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- EMDB-47746: Local refinement of Arp2 in the map of Coronin-7 CA bound to Arp2... -

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Basic information

Entry
Database: EMDB / ID: EMD-47746
TitleLocal refinement of Arp2 in the map of Coronin-7 CA bound to Arp2/3 complex
Map datamap
Sample
  • Complex: Local refinement of Arp2 in the map of Coronin-7 CA bound to Arp2/3 complex
    • Protein or peptide: Actin-related protein 2 (Arp2)
  • Protein or peptide: Actin-related protein 3 (Arp3)
  • Protein or peptide: ArpC1
  • Protein or peptide: ArpC2
  • Protein or peptide: ArpC3
  • Protein or peptide: ArpC4
  • Protein or peptide: ArpC5
  • Protein or peptide: Coronin-7 CA
Keywordscytoskeleton / actin / cell motility / PROTEIN BINDING
Biological speciesBos taurus (domestic cattle) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 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
DepositionNov 7, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47746.png

Downloads & links

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Map

FileDownload / File: emd_47746.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
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-0.08556205 - 0.20415412
Average (Standard dev.)0.00047843673 (±0.005492653)
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_47746_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 2

Fileemd_47746_half_map_1.map
Annotationhalf 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 1

Fileemd_47746_half_map_2.map
Annotationhalf 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Local refinement of Arp2 in the map of Coronin-7 CA bound to Arp2...

EntireName: Local refinement of Arp2 in the map of Coronin-7 CA bound to Arp2/3 complex
Components
  • Complex: Local refinement of Arp2 in the map of Coronin-7 CA bound to Arp2/3 complex
    • Protein or peptide: Actin-related protein 2 (Arp2)
  • Protein or peptide: Actin-related protein 3 (Arp3)
  • Protein or peptide: ArpC1
  • Protein or peptide: ArpC2
  • Protein or peptide: ArpC3
  • Protein or peptide: ArpC4
  • Protein or peptide: ArpC5
  • Protein or peptide: Coronin-7 CA

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Supramolecule #1: Local refinement of Arp2 in the map of Coronin-7 CA bound to Arp2...

SupramoleculeName: Local refinement of Arp2 in the map of Coronin-7 CA bound to Arp2/3 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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 ASELRSMLEV NYPMENGIVR NWDDMKHLWD YTFGPEKLNI DTRNCKILLT EPPMNPTKNR EKIVEVMFET YQFSGVYVAI QAVLTLYAQG LLTGVVVDSG DGVTHICPVY ...String:
MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTTKVGNI EIKDLMVGDE ASELRSMLEV NYPMENGIVR NWDDMKHLWD YTFGPEKLNI DTRNCKILLT EPPMNPTKNR EKIVEVMFET YQFSGVYVAI QAVLTLYAQG LLTGVVVDSG DGVTHICPVY EGFSLPHLTR RLDIAGRDIT RYLIKLLLLR GYAFNHSADF ETVRMIKEKL CYVGYNIEQE QKLALETTVL VESYTLPDGR IIKVGGERFE APEALFQPHL INVEGVGVAE LLFNTIQAAD IDTRSEFYKH IVLSGGSTMY PGLPSRLERE LKQLYLERVL KGDVEKLSKF KIRIEDPPRR KHMVFLGGAV LADIMKDKDN FWMTRQEYQE KGVRVLEKLG VTVR

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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 FIGDEAIEKP TYATKWPIRH GIVEDWDLME RFMEQVIFKY LRAEPEDHYF LLTEPPLNTP ENREYTAEIM FESFNVPGLY IAVQAVLALA ASWTSRQVGE RTLTGTVIDS ...String:
MAGRLPACVV DCGTGYTKLG YAGNTEPQFI IPSCIAIKES AKVGDQAQRR VMKGVDDLDF FIGDEAIEKP TYATKWPIRH GIVEDWDLME RFMEQVIFKY LRAEPEDHYF LLTEPPLNTP ENREYTAEIM FESFNVPGLY IAVQAVLALA ASWTSRQVGE RTLTGTVIDS GDGVTHVIPV AEGYVIGSCI KHIPIAGRDI TYFIQQLLRD REVGIPPEQS LETAKAVKER YSYVCPDLVK EFNKYDTDGS KWIKQYTGIN AISKKEFSID VGYERFLGPE IFFHPEFANP DFTQPISEVV DEVIQNCPID VRRPLYKNIV LSGGSTMFRD FGRRLQRDLK RTVDARLKLS EELSGGRLKP KPIDVQVITH HMQRYAVWFG GSMLASTPEF YQVCHTKKDY EEIGPSICRH NPVFGVMS

