Month	#19 - Jul 2001 Actin similarity (9) #18 - Jun 2001 Myosin similarity (9) #79 - Jul 2006 Amyloid-beta Precursor Protein similarity (1) #189 - Sep 2015 Amyloids similarity (1) #239 - Nov 2019 Phospholipase A2 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #167 - Nov 2013 SNARE Proteins similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #224 - Aug 2018 Legumain similarity (1) #128 - Aug 2010 Interferons similarity (1) #88 - Apr 2007 Clathrin similarity (1) #247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #14 - Feb 2001 Insulin similarity (1) #94 - Oct 2007 Superoxide Dismutase similarity (1) #12 - Dec 2000 Pepsin similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1) #64 - Apr 2005 Kinesin similarity (1) #222 - Jun 2018 Proteins and Nanoparticles similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (3)

EMDB pages

EMDB (EBI/PDBe) /

EMDataResource

Related items in Molecule of the Month

#19 - Jul 2001
Actin
similarity (9)
#18 - Jun 2001
Myosin
similarity (9)
#79 - Jul 2006
Amyloid-beta Precursor Protein
similarity (1)
#189 - Sep 2015
Amyloids
similarity (1)
#239 - Nov 2019
Phospholipase A2
similarity (1)
#194 - Feb 2016
Designer Insulins
similarity (1)
#167 - Nov 2013
SNARE Proteins
similarity (1)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#224 - Aug 2018
Legumain
similarity (1)
#128 - Aug 2010
Interferons
similarity (1)
#88 - Apr 2007
Clathrin
similarity (1)
#247 - Jul 2020
Myelin-associated Glycoprotein
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#14 - Feb 2001
Insulin
similarity (1)
#94 - Oct 2007
Superoxide Dismutase
similarity (1)
#12 - Dec 2000
Pepsin
similarity (1)
#205 - Jan 2017
Nuclear Pore Complex
similarity (1)
#209 - May 2017
Tissue Transglutaminase and Celiac Disease
similarity (1)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (1)
#63 - Mar 2005
T-Cell Receptor
similarity (1)
#64 - Apr 2005
Kinesin
similarity (1)
#222 - Jun 2018
Proteins and Nanoparticles
similarity (1)
#163 - Jul 2013
HIV Capsid
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (3)

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Map

File

Download / File: emd_25707.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Annotation

Main map post processed with deepEMhancer

Voxel size

X=Y=Z: 0.86 Å

Density

Contour Level	By AUTHOR: 0.066
Minimum - Maximum	-0.0018159297 - 1.8901378
Average (Standard dev.)	0.0017101009 (±0.028842943)

Symmetry

Space group: 1

Details

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Supplemental data

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Additional map: map post processed with global b factor sharpening

File

emd_25707_additional_1.map

Annotation

map post processed with global b factor sharpening

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

File

emd_25707_additional_2.map

Annotation

unsharpened map

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

File

emd_25707_half_map_1.map

Annotation

half map A

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

File

emd_25707_half_map_2.map

Annotation

half map B

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : bovine Arp2/3 complex and Actin, CapZ

Entire	Name: bovine Arp2/3 complex and Actin, CapZ
Components	Complex: bovine Arp2/3 complex and Actin, CapZ Complex: bovine Arp2/3 Protein or peptide: Actin-related protein 3 Protein or peptide: Actin-related protein 2 Protein or peptide: Actin-related protein 2/3 complex subunit 1A Protein or peptide: Actin-related protein 2/3 complex subunit 2 Protein or peptide: Actin-related protein 2/3 complex subunit 3 Protein or peptide: Actin-related protein 2/3 complex subunit 4 Protein or peptide: Actin-related protein 2/3 complex subunit 5 Complex: Actin skeletal muscle Protein or peptide: Actin, alpha skeletal muscle Complex: F-actin-capping protein Protein or peptide: F-actin-capping protein subunit alpha-1/Actin nucleation-promoting factor WASL chimera Protein or peptide: F-actin-capping protein subunit beta/Actin nucleation-promoting factor WASL chimera Ligand: MAGNESIUM ION Ligand: ADENOSINE-5'-TRIPHOSPHATE Ligand: ADENOSINE-5'-DIPHOSPHATE

