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- EMDB-20770: CryoEM structure of human Arp2/3 complex with bound NPFs -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-20770

Title

CryoEM structure of human Arp2/3 complex with bound NPFs

Map data

Cryo-EM structure of human Arp2/3 complex bound to two nucleation promoting factors (B-factor sharpened).

Sample

Complex: Cryo-EM structure of human Arp2/3 complex with bound NPFs
- Protein or peptide: Actin-related protein 3
- Protein or peptide: Actin-related protein 2
- Protein or peptide: Actin-related protein 2/3 complex subunit 1B
- 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
- Protein or peptide: Neural Wiskott-Aldrich syndrome protein
Ligand: MAGNESIUM ION
Ligand: ADENOSINE-5'-TRIPHOSPHATE

Keywords

actin / ATPase / actin related protein / arp / cytoskeleton / Arp2-3 complex / actin nucleation / actin branching / CONTRACTILE PROTEIN

Function / homology

Function and homology information

tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / meiotic cytokinesis / negative regulation of membrane tubulation / muscle cell projection membrane / spindle localization / positive regulation of clathrin-dependent endocytosis / actin polymerization-dependent cell motility ...tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / meiotic cytokinesis / negative regulation of membrane tubulation / muscle cell projection membrane / spindle localization / positive regulation of clathrin-dependent endocytosis / actin polymerization-dependent cell motility / Arp2/3 protein complex / asymmetric cell division / Arp2/3 complex-mediated actin nucleation / negative regulation of lymphocyte migration / actin nucleation / vesicle transport along actin filament / actin cap / vesicle organization / regulation of actin filament polymerization / vesicle budding from membrane / dendritic spine morphogenesis / protein-containing complex localization / regulation of postsynapse organization / positive regulation of filopodium assembly / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / filamentous actin / regulation of synaptic vesicle endocytosis / brush border / cilium assembly / RHO GTPases Activate WASPs and WAVEs / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / actin filament polymerization / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / cell projection / FCGR3A-mediated phagocytosis / response to bacterium / cellular response to nerve growth factor stimulus / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / cellular response to type II interferon / response to estrogen / synaptic vesicle membrane / azurophil granule lumen / cell-cell junction / cell migration / response to estradiol / lamellipodium / actin cytoskeleton / regulation of protein localization / Clathrin-mediated endocytosis / site of double-strand break / actin binding / actin cytoskeleton organization / cell cortex / cytoplasmic vesicle / secretory granule lumen / ficolin-1-rich granule lumen / postsynapse / neuron projection / endosome / cell division / focal adhesion / Neutrophil degranulation / protein-containing complex binding / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function

Biological species

Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) /

Homo sapiens (human) /

Mus musculus (house mouse)

Method

single particle reconstruction / cryo EM / Resolution: 3.9 Å

Authors

Zimmet A / van Eeuwen T

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: Sci Adv / Year: 2020
Title: Cryo-EM structure of NPF-bound human Arp2/3 complex and activation mechanism.
Authors: Austin Zimmet / Trevor Van Eeuwen / Malgorzata Boczkowska / Grzegorz Rebowski / Kenji Murakami / Roberto Dominguez /

Abstract: Actin-related protein (Arp) 2/3 complex nucleates branched actin networks that drive cell motility. It consists of seven proteins, including two actin-related subunits (Arp2 and Arp3). Two nucleation- ...

History

Deposition	Sep 27, 2019	-
Header (metadata) release	Nov 20, 2019	-
Map release	Jul 1, 2020	-
Update	Mar 20, 2024	-
Current status	Mar 20, 2024	Processing site: RCSB / Status: Released

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Structure visualization

Movie	Surface view with section colored by density value Surface level: 0.475 Imaged by UCSF Chimera Download Surface view colored by radius Surface level: 0.475 Imaged by UCSF Chimera Download Surface view with fitted model Atomic models: PDB-6uhc Surface level: 0.475 Imaged by UCSF Chimera Download Movie viewer
Structure viewer	EM map: SurfViewMolmilJmol/JSmol
Supplemental images	emd_20770.png

