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- EMDB-47898: Composite map of the CARMIL dimer bound to Capping Protein -

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Basic information

Entry
Database: EMDB / ID: EMD-47898
TitleComposite map of the CARMIL dimer bound to Capping Protein
Map datacomposite map
Sample
  • Complex: Complex of the CARMIL dimer bound to Capping Protein
    • Protein or peptide: F-actin-uncapping protein LRRC16A
    • Protein or peptide: F-actin-capping protein subunit alpha-1
    • Protein or peptide: F-actin-capping protein subunit beta
Keywordscytoskeleton / membrane / cell motility / STRUCTURAL PROTEIN
Function / homology
Function and homology information


barbed-end actin filament uncapping / positive regulation of lamellipodium organization / negative regulation of barbed-end actin filament capping / macropinosome / actin filament network formation / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / macropinocytosis / regulation of Arp2/3 complex-mediated actin nucleation ...barbed-end actin filament uncapping / positive regulation of lamellipodium organization / negative regulation of barbed-end actin filament capping / macropinosome / actin filament network formation / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / macropinocytosis / regulation of Arp2/3 complex-mediated actin nucleation / urate metabolic process / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / ruffle organization / RHOD GTPase cycle / regulation of cell morphogenesis / RHOF GTPase cycle / COPI-independent Golgi-to-ER retrograde traffic / Sensory processing of sound by inner hair cells of the cochlea / lamellipodium assembly / filamentous actin / cortical cytoskeleton / positive regulation of actin filament polymerization / cell leading edge / brush border / Advanced glycosylation endproduct receptor signaling / COPI-mediated anterograde transport / positive regulation of stress fiber assembly / cytoskeleton organization / positive regulation of substrate adhesion-dependent cell spreading / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / actin filament organization / hippocampal mossy fiber to CA3 synapse / sarcomere / Schaffer collateral - CA1 synapse / actin filament binding / cell migration / actin cytoskeleton / lamellipodium / Factors involved in megakaryocyte development and platelet production / actin binding / actin cytoskeleton organization / protein-containing complex assembly / cytoskeleton / postsynaptic density / nuclear speck / positive regulation of cell migration / cadherin binding / protein-containing complex binding / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
CARMIL, C-terminal domain / CARMIL, pleckstrin homology domain / CARMIL C-terminus / Carmil pleckstrin homology domain / : / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. ...CARMIL, C-terminal domain / CARMIL, pleckstrin homology domain / CARMIL C-terminus / Carmil pleckstrin homology domain / : / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
F-actin-capping protein subunit beta / F-actin-capping protein subunit alpha-1 / F-actin-uncapping protein LRRC16A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBarrie KR / Dominguez R
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM073791 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM152412 United States
CitationJournal: To Be Published
Title: Structural basis for regulation of Capping Protein by the CARMIL dimer
Authors: Barrie KR / Dominguez R
History
DepositionNov 13, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47898.png

Downloads & links

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Map

FileDownload / File: emd_47898.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 317.184 Å		0.83 Å/pix.
x 384 pix.
= 317.184 Å		0.83 Å/pix.
x 384 pix.
= 317.184 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum0.0 - 0.015393789
Average (Standard dev.)0.000037741524 (±0.00037004362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 317.184 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Complex of the CARMIL dimer bound to Capping Protein

EntireName: Complex of the CARMIL dimer bound to Capping Protein
Components
  • Complex: Complex of the CARMIL dimer bound to Capping Protein
    • Protein or peptide: F-actin-uncapping protein LRRC16A
    • Protein or peptide: F-actin-capping protein subunit alpha-1
    • Protein or peptide: F-actin-capping protein subunit beta

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Supramolecule #1: Complex of the CARMIL dimer bound to Capping Protein

SupramoleculeName: Complex of the CARMIL dimer bound to Capping Protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 370 KDa

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Macromolecule #1: F-actin-uncapping protein LRRC16A