Entire

Name: bovine Arp2/3 complex and Actin, CapZ

Components

Complex: bovine Arp2/3 complex and Actin, CapZ
- Complex: bovine Arp2/3
  - Protein or peptide: Actin-related protein 3
  - Protein or peptide: Actin-related protein 2
  - Protein or peptide: Actin-related protein 2/3 complex subunit 1A
  - Protein or peptide: Actin-related protein 2/3 complex subunit 2
  - Protein or peptide: Actin-related protein 2/3 complex subunit 3
  - Protein or peptide: Actin-related protein 2/3 complex subunit 4
  - Protein or peptide: Actin-related protein 2/3 complex subunit 5
- Complex: Actin skeletal muscle
  - Protein or peptide: Actin, alpha skeletal muscle
- Complex: F-actin-capping protein
  - Protein or peptide: F-actin-capping protein subunit alpha-1/Actin nucleation-promoting factor WASL chimera
  - Protein or peptide: F-actin-capping protein subunit beta/Actin nucleation-promoting factor WASL chimera
Ligand: MAGNESIUM ION
Ligand: ADENOSINE-5'-TRIPHOSPHATE
Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: bovine Arp2/3 complex and Actin, CapZ

Supramolecule	Name: bovine Arp2/3 complex and Actin, CapZ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Molecular weight	Theoretical: 248.9 KDa

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Supramolecule #2: bovine Arp2/3

Supramolecule	Name: bovine Arp2/3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#7
Source (natural)	Organism: Bos taurus (cattle) / Organ: brain

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Supramolecule #3: Actin skeletal muscle

Supramolecule	Name: Actin skeletal muscle / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8
Source (natural)	Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #4: F-actin-capping protein

Supramolecule	Name: F-actin-capping protein / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #9-#10 / Details: subunit alpha and beta
Source (natural)	Organism: Homo sapiens (human)

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Macromolecule #1: Actin-related protein 3

Macromolecule	Name: Actin-related protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: cattle (cattle)
Molecular weight	Theoretical: 47.428031 KDa
Sequence	String: MAGRLPACVV DCGTGYTKLG YAGNTEPQFI IPSCIAIKES AKVGDQAQRR VMKGVDDLDF FIGDEAIEKP TYATKWPIRH GIVEDWDLM ERFMEQVIFK YLRAEPEDHY FLLTEPPLNT PENREYTAEI MFESFNVPGL YIAVQAVLAL AASWTSRQVG E RTLTGTVI ...String: MAGRLPACVV DCGTGYTKLG YAGNTEPQFI IPSCIAIKES AKVGDQAQRR VMKGVDDLDF FIGDEAIEKP TYATKWPIRH GIVEDWDLM ERFMEQVIFK YLRAEPEDHY FLLTEPPLNT PENREYTAEI MFESFNVPGL YIAVQAVLAL AASWTSRQVG E RTLTGTVI DSGDGVTHVI PVAEGYVIGS CIKHIPIAGR DITYFIQQLL RDREVGIPPE QSLETAKAVK ERYSYVCPDL VK EFNKYDT DGSKWIKQYT GINAISKKEF SIDVGYERFL GPEIFFHPEF ANPDFTQPIS EVVDEVIQNC PIDVRRPLYK NIV LSGGST MFRDFGRRLQ RDLKRTVDAR LKLSEELSGG RLKPKPIDVQ VITHHMQRYA VWFGGSMLAS TPEFYQVCHT KKDY EEIGP SICRHNPVFG VMS UniProtKB: Actin-related protein 3

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Macromolecule #2: Actin-related protein 2

Macromolecule	Name: Actin-related protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: cattle (cattle)
Molecular weight	Theoretical: 44.818711 KDa
Sequence	String: MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTTKVGNI EIKDLMVGDE ASELRSMLEV NYPMENGIVR NWDDMKHLW DYTFGPEKLN IDTRNCKILL TEPPMNPTKN REKIVEVMFE TYQFSGVYVA IQAVLTLYAQ GLLTGVVVDS G DGVTHICP ...String: MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTTKVGNI EIKDLMVGDE ASELRSMLEV NYPMENGIVR NWDDMKHLW DYTFGPEKLN IDTRNCKILL TEPPMNPTKN REKIVEVMFE TYQFSGVYVA IQAVLTLYAQ GLLTGVVVDS G DGVTHICP VYEGFSLPHL TRRLDIAGRD ITRYLIKLLL LRGYAFNHSA DFETVRMIKE KLCYVGYNIE QEQKLALETT VL VESYTLP DGRIIKVGGE RFEAPEALFQ PHLINVEGVG VAELLFNTIQ AADIDTRSEF YKHIVLSGGS TMYPGLPSRL ERE LKQLYL ERVLKGDVEK LSKFKIRIED PPRRKHMVFL GGAVLADIMK DKDNFWMTRQ EYQEKGVRVL EKLGVTVR UniProtKB: Actin-related protein 2