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Downloads & links

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EMDB archive

Map data	emd_20770.map.gz	117.9 MB		EMDB map data format
Header (meta data)	emd-20770-v30.xml emd-20770.xml	28.7 KB 28.7 KB	Display Display	EMDB header
FSC (resolution estimation)	emd_20770_fsc.xml	11.5 KB	Display	FSC data file
Images	emd_20770.png	41.8 KB
Filedesc metadata	emd-20770.cif.gz	8.6 KB
Others	emd_20770_additional.map.gz	62.4 MB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-20770 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20770	HTTPS FTP

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Validation report

Summary document	emd_20770_validation.pdf.gz	525.5 KB	Display	EMDB validaton report
Full document	emd_20770_full_validation.pdf.gz	525.1 KB	Display
Data in XML	emd_20770_validation.xml.gz	12.4 KB	Display
Data in CIF	emd_20770_validation.cif.gz	16.4 KB	Display
Arichive directory	https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20770 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20770	HTTPS FTP

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Related structure data

Related structure data	6uhcMC M: atomic model generated by this map C: citing same article (ref.)
Similar structure data	6uhc-d 2p9k-d 2p9i-d 6yw6-d 4xf2-2 4xf2-1 4jd2-d 3ule-d 6yw7-d 1u2v-d Search similar-shape structures by Omokage search (details) 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 (5) #18 - Jun 2001 Myosin similarity (5) #148 - Apr 2012 Ras Protein similarity (1) #245 - May 2020 Spliceosomes similarity (2) #43 - Jul 2003 Src Tyrosine Kinase similarity (2) #195 - Mar 2016 RAF Protein Kinases similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (3)

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Map

File

Download / File: emd_20770.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Annotation

Cryo-EM structure of human Arp2/3 complex bound to two nucleation promoting factors (B-factor sharpened).

Projections & slices

Image control

Size
Brightness
Contrast
Others	InvertY flip

Axes	Z (Sec.)	Y (Row.)	X (Col.)
	0.84 Å/pix. x 320 pix. = 267.52 Å	0.84 Å/pix. x 320 pix. = 267.52 Å	0.84 Å/pix. x 320 pix. = 267.52 Å
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider.

Voxel size

X=Y=Z: 0.836 Å

Density

Histogram

Histogram (log scale)

Contour Level	By AUTHOR: 0.475 / Movie #1: 0.475
Minimum - Maximum	-1.97515 - 3.0070715
Average (Standard dev.)	0.00638433 (±0.08849225)

Symmetry

Space group: 1

Details

EMDB XML:

Map geometry

Axis order	X	Y	Z
Origin	0	0	0
Dimensions	320	320	320
Spacing	320	320	320

Cell

A=B=C: 267.52002 Å
α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	0.836	0.836	0.836
M x/y/z	320	320	320
origin x/y/z	0.000	0.000	0.000
length x/y/z	267.520	267.520	267.520
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	320	320	320
D min/max/mean	-1.975	3.007	0.006

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Supplemental data

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Additional map: Cryo-EM structure of human Arp2/3 complex bound to...

File

emd_20770_additional.map

Annotation

Cryo-EM structure of human Arp2/3 complex bound to two nucleation promoting factors

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 : Cryo-EM structure of human Arp2/3 complex with bound NPFs

Entire	Name: Cryo-EM structure of human Arp2/3 complex with bound NPFs
Components	Complex: Cryo-EM structure of human Arp2/3 complex with bound NPFs Protein or peptide: Actin-related protein 3 Protein or peptide: Actin-related protein 2 Protein or peptide: Actin-related protein 2/3 complex subunit 1B 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 Protein or peptide: Neural Wiskott-Aldrich syndrome protein Ligand: MAGNESIUM ION Ligand: ADENOSINE-5'-TRIPHOSPHATE

Entire

Name: Cryo-EM structure of human Arp2/3 complex with bound NPFs

Components

Complex: Cryo-EM structure of human Arp2/3 complex with bound NPFs
- Protein or peptide: Actin-related protein 3
- Protein or peptide: Actin-related protein 2
- Protein or peptide: Actin-related protein 2/3 complex subunit 1B
- 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
- Protein or peptide: Neural Wiskott-Aldrich syndrome protein
Ligand: MAGNESIUM ION
Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Cryo-EM structure of human Arp2/3 complex with bound NPFs

