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- EMDB-11869: Structure of the actin filament Arp2/3 complex branch junction in... -

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Basic information

Entry
Database: EMDB / ID: EMD-11869
TitleStructure of the actin filament Arp2/3 complex branch junction in cells
Map dataStructure of the actin filament Arp2/3 complex branch junction
Sample
  • Cell: Actin Filament Arp2/3 Complex Branch Junction
    • Protein or peptide: Actin-related protein 2, Arp2
    • Protein or peptide: Actin-related protein 3, Arp3
    • Protein or peptide: Actin-related protein 2/3 complex subunit 1b, ArpC1b
    • Protein or peptide: Actin-related protein 2/3 complex subunit 2, ArpC2
    • Protein or peptide: Actin-related protein 2/3 complex subunit 3, ArpC3
    • Protein or peptide: Actin-related protein 2/3 complex subunit 4, ArpC4
    • Protein or peptide: Actin-related protein 2/3 complex subunit 5, ArpC5
    • Protein or peptide: Actin, alpha skeletal muscle, ACTA1
KeywordsActin / Arp2-3 complex / Cytoskeleton / STRUCTURAL PROTEIN
Function / homology
Function and homology information


podosome core / concave side of sperm head / actin filament branch point / ventral surface of cell / microtubule organizing center localization / negative regulation of bleb assembly / positive regulation of barbed-end actin filament capping / apical tubulobulbar complex / tubulobulbar complex / regulation of myosin II filament organization ...podosome core / concave side of sperm head / actin filament branch point / ventral surface of cell / microtubule organizing center localization / negative regulation of bleb assembly / positive regulation of barbed-end actin filament capping / apical tubulobulbar complex / tubulobulbar complex / regulation of myosin II filament organization / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / peripheral region of growth cone / muscle cell projection membrane / meiotic cytokinesis / apical ectoplasmic specialization / basal ectoplasmic specialization / lamellipodium organization / spindle localization / skeletal muscle fiber adaptation / leading edge of lamellipodium / Striated Muscle Contraction / EPHB-mediated forward signaling / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / hemidesmosome / actin filament network formation / asymmetric cell division / Arp2/3 complex-mediated actin nucleation / protein kinase C signaling / cellular response to rapamycin / postsynapse organization / podosome ring / actin cap / postsynaptic actin cytoskeleton organization / Regulation of actin dynamics for phagocytic cup formation / apical dendrite / negative regulation of axon extension / maintenance of cell polarity / Clathrin-mediated endocytosis / positive regulation of astrocyte differentiation / regulation of actin filament polymerization / : / positive regulation of dendritic spine morphogenesis / astrocyte differentiation / positive regulation of fibroblast migration / positive regulation of podosome assembly / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / response to steroid hormone / podosome / positive regulation of filopodium assembly / regulation of synaptic vesicle endocytosis / smooth muscle cell migration / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / mesenchyme migration / positive regulation of smooth muscle cell migration / cell leading edge / cellular response to platelet-derived growth factor stimulus / filamentous actin / brush border / skeletal muscle thin filament assembly / striated muscle thin filament / excitatory synapse / positive regulation of double-strand break repair via homologous recombination / cilium assembly / positive regulation of protein targeting to membrane / glutamate receptor binding / response to mechanical stimulus / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / skeletal muscle fiber development / stress fiber / cellular response to transforming growth factor beta stimulus / axon terminus / ruffle / cytoskeletal protein binding / cellular response to epidermal growth factor stimulus / positive regulation of neuron differentiation / actin filament polymerization / Neutrophil degranulation / secretory granule / filopodium / dendritic shaft / cell projection / meiotic cell cycle / actin filament / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / cellular response to type II interferon / structural constituent of cytoskeleton / ruffle membrane / synaptic vesicle membrane / actin filament binding / cell-cell junction / cell migration
Similarity search - Function
Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 5 superfamily / 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 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc ...Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 5 superfamily / 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 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit / ARP2/3 complex 20 kDa subunit (ARPC4) / 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 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2 / Actin, alpha skeletal muscle / Actin-related protein 3 / 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 1B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 9.0 Å
AuthorsFaessler F / Dimchev G
Funding support Austria, 1 items
OrganizationGrant numberCountry
Austrian Science FundP33367 Austria
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction.
Authors: Florian Fäßler / Georgi Dimchev / Victor-Valentin Hodirnau / William Wan / Florian K M Schur /
Abstract: The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves ...The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.
History
DepositionOct 22, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00404
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.00404
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7aqk
  • Surface level: 0.00404
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7aqk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11869.png