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Macromolecule #3: Actin-related protein 2/3 complex subunit 1A

Macromolecule	Name: Actin-related protein 2/3 complex subunit 1A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: cattle (cattle)
Molecular weight	Theoretical: 41.594238 KDa
Sequence	String: MSLHQFLLEP ITCHAWNRDR TQIALSPNNH EVHIYKKNGG QWVKAHELKE HNGHITGIDW APKSDRIVTC GADRNAYVWS QKDGVWKPT LVILRINRAA TFVKWSPLEN KFAVGSGARL ISVCYFESEN DWWVSKHIKK PIRSTVLSLD WHPNNVLLAA G SCDFKCRV ...String: MSLHQFLLEP ITCHAWNRDR TQIALSPNNH EVHIYKKNGG QWVKAHELKE HNGHITGIDW APKSDRIVTC GADRNAYVWS QKDGVWKPT LVILRINRAA TFVKWSPLEN KFAVGSGARL ISVCYFESEN DWWVSKHIKK PIRSTVLSLD WHPNNVLLAA G SCDFKCRV FSAYIKEVDE KPASTPWGSK MPFGQLMSEF GGSGTGGWVH GVSFSASGSR LAWVSHDSTV SVADASKSVQ VS TLKTEFL PLLSVSFVSE NSVVAAGHDC CPMLFNYDDR GCLTFVSKLD IPKQSIQRNM SAMERFRNMD KRATTEDRNT ALE TLHQNS ITQVSIYEVD KQDCRKFCTT GIDGAMTIWD FKTLESSIQG LRIM UniProtKB: Actin-related protein 2/3 complex subunit 1A

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Macromolecule #4: Actin-related protein 2/3 complex subunit 2

Macromolecule	Name: Actin-related protein 2/3 complex subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: cattle (cattle)
Molecular weight	Theoretical: 34.402043 KDa
Sequence	String: MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSYLVNPES GYNVSLLYDL ENLPASKDSI VHQAGMLKRN CFASVFEKYF QFQEEGKEGE NRAVIHYRDD ETMYVESKKD R VTVVFSTV ...String: MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSYLVNPES GYNVSLLYDL ENLPASKDSI VHQAGMLKRN CFASVFEKYF QFQEEGKEGE NRAVIHYRDD ETMYVESKKD R VTVVFSTV FKDDDDVVIG KVFMQEFKEG RRASHTAPQV LFSHREPPLE LKDTDAAVGD NIGYITFVLF PRHTNASARD NT INLIHTF RDYLHYHIKC SKAYIHTRMR AKTSDFLKVL NRARPDAEKK EMKTITGKTF SSR UniProtKB: Actin-related protein 2/3 complex subunit 2

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Macromolecule #5: Actin-related protein 2/3 complex subunit 3

Macromolecule	Name: Actin-related protein 2/3 complex subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: cattle (cattle)
Molecular weight	Theoretical: 20.572666 KDa
Sequence	String: MPAYHSSLMD PDTKLIGNMA LLPIRSQFKG PAPRETKDTD IVDEAIYYFK ANVFFKNYEI KNEADRTLIY ITLYISECLK KLQKCNSKS QGEKEMYTLG ITNFPIPGEP GFPLNAIYAK PANKQEDEVM RAYLQQLRQE TGLRLCEKVF DPQNDKPSKW W TCFVKRQF MNKSLSGPGQ UniProtKB: Actin-related protein 2/3 complex subunit 3

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Macromolecule #6: Actin-related protein 2/3 complex subunit 4

Macromolecule	Name: Actin-related protein 2/3 complex subunit 4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: cattle (cattle)
Molecular weight	Theoretical: 19.697047 KDa
Sequence	String: MTATLRPYLS AVRATLQAAL CLENFSSQVV ERHNKPEVEV RSSKELLLQP VTISRNEKEK VLIEGSINSV RVSIAVKQAD EIEKILCHK FMRFMMMRAE NFFILRRKPV EGYDISFLIT NFHTEQMYKH KLVDFVIHFM EEIDKEISEM KLSVNARARI V AEEFLKNF UniProtKB: Actin-related protein 2/3 complex subunit 4

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Macromolecule #7: Actin-related protein 2/3 complex subunit 5

