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- EMDB-47408: Consensus map of Coronin-7 CA bound to Arp2/3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-47408
TitleConsensus map of Coronin-7 CA bound to Arp2/3 complex
Map dataConsensus map of Coronin-7 CA bound to Arp2/3 complex
Sample
  • Complex: Arp2/3 complex with Coronin-7 peptide
    • 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 1A (ArpC1)
    • 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: Coronin-7
Keywordscytoskeleton / actin / cell motility / PROTEIN BINDING
Biological speciesBos taurus (domestic cattle) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsFregoso FE / Barrie KR / Dominguez R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM073791 United States
CitationJournal: To Be Published
Title: Coronin-7 is an Arp2/3 complex debrancher
Authors: Fregoso FE / Barrie KR / Saks AJ / Dominguez R
History
DepositionOct 21, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47408.png

Downloads & links

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Map

FileDownload / File: emd_47408.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map of Coronin-7 CA bound to Arp2/3 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 273.92 Å		0.86 Å/pix.
x 320 pix.
= 273.92 Å		0.86 Å/pix.
x 320 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.08163942 - 0.23135878
Average (Standard dev.)0.0004941094 (±0.0060950844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47408_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_47408_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_47408_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Arp2/3 complex with Coronin-7 peptide

EntireName: Arp2/3 complex with Coronin-7 peptide
Components
  • Complex: Arp2/3 complex with Coronin-7 peptide
    • 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 1A (ArpC1)
    • 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: Coronin-7

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Supramolecule #1: Arp2/3 complex with Coronin-7 peptide

SupramoleculeName: Arp2/3 complex with Coronin-7 peptide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 230 KDa

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Macromolecule #1: Actin-related protein 2 (Arp2)

MacromoleculeName: Actin-related protein 2 (Arp2) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString: MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTTKVGNI EIKDLMVGDE ASELRSMLE VNYPMENGIV RNWDDMKHLW DYTFGPEKLN IDTRNCKILL TEPPMNPTKN R EKIVEVMF ETYQFSGVYV AIQAVLTLYA QGLLTGVVVD SGDGVTHICP ...String:
MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTTKVGNI EIKDLMVGDE ASELRSMLE VNYPMENGIV RNWDDMKHLW DYTFGPEKLN IDTRNCKILL TEPPMNPTKN R EKIVEVMF ETYQFSGVYV AIQAVLTLYA QGLLTGVVVD SGDGVTHICP VYEGFSLPHL TR RLDIAGR DITRYLIKLL LLRGYAFNHS ADFETVRMIK EKLCYVGYNI EQEQKLALET TVL VESYTL PDGRIIKVGG ERFEAPEALF QPHLINVEGV GVAELLFNTI QAADIDTRSE FYKH IVLSG GSTMYPGLPS RLERELKQLY LERVLKGDVE KLSKFKIRIE DPPRRKHMVF LGGAV LADI MKDKDNFWMT RQEYQEKGVR VLEKLGVTVR

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Macromolecule #2: Actin-related protein 3 (Arp3)

MacromoleculeName: Actin-related protein 3 (Arp3) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString: MAGRLPACVV DCGTGYTKLG YAGNTEPQFI IPSCIAIKES AKVGDQAQRR VMKGVDDLDF FIGDEAIEK PTYATKWPIR HGIVEDWDLM ERFMEQVIFK YLRAEPEDHY FLLTEPPLNT P ENREYTAE IMFESFNVPG LYIAVQAVLA LAASWTSRQV GERTLTGTVI ...String:
MAGRLPACVV DCGTGYTKLG YAGNTEPQFI IPSCIAIKES AKVGDQAQRR VMKGVDDLDF FIGDEAIEK PTYATKWPIR HGIVEDWDLM ERFMEQVIFK YLRAEPEDHY FLLTEPPLNT P ENREYTAE IMFESFNVPG LYIAVQAVLA LAASWTSRQV GERTLTGTVI DSGDGVTHVI PV AEGYVIG SCIKHIPIAG RDITYFIQQL LRDREVGIPP EQSLETAKAV KERYSYVCPD LVK EFNKYD TDGSKWIKQY TGINAISKKE FSIDVGYERF LGPEIFFHPE FANPDFTQPI SEVV DEVIQ NCPIDVRRPL YKNIVLSGGS TMFRDFGRRL QRDLKRTVDA RLKLSEELSG GRLKP KPID VQVITHHMQR YAVWFGGSML ASTPEFYQVC HTKKDYEEIG PSICRHNPVF GVMS

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Macromolecule #3: Actin-related protein 2/3 complex subunit 1A (ArpC1)

MacromoleculeName: Actin-related protein 2/3 complex subunit 1A (ArpC1) / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString: MSLHQFLLEP ITCHAWNRDR TQIALSPNNH EVHIYKKNGG QWVKAHELKE HNGHITGIDW APKSDRIVT CGADRNAYVW SQKDGVWKPT LVILRINRAA TFVKWSPLEN KFAVGSGARL I SVCYFESE NDWWVSKHIK KPIRSTVLSL DWHPNNVLLA AGSCDFKCRV ...String:
MSLHQFLLEP ITCHAWNRDR TQIALSPNNH EVHIYKKNGG QWVKAHELKE HNGHITGIDW APKSDRIVT CGADRNAYVW SQKDGVWKPT LVILRINRAA TFVKWSPLEN KFAVGSGARL I SVCYFESE NDWWVSKHIK KPIRSTVLSL DWHPNNVLLA AGSCDFKCRV FSAYIKEVDE KP ASTPWGS KMPFGQLMSE FGGSGTGGWV HGVSFSASGS RLAWVSHDST VSVADASKSV QVS TLKTEF LPLLSVSFVS ENSVVAAGHD CCPMLFNYDD RGCLTFVSKL DIPKQSIQRN MSAM ERFRN MDKRATTEDR NTALETLHQN SITQVSIYEV DKQDCRKFCT TGIDGAMTIW DFKTL ESSI QGLRIM

