[English] 日本語
Yorodumi
- EMDB-52580: SPIN90-Arp2/3 nucleated bidirectional actin filaments -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52580
TitleSPIN90-Arp2/3 nucleated bidirectional actin filaments
Map data
Sample
  • Complex: The SPIN90-Arp2/3 complex in the presence of actin
    • Complex: The Arp2/3 complex
      • Protein or peptide: x 7 types
    • Complex: Actin, cytoplasmic 1
      • Protein or peptide: x 1 types
    • Complex: Phalloidin
      • Protein or peptide: x 1 types
    • Complex: SPIN90
      • Protein or peptide: x 1 types
  • Ligand: x 2 types
KeywordsCytoskeleton / Branched actin network / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / spindle localization / meiotic cytokinesis / actin polymerization-dependent cell motility / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions ...tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / spindle localization / meiotic cytokinesis / actin polymerization-dependent cell motility / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / UCH proteinases / muscle cell projection membrane / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / Clathrin-mediated endocytosis / Formation of the dystrophin-glycoprotein complex (DGC) / asymmetric cell division / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / actin nucleation / Arp2/3 complex binding / actin cap / cellular response to cytochalasin B / regulation of actin filament polymerization / regulation of transepithelial transport / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / postsynaptic actin cytoskeleton / Tat protein binding / adherens junction assembly / apical protein localization / intermediate filament / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / tight junction / apical junction complex / regulation of norepinephrine uptake / transporter regulator activity / nitric-oxide synthase binding / cortical cytoskeleton / positive regulation of actin filament polymerization / filamentous actin / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / brush border / regulation of postsynapse assembly / kinesin binding / cilium assembly / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / cytoskeletal protein binding / positive regulation of lamellipodium assembly / actin filament polymerization / EPHB-mediated forward signaling / cytoskeleton organization / positive regulation of substrate adhesion-dependent cell spreading / axonogenesis / calyx of Held / nitric-oxide synthase regulator activity / cell projection / FCGR3A-mediated phagocytosis / actin filament / adherens junction / cell motility / positive regulation of neuron projection development / cellular response to nerve growth factor stimulus / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / cellular response to type II interferon / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to estrogen / Schaffer collateral - CA1 synapse / cytoplasmic ribonucleoprotein granule / endocytosis / actin filament binding / azurophil granule lumen / cell-cell junction / synaptic vesicle membrane / cell migration / response to estradiol / nucleosome / lamellipodium / actin cytoskeleton / Clathrin-mediated endocytosis / site of double-strand break / actin binding / cell cortex / ficolin-1-rich granule lumen / cytoskeleton / postsynapse
Similarity search - Function
SPIN90, SH3 domain / SPIN90/Ldb17, leucine-rich domain / SPIN90/Ldb17 / SPIN90/Ldb17, leucine-rich domain / Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / 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 ...SPIN90, SH3 domain / SPIN90/Ldb17, leucine-rich domain / SPIN90/Ldb17 / SPIN90/Ldb17, leucine-rich domain / Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / 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 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 / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / ATPase, nucleotide binding domain / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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 1B / 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 3 / Actin-related protein 2 / Actin, cytoplasmic 1 / Actin-related protein 2/3 complex subunit 5-like protein / NCK-interacting protein with SH3 domain
Similarity search - Component
Biological speciesHomo sapiens (human) / Sus scrofa (pig) / Amanita phalloides (death cap)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLiu T / Moores CA
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Arp2/3-mediated bidirectional actin assembly by SPIN90 dimers.
Authors: Tianyang Liu / Luyan Cao / Miroslav Mladenov / Guillaume Romet-Lemonne / Michael Way / Carolyn A Moores /
Abstract: Branched actin networks nucleated by the Arp2/3 complex have critical roles in various cellular processes, from cell migration to intracellular transport. However, when activated by WISH/DIP/SPIN90- ...Branched actin networks nucleated by the Arp2/3 complex have critical roles in various cellular processes, from cell migration to intracellular transport. However, when activated by WISH/DIP/SPIN90-family proteins, Arp2/3 nucleates linear actin filaments. Here we found that human SPIN90 is a dimer that can nucleate bidirectional actin filaments. To understand the basis for this, we determined a 3-Å-resolution structure of human SPIN90-Arp2/3 complex nucleating actin filaments. Our structure shows that SPIN90 dimerizes through a three-helix bundle and interacts with two Arp2/3 complexes. Each SPIN90 molecule binds both Arp2/3 complexes to promote their activation. Our analysis demonstrates that single-filament nucleation by Arp2/3 is mechanistically more like branch formation than previously appreciated. The dimerization domain in SPIN90 orthologs is conserved in metazoans, suggesting that this mode of bidirectional nucleation is a common strategy to generate antiparallel actin filaments.
History
DepositionJan 20, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_52580.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 368 pix.
= 390.08 Å
1.06 Å/pix.
x 368 pix.
= 390.08 Å
1.06 Å/pix.
x 368 pix.
= 390.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.3376114 - 0.91795856
Average (Standard dev.)-0.0009883371 (±0.028455766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 390.08 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_52580_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #1

Fileemd_52580_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire : The SPIN90-Arp2/3 complex in the presence of actin