Downloads & links

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Map

FileDownload / File: emd_11869.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the actin filament Arp2/3 complex branch junction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.14 Å/pix.
x 240 pix.
= 512.88 Å		2.14 Å/pix.
x 240 pix.
= 512.88 Å		2.14 Å/pix.
x 240 pix.
= 512.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.137 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00404 / Movie #1: 0.00404
Minimum - Maximum-0.0034114548 - 0.014956028
Average (Standard dev.)0.0000346011 (±0.00058454473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 512.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.1372.1372.137
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z512.880512.880512.880
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0030.0150.000

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Supplemental data

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Mask #1

Fileemd_11869_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_11869_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_11869_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Actin Filament Arp2/3 Complex Branch Junction

EntireName: Actin Filament Arp2/3 Complex Branch Junction
Components
  • Cell: Actin Filament Arp2/3 Complex Branch Junction
    • Protein or peptide: Actin-related protein 2, Arp2
    • Protein or peptide: Actin-related protein 3, Arp3
    • Protein or peptide: Actin-related protein 2/3 complex subunit 1b, ArpC1b
    • Protein or peptide: Actin-related protein 2/3 complex subunit 2, ArpC2
    • Protein or peptide: Actin-related protein 2/3 complex subunit 3, ArpC3
    • Protein or peptide: Actin-related protein 2/3 complex subunit 4, ArpC4
    • Protein or peptide: Actin-related protein 2/3 complex subunit 5, ArpC5
    • Protein or peptide: Actin, alpha skeletal muscle, ACTA1

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Supramolecule #1: Actin Filament Arp2/3 Complex Branch Junction

SupramoleculeName: Actin Filament Arp2/3 Complex Branch Junction / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Structure obtained from the actin network of extracted and fixed mouse fibroblast lamellipodia
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Actin-related protein 2, Arp2

MacromoleculeName: Actin-related protein 2, Arp2 / type: protein_or_peptide / ID: 1
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 44.818711 KDa
SequenceString: 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

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Macromolecule #2: Actin-related protein 3, Arp3

MacromoleculeName: Actin-related protein 3, Arp3 / type: protein_or_peptide / ID: 2
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 47.428031 KDa
SequenceString: 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

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Macromolecule #3: Actin-related protein 2/3 complex subunit 1b, ArpC1b

MacromoleculeName: Actin-related protein 2/3 complex subunit 1b, ArpC1b / type: protein_or_peptide / ID: 3
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 41.016738 KDa
SequenceString: MAYHSFLVEP ISCHAWNKDR TQIAICPNNH EVHIYEKSGN KWVQVHELKE HNGQVTGVDW APDSNRIVTC GTDRNAYVWT LKGRTWKPT LVILRINRAA RCVRWAPNEK KFAVGSGSRV ISICYFEQEN DWWVCKHIKK PIRSTVLSLD WHPNSVLLAA G SCDFKCRI ...String:
MAYHSFLVEP ISCHAWNKDR TQIAICPNNH EVHIYEKSGN KWVQVHELKE HNGQVTGVDW APDSNRIVTC GTDRNAYVWT LKGRTWKPT LVILRINRAA RCVRWAPNEK KFAVGSGSRV ISICYFEQEN DWWVCKHIKK PIRSTVLSLD WHPNSVLLAA G SCDFKCRI FSAYIKEVEE RPAPTPWGSK MPFGELMFES SSSCGWVHGV CFSANGSRVA WVSHDSTVCL ADADKKMAVA TL ASETLPL LAVTFITESS LVAAGHDCFP VLFTYDSAAG KLSFGGRLDV PKQSSQRGLT ARERFQNLDK KASSEGSAAA GAG LDSLHK NSVSQISVLS GGKAKCSQFC TTGMDGGMSI WDVRSLESAL KDLKIV

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Macromolecule #4: Actin-related protein 2/3 complex subunit 2, ArpC2

MacromoleculeName: Actin-related protein 2/3 complex subunit 2, ArpC2 / type: protein_or_peptide / ID: 4
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 34.402043 KDa
SequenceString: 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

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Macromolecule #5: Actin-related protein 2/3 complex subunit 3, ArpC3

MacromoleculeName: Actin-related protein 2/3 complex subunit 3, ArpC3 / type: protein_or_peptide / ID: 5
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 20.572666 KDa
SequenceString:
MPAYHSSLMD PDTKLIGNMA LLPIRSQFKG PAPRETKDTD IVDEAIYYFK ANVFFKNYEI KNEADRTLIY ITLYISECLK KLQKCNSKS QGEKEMYTLG ITNFPIPGEP GFPLNAIYAK PANKQEDEVM RAYLQQLRQE TGLRLCEKVF DPQNDKPSKW W TCFVKRQF MNKSLSGPGQ