Macromolecule	Name: Actin-related protein 2/3 complex subunit 5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: cattle (cattle)
Molecular weight	Theoretical: 16.251308 KDa
Sequence	String: MSKNTVSSAR FRKVDVGEYD ENKFVDEEDG GDGQAGPDEG EVDSCLRQGN MTAALQAALK NPPINTKSQA VKDRAGSIVL KVLISFKAN DIEKAVQSLD KNGVDLLMKY IYKGFESPSD NSSAVLLQWH EKALAAGGVG SIVRVLTARK TV UniProtKB: Actin-related protein 2/3 complex subunit 5

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Macromolecule #8: Actin, alpha skeletal muscle

Macromolecule	Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: rabbit (rabbit)
Molecular weight	Theoretical: 41.875633 KDa
Sequence	String: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG ...String: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #9: F-actin-capping protein subunit alpha-1/Actin nucleation-promotin...

Macromolecule	Name: F-actin-capping protein subunit alpha-1/Actin nucleation-promoting factor WASL chimera type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Mus musculus (house mouse)
Molecular weight	Theoretical: 39.600566 KDa
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: MADFDDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY EDQVLITEHG DLGNSRFLD PRNKISFKFD HLRKEASDPQ PEEADGGLKS WRESCDSALR AYVKDHYSNG FCTVYAKTID GQQTIIACIE S HQFQPKNF ...String: MADFDDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY EDQVLITEHG DLGNSRFLD PRNKISFKFD HLRKEASDPQ PEEADGGLKS WRESCDSALR AYVKDHYSNG FCTVYAKTID GQQTIIACIE S HQFQPKNF WNGRWRSEWK FTITPPTAQV VGVLKIQVHY YEDGNVQLVS HKDVQDSLTV SNEAQTAKEF IKIIENAENE YQ TAISENY QTMSDTTFKA LRRQLPVTRT KIDWNKILSY KIGQIRQGIQ LKSVSDGQES TPPTPAPTSG IVGALMEVMQ KRS KAIHSS DEDEDDDDEE DFEDDDEWED UniProtKB: F-actin-capping protein subunit alpha-1, Actin nucleation-promoting factor WASL

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Macromolecule #10: F-actin-capping protein subunit beta/Actin nucleation-promoting f...

Macromolecule	Name: F-actin-capping protein subunit beta/Actin nucleation-promoting factor WASL chimera type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Mus musculus (house mouse)
Molecular weight	Theoretical: 37.470754 KDa
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMP SARLRKLEVE ANNAFDQYRD LYFEGGVSSV YLWDLDHGFA GVILIKKAGD GSKKIKGCWD SIHVVEVQEK S SGRTAHYK ...String: MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMP SARLRKLEVE ANNAFDQYRD LYFEGGVSSV YLWDLDHGFA GVILIKKAGD GSKKIKGCWD SIHVVEVQEK S SGRTAHYK LTSTVMLWLQ TNKSGSGTMN LGGSLTRQME KDETVSDCSP HIANIGRLVE DMENKIRSTL NEIYFGKTKD IV NGLRSID AIPDNQKFKQ LQRELSQVLT QRQIGIQLKS VSDGQESTPP TPAPTSGIVG ALMEVMQKRS KAIHSSDEDE DDD DEEDFE DDDEWED UniProtKB: F-actin-capping protein subunit beta, Actin nucleation-promoting factor WASL

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Macromolecule #11: MAGNESIUM ION

Macromolecule	Name: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 3 / Formula: MG
Molecular weight	Theoretical: 24.305 Da

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Macromolecule #12: ADENOSINE-5'-TRIPHOSPHATE

Macromolecule	Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 2 / Formula: ATP
Molecular weight	Theoretical: 507.181 Da
Chemical component information	ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

Macromolecule	Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 1 / Formula: ADP
Molecular weight	Theoretical: 427.201 Da
Chemical component information	ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Experimental details

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Structure determination

Method	cryo EM
Processing	single particle reconstruction
Aggregation state	particle

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Sample preparation

Concentration

5 mg/mL

Buffer

pH: 7
Component:

Concentration	Formula	Name
20.0 mM	C₈H₁₈N₂O₄S	HEPES
100.0 mM	NaClSodium chloride	sodium chloride
1.0 mM	HSCH₂CH(OH)CH(OH)CH₂SH	Dithiothreitol
0.2 mM	C₁₀H₁₄N₅O₁₃P₃Na₂	Adenosine triphosphate disodium salt
0.2 mM	MgCl₂	magnesium chloride

Vitrification

Cryogen name: ETHANE / Instrument: LEICA EM CPC
Details: Grids were manually blotted for 3 seconds with Whatman 41 filter paper and manually plunged using a Leica EM CPC manual plunger..