Supramolecule	Name: Cryo-EM structure of human Arp2/3 complex with bound NPFs type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)	Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Molecular weight	Theoretical: 243 kDa/nm

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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: Homo sapiens (human)
Molecular weight	Theoretical: 47.428031 KDa
Recombinant expression	Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
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: Homo sapiens (human)
Molecular weight	Theoretical: 44.818711 KDa
Recombinant expression	Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
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 1B

Macromolecule	Name: Actin-related protein 2/3 complex subunit 1B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Homo sapiens (human)
Molecular weight	Theoretical: 41.004781 KDa
Recombinant expression	Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Sequence	String: MAYHSFLVEP ISCHAWNKDR TQIAICPNNH EVHIYEKSGA KWTKVHELKE HNGQVTGIDW APESNRIVTC GTDRNAYVWT LKGRTWKPT LVILRINRAA RCVRWAPNEN KFAVGSGSRV ISICYFEQEN DWWVCKHIKK PIRSTVLSLD WHPNNVLLAA G SCDFKCRI ...String: MAYHSFLVEP ISCHAWNKDR TQIAICPNNH EVHIYEKSGA KWTKVHELKE HNGQVTGIDW APESNRIVTC GTDRNAYVWT LKGRTWKPT LVILRINRAA RCVRWAPNEN KFAVGSGSRV ISICYFEQEN DWWVCKHIKK PIRSTVLSLD WHPNNVLLAA G SCDFKCRI FSAYIKEVEE RPAPTPWGSK MPFGELMFES SSSCGWVHGV CFSASGSRVA WVSHDSTVCL ADADKKMAVA TL ASETLPL LALTFITDNS LVAAGHDCFP VLFTYDAAAG MLSFGGRLDV PKQSSQRGLT ARERFQNLDK KASSEGGTAA GAG LDSLHK NSVSQISVLS GGKAKCSQFC TTGMDGGMSI WDVKSLESAL KDLKIK UniProtKB: Actin-related protein 2/3 complex subunit 1B

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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: Homo sapiens (human)
Molecular weight	Theoretical: 34.386043 KDa
Recombinant expression	Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Sequence	String: MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSFLVNPES GYNVSLLYDL ENLPASKDSI VHQAGMLKRN CFASVFEKYF QFQEEGKEGE NRAVIHYRDD ETMYVESKKD R VTVVFSTV ...String: MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSFLVNPES 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 / Details: C-terminal Flag tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Homo sapiens (human)
Molecular weight	Theoretical: 23.19633 KDa
Recombinant expression	Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Sequence	String: MPAYHSSLMD PDTKLIGNMA LLPIRSQFKG PAPRETKDTD IVDEAIYYFK ANVFFKNYEI KNEADRTLIY ITLYISECLK KLQKCNSKS QGEKEMYTLG ITNFPIPGEP GFPLNAIYAK PANKQEDEVM RAYLQQLRQE TGLRLCEKVF DPQNDKPSKW W TCFVKRQF ...String: MPAYHSSLMD PDTKLIGNMA LLPIRSQFKG PAPRETKDTD IVDEAIYYFK ANVFFKNYEI KNEADRTLIY ITLYISECLK KLQKCNSKS QGEKEMYTLG ITNFPIPGEP GFPLNAIYAK PANKQEDEVM RAYLQQLRQE TGLRLCEKVF DPQNDKPSKW W TCFVKRQF MNKSLSGPGQ GTSENLYQGG GDYKDDDDKC GRASS 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: Homo sapiens (human)
Molecular weight	Theoretical: 19.697047 KDa
Recombinant expression	Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
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: Homo sapiens (human)
Molecular weight	Theoretical: 16.341407 KDa
Recombinant expression	Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Sequence	String: MSKNTVSSAR FRKVDVDEYD ENKFVDEEDG GDGQAGPDEG EVDSCLRQGN MTAALQAALK NPPINTKSQA VKDRAGSIVL KVLISFKAN DIEKAVQSLD KNGVDLLMKY IYKGFESPSD NSSAMLLQWH EKALAAGGVG SIVRVLTARK TV UniProtKB: Actin-related protein 2/3 complex subunit 5