MacromoleculeName: F-actin-uncapping protein LRRC16A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.676219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHGMT EESSDVPREL IESIKDVIGR KIKISVKKKV KLEVKGDKVE NKVLVLTSCR AFLVTARIPT KLELTFSYLE IHGVVCSKS AQMIVETEKC SISMKMASPE DVSEVLAHIG TCLRKIFPGL SPVRIMKKVS MEPSERLASL QALWDSQTVA E QGPCGGFS ...String:
MHHHHHHGMT EESSDVPREL IESIKDVIGR KIKISVKKKV KLEVKGDKVE NKVLVLTSCR AFLVTARIPT KLELTFSYLE IHGVVCSKS AQMIVETEKC SISMKMASPE DVSEVLAHIG TCLRKIFPGL SPVRIMKKVS MEPSERLASL QALWDSQTVA E QGPCGGFS QMYACVCDWL GFSYREEVQW DVDTIYLTQD TRELNLQDFS HLDHRDLIPI IAALEYNQWF TKLSSKDLKL ST DVCEQIL RVVSRSNRLE ELVLENAGLR TDFAQKLASA LAHNPNSGLH TINLAGNPLE DRGVSSLSIQ FAKLPKGLKH LNL SKTSLS PKGVNSLSQS LSANPLTAST LVHLDLSGNV LRGDDLSHMY NFLAQPNAIV HLDLSNTECS LDMVCGALLR GCLQ YLAVL NLSRTVFSHR KGKEVPPSFK QFFSSSLALM HINLSGTKLS PEPLKALLLG LACNHNLKGV SLDLSNCELR SGGAQ VLEG CIAEIHNITS LDISDNGLES DLSTLIVWLS KNRSIQHLAL GKNFNNMKSK NLTPVLDNLV QMIQDEESPL QSLSLA DSK LKTEVTIIIN ALGSNTSLTK VDISGNGMGD MGAKMLAKAL QINTKLRTVI WDKNNITAQG FQDIAVAMEK NYTLRFM PI PMYDASQALK TNPEKTEDAL QKIENYLLRN HETRKYLQEQ AYRLQQGIVT STTQQMIDRI CVKVQDHLNS LRNCGGDA I QEDLKSAERL MRDAKNSKTL LPNLYHVGGA SWAGASGLLS SPIQETLESM AGEVTRVVDE QLKALLESMV DAAENLCPN VMKKAHIRQD LIHASTEKIS IPRTFVKNVL LEQSGIDILN KISEVKLTVA SFLSDRIVDE ILDALSHCHH KLADHFSRRG KTLPQQESL EIELAEEKPV KRSIITVEEL TEIERLEDLD TCMMTPKSKR KSIHSRMLRP VSRAFEMEFD LDKALEEVPI H IEDPPFPS LRQEKRSSGF ISELPSEEGK KLEHFTKLRP KRNKKQQPTQ AAVCAANIVS QDGEQNGLMG RVDEGVDEFF TK KVTKMDS KKWSTRGWSH PQFEK

UniProtKB: F-actin-uncapping protein LRRC16A

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Macromolecule #2: F-actin-capping protein subunit alpha-1

MacromoleculeName: F-actin-capping protein subunit alpha-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.964727 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADFDDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY EDQVLITEHG DLGNSRFLD PRNKISFKFD HLRKEASDPQ PEEADGGLKS WRESCDSALR AYVKDHYSNG FCTVYAKTID GQQTIIACIE S HQFQPKNF ...String:
MADFDDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY EDQVLITEHG DLGNSRFLD PRNKISFKFD HLRKEASDPQ PEEADGGLKS WRESCDSALR AYVKDHYSNG FCTVYAKTID GQQTIIACIE S HQFQPKNF WNGRWRSEWK FTITPPTAQV VGVLKIQVHY YEDGNVQLVS HKDVQDSLTV SNEAQTAKEF IKIIENAENE YQ TAISENY QTMSDTTFKA LRRQLPVTRT KIDWNKILSY KIGKEMQNA

UniProtKB: F-actin-capping protein subunit alpha-1

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Macromolecule #3: F-actin-capping protein subunit beta

MacromoleculeName: F-actin-capping protein subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.258289 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDQQLDCALD LMRRLPPQQI EKNLSDLIDL VPSLCEDLLS SVDQPLKIAR DKVVGKDYLL CDYNRDGDSY RSPWSNKYDP PLEDGAMPS ARLRKLEVEA NNAFDQYRDL YFEGGVSSVY LWDLDHGFAG VILIKKAGDG SKKIKGCWDS IHVVEVQEKS S GRTAHYKL ...String:
SDQQLDCALD LMRRLPPQQI EKNLSDLIDL VPSLCEDLLS SVDQPLKIAR DKVVGKDYLL CDYNRDGDSY RSPWSNKYDP PLEDGAMPS ARLRKLEVEA NNAFDQYRDL YFEGGVSSVY LWDLDHGFAG VILIKKAGDG SKKIKGCWDS IHVVEVQEKS S GRTAHYKL TSTVMLWLQT NKSGSGTMNL GGSLTRQMEK DETVSDCSPH IANIGRLVED MENKIRSTLN EIYFGKTKDI VN GLRSIDA IPDNQKFKQL QRELSQVLTQ RQIYIQPDN

UniProtKB: F-actin-capping protein subunit beta

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / 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 / Details: ab-initio model generated in cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Please note that this is a composite map (used for model building and refinement) and therefore does not have a single particle number or resolution associated with it. Instead, the map was ...Details: Please note that this is a composite map (used for model building and refinement) and therefore does not have a single particle number or resolution associated with it. Instead, the map was obtained by combining multiple different maps (already deposited as separate EMDB entries) each at different resolutions and with different numbers of particles. Since the number of particles and resolution are required, the values included here reflect the consensus map (EMD-47891). Thank you.
Number images used: 690592
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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