Details

This sample was monodisperse.

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Electron microscopy

Microscope	FEI TITAN KRIOS
Electron beam	Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics	C2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 165000
Specialist optics	Energy filter - Slit width: 20 eV
Sample stage	Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Details	Data were collected in super-resolution mode with an illuminated area of 1.01 um, nominal dose of 40 e-/A^2, a dose rate of 4.87 e-/s/pixel, and 2 or 5 exposures per hole by image shift.
Image recording	Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 9661 / Average exposure time: 2.6 sec. / Average electron dose: 50.0 e/Å²
Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selection	Number selected: 4485066 / Details: Particles autopicked in cryoSPARC
Startup model	Type of model: OTHER / Details: ab initio model generated by cryoSPARC
Initial angle assignment	Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classification	Number classes: 6 / Avg.num./class: 150000 / Software - Name: RELION (ver. 3.1)
Final angle assignment	Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstruction	Number classes used: 1 / Applied symmetry - Point group: C₁ (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Software - details: non-uniform refinement / Details: Composite map after multibody refinement / Number images used: 269760
Details	Super resolution mode; micrographs binned during motion correction
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model	PDB ID: 4jd2 Chain - Source name: PDB / Chain - Initial model type: experimental model
Refinement	Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 132 / Target criteria: correlation
Output model	PDB-7t5q: Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation

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+Entire : bovine Arp2/3 complex and Actin, CapZ

+Supramolecule #1: bovine Arp2/3 complex and Actin, CapZ

+Supramolecule #2: bovine Arp2/3

+Supramolecule #3: Actin skeletal muscle

+Supramolecule #4: F-actin-capping protein

+Macromolecule #1: Actin-related protein 3

+Macromolecule #2: Actin-related protein 2

+Macromolecule #3: Actin-related protein 2/3 complex subunit 1A

+Macromolecule #4: Actin-related protein 2/3 complex subunit 2

+Macromolecule #5: Actin-related protein 2/3 complex subunit 3

+Macromolecule #6: Actin-related protein 2/3 complex subunit 4

+Macromolecule #7: Actin-related protein 2/3 complex subunit 5

+Macromolecule #8: Actin, alpha skeletal muscle

+Macromolecule #9: F-actin-capping protein subunit alpha-1/Actin nucleation-promotin...

+Macromolecule #10: F-actin-capping protein subunit beta/Actin nucleation-promoting f...

+Macromolecule #11: MAGNESIUM ION

+Macromolecule #12: ADENOSINE-5'-TRIPHOSPHATE

+Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

-Experimental details

-Structure determination

-Sample preparation

-Electron microscopy

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-Atomic model buiding 1

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Viewer log

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This page

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Options

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Open data

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Downloads & links

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Related structure data

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Links

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Map

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Supplemental data

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Additional map: map post processed with global b factor sharpening

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Additional map: unsharpened map

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Half map: half map A

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Half map: half map B

-
Sample components

+
Entire : bovine Arp2/3 complex and Actin, CapZ

+
Supramolecule #1: bovine Arp2/3 complex and Actin, CapZ

+
Supramolecule #2: bovine Arp2/3

+
Supramolecule #3: Actin skeletal muscle

+
Supramolecule #4: F-actin-capping protein

+
Macromolecule #1: Actin-related protein 3

+
Macromolecule #2: Actin-related protein 2

+
Macromolecule #3: Actin-related protein 2/3 complex subunit 1A

+
Macromolecule #4: Actin-related protein 2/3 complex subunit 2

+
Macromolecule #5: Actin-related protein 2/3 complex subunit 3

+
Macromolecule #6: Actin-related protein 2/3 complex subunit 4

+
Macromolecule #7: Actin-related protein 2/3 complex subunit 5

+
Macromolecule #8: Actin, alpha skeletal muscle

+
Macromolecule #9: F-actin-capping protein subunit alpha-1/Actin nucleation-promotin...

+
Macromolecule #10: F-actin-capping protein subunit beta/Actin nucleation-promoting f...

+
Macromolecule #11: MAGNESIUM ION

+
Macromolecule #12: ADENOSINE-5'-TRIPHOSPHATE

+
Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

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Experimental details

-
Structure determination

-
Sample preparation

-
Electron microscopy

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Image processing

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Atomic model buiding 1

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