EntireName: The SPIN90-Arp2/3 complex in the presence of actin
Components
  • Complex: The SPIN90-Arp2/3 complex in the presence of actin
    • Complex: The Arp2/3 complex
      • Protein or peptide: Actin-related protein 2
      • 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-like protein
      • Protein or peptide: Actin-related protein 2/3 complex subunit 1B
      • Protein or peptide: Actin-related protein 3
    • Complex: Actin, cytoplasmic 1
      • Protein or peptide: Actin, cytoplasmic 1
    • Complex: Phalloidin
      • Protein or peptide: Phalloidin
    • Complex: SPIN90
      • Protein or peptide: NCK-interacting protein with SH3 domain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: The SPIN90-Arp2/3 complex in the presence of actin

SupramoleculeName: The SPIN90-Arp2/3 complex in the presence of actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #2: The Arp2/3 complex

SupramoleculeName: The Arp2/3 complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5, #9-#10
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: Actin, cytoplasmic 1

SupramoleculeName: Actin, cytoplasmic 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Sus scrofa (pig)

+
Supramolecule #4: Phalloidin

SupramoleculeName: Phalloidin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Amanita phalloides (death cap)

+
Supramolecule #5: SPIN90

SupramoleculeName: SPIN90 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Actin-related protein 2

MacromoleculeName: Actin-related protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.818711 KDa
Recombinant expressionOrganism: unidentified baculovirus
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

UniProtKB: Actin-related protein 2

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

MacromoleculeName: Actin-related protein 2/3 complex subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.386043 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: 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

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

MacromoleculeName: Actin-related protein 2/3 complex subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.572666 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString:
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

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

MacromoleculeName: Actin-related protein 2/3 complex subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.697047 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString:
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

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

MacromoleculeName: Actin-related protein 2/3 complex subunit 5-like protein
type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.96418 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString:
MARNTLSSRF RRVDIDEFDE NKFVDEQEEA AAAAAEPGPD PSEVDGLLRQ GDMLRAFHAA LRNSPVNTKN QAVKERAQGV VLKVLTNFK SSEIEQAVQS LDRNGVDLLM KYIYKGFEKP TENSSAVLLQ WHEKALAVGG LGSIIRVLTA RKTV

UniProtKB: Actin-related protein 2/3 complex subunit 5-like protein

+
Macromolecule #6: Actin, cytoplasmic 1

MacromoleculeName: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 41.78266 KDa
SequenceString: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG ...String:
MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

+
Macromolecule #7: Phalloidin

MacromoleculeName: Phalloidin / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Amanita phalloides (death cap)
Molecular weightTheoretical: 808.899 Da
SequenceString:
W(EEP)A(DTH)C(HYP)A

+
Macromolecule #8: NCK-interacting protein with SH3 domain

MacromoleculeName: NCK-interacting protein with SH3 domain / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 79.054094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYRALYAFRS AEPNALAFAA GETFLVLERS SAHWWLAARA RSGETGYVPP AYLRRLQGLE QDVLQAIDRA IEAVHNTAMR DGGKYSLEQ RGVLQKLIHH RKETLSRRGP SASSVAVMTS STSDHHLDAA AARQPNGVCR AGFERQHSLP SSEHLGADGG L YQIPLPSS ...String:
MYRALYAFRS AEPNALAFAA GETFLVLERS SAHWWLAARA RSGETGYVPP AYLRRLQGLE QDVLQAIDRA IEAVHNTAMR DGGKYSLEQ RGVLQKLIHH RKETLSRRGP SASSVAVMTS STSDHHLDAA AARQPNGVCR AGFERQHSLP SSEHLGADGG L YQIPLPSS QIPPQPRRAA PTTPPPPVKR RDREALMASG SGGHNTMPSG GNSVSSGSSV SSTSLDTLYT SSSPSEPGSS CS PTPPPVP RRGTHTTVSQ VQPPPSKASA PEPPAEEEVA TGTTSASDDL EALGTLSLGT TEEKAAAEAA VPRTIGAELM ELV RRNTGL SHELCRVAIG IIVGHIQASV PASSPVMEQV LLSLVEGKDL SMALPSGQVC HDQQRLEVIF ADLARRKDDA QQRS WALYE DEGVIRCYLE ELLHILTDAD PEVCKKMCKR NEFESVLALV AYYQMEHRAS LRLLLLKCFG AMCSLDAAII STLVS SVLP VELARDMQTD TQDHQKLCYS ALILAMVFSM GEAVPYAHYE HLGTPFAQFL LNIVEDGLPL DTTEQLPDLC VNLLLA LNL HLPAADQNVI MAALSKHANV KIFSEKLLLL LNRGDDPVRI FKHEPQPPHS VLKFLQDVFG SPATAAIFYH TDMMALI DI TVRHIADLSP GDKLRMEYLS LMHAIVRTTP YLQHRHRLPD LQAILRRILN EEETSPQCQM DRMIVREMCK EFLVLGEA P S

UniProtKB: NCK-interacting protein with SH3 domain

+
Macromolecule #9: Actin-related protein 2/3 complex subunit 1B

MacromoleculeName: Actin-related protein 2/3 complex subunit 1B / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.004781 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: 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

+
Macromolecule #10: Actin-related protein 3

MacromoleculeName: Actin-related protein 3 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.428031 KDa
Recombinant expressionOrganism: unidentified baculovirus
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

UniProtKB: Actin-related protein 3

+
Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 8 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

+
Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298.15 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.2 e/Å2
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 / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 39104
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-9i2b:
SPIN90-Arp2/3 nucleated bidirectional actin filaments

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more