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Macromolecule #3: ArpC1

MacromoleculeName: ArpC1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString: MSLHQFLLEP ITCHAWNRDR TQIALSPNNH EVHIYKKNGG QWVKAHELKE HNGHITGIDW APKSDRIVTC GADRNAYVWS QKDGVWKPTL VILRINRAAT FVKWSPLENK FAVGSGARLI SVCYFESEND WWVSKHIKKP IRSTVLSLDW HPNNVLLAAG SCDFKCRVFS ...String:
MSLHQFLLEP ITCHAWNRDR TQIALSPNNH EVHIYKKNGG QWVKAHELKE HNGHITGIDW APKSDRIVTC GADRNAYVWS QKDGVWKPTL VILRINRAAT FVKWSPLENK FAVGSGARLI SVCYFESEND WWVSKHIKKP IRSTVLSLDW HPNNVLLAAG SCDFKCRVFS AYIKEVDEKP ASTPWGSKMP FGQLMSEFGG SGTGGWVHGV SFSASGSRLA WVSHDSTVSV ADASKSVQVS TLKTEFLPLL SVSFVSENSV VAAGHDCCPM LFNYDDRGCL TFVSKLDIPK QSIQRNMSAM ERFRNMDKRA TTEDRNTALE TLHQNSITQV SIYEVDKQDC RKFCTTGIDG AMTIWDFKTL ESSIQGLRIM

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Macromolecule #4: ArpC2

MacromoleculeName: ArpC2 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString: MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSYLVNPESG YNVSLLYDLE NLPASKDSIV HQAGMLKRNC FASVFEKYFQ FQEEGKEGEN RAVIHYRDDE TMYVESKKDR VTVVFSTVFK ...String:
MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSYLVNPESG YNVSLLYDLE NLPASKDSIV HQAGMLKRNC FASVFEKYFQ FQEEGKEGEN RAVIHYRDDE TMYVESKKDR VTVVFSTVFK DDDDVVIGKV FMQEFKEGRR ASHTAPQVLF SHREPPLELK DTDAAVGDNI GYITFVLFPR HTNASARDNT INLIHTFRDY LHYHIKCSKA YIHTRMRAKT SDFLKVLNRA RPDAEKKEMK TITGKTFSSR

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Macromolecule #5: ArpC3

MacromoleculeName: ArpC3 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString:
MPAYHSSLMD PDTKLIGNMA LLPIRSQFKG PAPRETKDTD IVDEAIYYFK ANVFFKNYEI KNEADRTLIY ITLYISECLK KLQKCNSKSQ GEKEMYTLGI TNFPIPGEPG FPLNAIYAKP ANKQEDEVMR AYLQQLRQET GLRLCEKVFD PQNDKPSKWW TCFVKRQFMN KSLSGPGQ

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Macromolecule #6: ArpC4

MacromoleculeName: 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: ArpC5

MacromoleculeName: ArpC5 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString:
MSKNTVSSAR FRKVDVGEYD ENKFVDEEDG GDGQAGPDEG EVDSCLRQGN MTAALQAALK NPPINTKSQA VKDRAGSIVL KVLISFKAND IEKAVQSLDK NGVDLLMKYI YKGFESPSDN SSAVLLQWHE KALAAGGVGS IVRVLTARKT V

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Macromolecule #8: Coronin-7 CA

MacromoleculeName: Coronin-7 CA / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SDQQKKEELL NAMVAKLGNR EDPLPQDSFE GVDEDEWD

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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

MicroscopeTFS 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: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59592
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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