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Macromolecule #6: Actin-related protein 2/3 complex subunit 4, ArpC4

MacromoleculeName: Actin-related protein 2/3 complex subunit 4, ArpC4 / type: protein_or_peptide / ID: 6
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 19.697047 KDa
SequenceString:
MTATLRPYLS AVRATLQAAL CLENFSSQVV ERHNKPEVEV RSSKELLLQP VTISRNEKEK VLIEGSINSV RVSIAVKQAD EIEKILCHK FMRFMMMRAE NFFILRRKPV EGYDISFLIT NFHTEQMYKH KLVDFVIHFM EEIDKEISEM KLSVNARARI V AEEFLKNF

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Macromolecule #7: Actin-related protein 2/3 complex subunit 5, ArpC5

MacromoleculeName: Actin-related protein 2/3 complex subunit 5, ArpC5 / type: protein_or_peptide / ID: 7
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 16.295317 KDa
SequenceString:
MSKNTVSSAR FRKVDVDEYD ENKFVDEDDG GDGQAGPDEG EVDSCLRQGN MTAALQAALK NPPINTKSQA VKDRAGSIVL KVLISFKAN DIEKAVQSLD KNGVDLLMKY IYKGFESPSD NSSAVLLQWH EKALAAGGVG SIVRVLTARK TV

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Macromolecule #8: Actin, alpha skeletal muscle, ACTA1

MacromoleculeName: Actin, alpha skeletal muscle, ACTA1 / type: protein_or_peptide / ID: 8
Details: As models derived from Oryctolagus cuniculus actin have been used for fitting, also the Oryctolagus cuniculus sequence (as well as the corresponding UniProt identifier) is given here, even ...Details: As models derived from Oryctolagus cuniculus actin have been used for fitting, also the Oryctolagus cuniculus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 42.096953 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 6.1
Component:
ConcentrationName
10.0 mMMES
150.0 mMsodium chloride
5.0 mMEGTA
5.0 mMGlucose
5.0 mMMagnesium chloride

Details: Adjust to pH 6.1 using NaOH
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
Details: After glow discharging of the grid and prior to the seeding of cells, the grid was coated using 25ug/ml Fibronectin
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K
Details: Leica GP2, 3,5sec back-blotting, sensor on, 0,1mm movement after contact, manually pre-blotted within the chamber prior to the application of fiducials.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.21 sec. / Average electron dose: 2.79 e/Å2
Details: Images were collected in movie-mode at 7 frames per tilt
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -0.0055 µm / Nominal defocus min: -0.00175 µm / Nominal magnification: 42000
Sample stageSpecimen 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

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.9)
Details: Final reconstruction in RELION was performed after Multiple particle refinement in M version 1.0.9.
Number subtomograms used: 14296
ExtractionNumber tomograms: 131 / Number images used: 39300
Reference model: Reference generated from manually selected particles
Method: Template Matching / Software: (Name: Dynamo (ver. 1.133), Warp (ver. 1.07))
Details: After first classification in Dynamo and re-extraction in Warp 17,146 subvolumes remained.
Final 3D classificationNumber classes: 1 / Avg.num./class: 14296 / Software - Name: RELION (ver. 3.0.9)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.9)
Details: Multiple particle refinement in M version 1.0.9 was performed after 3D Refinement in RELION.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1tyq

chain_id: A, residue_range: 2-39, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: A, residue_range: 52-353, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: A, residue_range: 360-418, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: B, residue_range: 151-345, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: C, residue_range: 1-288, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: C, residue_range: 319-372, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: D, residue_range: 1-208, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: D, residue_range: 217-281, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: E, residue_range: 2-150, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: E, residue_range: 155-174, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: F, residue_range: 3-168, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: G, residue_range: 36-151, source_name: PDB, initial_model_type: experimental model

4jd2

chain_id: B, residue_range: 4-150, source_name: PDB, initial_model_type: experimental model

4jd2

chain_id: B, residue_range: 346-387, source_name: PDB, initial_model_type: experimental model

1k8k

chain_id: C, residue_range: 297-309, source_name: PDB, initial_model_type: experimental model

6t20

chain_id: A, residue_range: 5-375, source_name: PDB, initial_model_type: experimental model

6t20

chain_id: B, residue_range: 5-375, source_name: PDB, initial_model_type: experimental model

6t20

chain_id: C, residue_range: 5-375, source_name: PDB, initial_model_type: experimental model

6t20

chain_id: D, residue_range: 5-375, source_name: PDB, initial_model_type: experimental model

6t20

chain_id: E, residue_range: 5-375, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7aqk:
Model of the actin filament Arp2/3 complex branch junction in cells

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