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Macromolecule #8: Neural Wiskott-Aldrich syndrome protein

Macromolecule	Name: Neural Wiskott-Aldrich syndrome protein / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)	Organism: Mus musculus (house mouse)
Molecular weight	Theoretical: 54.342023 KDa
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: MSSGQQPPRR VTNVGSLLLT PQENESLFSF LGKKCVTMSS AVVQLYAADR NCMWAKKCSG VACLVKDNPQ RSYFLRIFDI KDGKLLWEQ ELYNNFVYNS PRGYFHTFAG DTCQVALNFA NEEEAKKFRK AVTDLLGRRQ RKSEKRRDAP NGPNLPMATV D IKNPEITT ...String: MSSGQQPPRR VTNVGSLLLT PQENESLFSF LGKKCVTMSS AVVQLYAADR NCMWAKKCSG VACLVKDNPQ RSYFLRIFDI KDGKLLWEQ ELYNNFVYNS PRGYFHTFAG DTCQVALNFA NEEEAKKFRK AVTDLLGRRQ RKSEKRRDAP NGPNLPMATV D IKNPEITT NRFYGSQVNN ISHTKEKKKG KAKKKRLTKA DIGTPSNFQH IGHVGWDPNT GFDLNNLDPE LKNLFDMCGI SE AQLKDRE TSKVIYDFIE KTGGVEAVKN ELRRQAPPPP PPSRGGPPPP PPPPHSSGPP PPPARGRGAP PPPPSRAPTA APP PPPPSR PGVVVPPPPP NRMYPPPPPA LPSSAPSGPP PPPPPSMAGS TAPPPPPPPP PPPGPPPPPG LPSDGDHQVP APSG NKAAL LDQIREGAQL KKVEQNSRPV SCSGRDALLD QIRQGIQLKS VSDGQESTPP TPAPTSGIVG ALMEVMQKRS KAIHS SDED EDDDDEEDFE DDDEWED UniProtKB: Actin nucleation-promoting factor WASL

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Macromolecule #9: MAGNESIUM ION

Macromolecule	Name: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: MG
Molecular weight	Theoretical: 24.305 Da

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Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

Macromolecule	Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / 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

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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	NaCl	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
0.00025 V/V		TERGITOL

Grid

Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: Grids glow discharged with easiGLOW glow discharger at 0.3 mBar, 25mA for 1 minute

Vitrification

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

Details

This sample was monodisperse

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Electron microscopy

Microscope	FEI TITAN KRIOS
Specialist optics	Energy filter - Slit width: 20 eV
Details	Data collected in super resolution mode. Illuminated area of 1.01um. Nominal Dose of 40a/A^2 and a dose rate of 4.87 e-/s/pixel. 2 or 5 exposures per hole by image shift.
Image recording	Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 2 / Number real images: 5004 / Average exposure time: 7.0 sec. / Average electron dose: 40.0 e/Å²
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 FIELD / Cs: 2.7 mm / Nominal defocus max: -3.5 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 165000
Sample stage	Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selection	Number selected: 627163
Startup model	Type of model: NONE / Details: ab initio model generated by cryoSPARC.
Final reconstruction	Number classes used: 1 / Applied symmetry - Point group: C₁ (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.9.0) / Number images used: 123198
Initial angle assignment	Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignment	Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classification	Number classes: 4 / Avg.num./class: 100000 / Software - Name: cryoSPARC (ver. 2.9.0)
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-6uhc: CryoEM structure of human Arp2/3 complex with bound NPFs

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Additional map: Cryo-EM structure of human Arp2/3 complex bound to...

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+Entire : Cryo-EM structure of human Arp2/3 complex with bound NPFs

+Supramolecule #1: Cryo-EM structure of human Arp2/3 complex with bound NPFs

+Macromolecule #1: Actin-related protein 3

+Macromolecule #2: Actin-related protein 2

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

+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: Neural Wiskott-Aldrich syndrome protein

+Macromolecule #9: MAGNESIUM ION

+Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

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