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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 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString: MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQA HGADELLKRV YGSYLVNPES GYNVSLLYDL ENLPASKDSI VHQAGMLKRN C FASVFEKY FQFQEEGKEG ENRAVIHYRD DETMYVESKK DRVTVVFSTV ...String:
MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQA HGADELLKRV YGSYLVNPES GYNVSLLYDL ENLPASKDSI VHQAGMLKRN C FASVFEKY FQFQEEGKEG ENRAVIHYRD DETMYVESKK DRVTVVFSTV FKDDDDVVIG KV FMQEFKE GRRASHTAPQ VLFSHREPPL ELKDTDAAVG DNIGYITFVL FPRHTNASAR DNT INLIHT FRDYLHYHIK CSKAYIHTRM RAKTSDFLKV LNRARPDAEK KEMKTITGKT FSSR

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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 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString:
MPAYHSSLMD PDTKLIGNMA LLPIRSQFKG PAPRETKDTD IVDEAIYYFK ANVFFKNYEI KNEADRTLI YITLYISECL KKLQKCNSKS QGEKEMYTLG ITNFPIPGEP GFPLNAIYAK P ANKQEDEV MRAYLQQLRQ ETGLRLCEKV FDPQNDKPSK WWTCFVKRQF 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 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString:
MTATLRPYLS AVRATLQAAL CLENFSSQVV ERHNKPEVEV RSSKELLLQP VTISRNEKEK VLIEGSINSV RVSIAVKQAD EIEKILCHKF MRFMMMRAEN FFILRRKPVE GYDISFLITN FHTEQMYKHK LVDFVIHFME EIDKEISEMK LSVNARARIV 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 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString:
MSKNTVSSAR FRKVDVDEYD ENKFVDEEDG GDGQAGPDEG EVDSCLRQGN MTAALQAALK NPPINTKSQA VKDRAGSIVL KVLISFKAND IEKAVQSLDK NGVDLLMKYI YKGFESPSDN SSAVLLQWHE KALAAGGVGS IVRVLTARKT V

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Macromolecule #8: Coronin-7

MacromoleculeName: Coronin-7 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNRFRVSKFR HTEARPPRRE SWISDIRAGT APSCRNHIKS SCSLIAFNSD RPGVLGIVPL QGQGEDKRRV AHLGCHSDLV TDLDFSPFDD FLLATGSADR TVKLWRLPGP GQALPSAPGV VLGPEDLPVE VLQFHPTSDG ILVSAAGTTV KVWDAAKQQP LTELAAHGDL ...String:
MNRFRVSKFR HTEARPPRRE SWISDIRAGT APSCRNHIKS SCSLIAFNSD RPGVLGIVPL QGQGEDKRRV AHLGCHSDLV TDLDFSPFDD FLLATGSADR TVKLWRLPGP GQALPSAPGV VLGPEDLPVE VLQFHPTSDG ILVSAAGTTV KVWDAAKQQP LTELAAHGDL VQSAVWSRDG ALVGTACKDK QLRIFDPRTK PRASQSTQAH ENSRDSRLAW MGTWEHLVST GFNQMREREV KLWDTRFFSS ALASLTLDTS LGCLVPLLDP DSGLLVLAGK GERQLYCYEV VPQQPALSPV TQCVLESVLR GAALVPRQAL AVMSCEVLRV LQLSDTAIVP IGYHVPRKAV EFHEDLFPDT AGCVPATDPH SWWAGDNQQV QKVSLNPACR PHPSFTSCLV PPAEPLPDTA QPAVMETPVG DADASEGFSS PPSSLTSPST PSSLGPSLSS TSGIGTSPSL RSLQSLLGPS SKFRHAQGTV LHRDSHITNL KGLNLTTPGE SDGFCANKLR VAVPLLSSGG QVAVLELRKP GRLPDTALPT LQNGAAVTDL AWDPFDPHRL AVAGEDARIR LWRVPAEGLE EVLTTPETVL TGHTEKICSL RFHPLAANVL ASSSYDLTVR IWDLQAGADR LKLQGHQDQI FSLAWSPDGQ QLATVCKDGR VRVYRPRSGP EPLQEGPGPK GGRGARIVWV CDGRCLLVSG FDSQSERQLL LYEAEALAGG PLAVLGLDVA PSTLLPSYDP DTGLVLLTGK GDTRVFLYEL LPESPFFLEC NSFTSPDPHK GLVLLPKTEC DVREVELMRC LRLRQSSLEP VAFRLPRVRK EFFQDDVFPD TAVIWEPVLS AEAWLQGANG QPWLLSLQPP DMSPVSQAPR EAPARRAPSS AQYLEEKSDQ QKKEELLNAM VAKLGNREDP LPQDSFEGVD EDEWD

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116851
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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