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- EMDB-47896: Focused map of the PH domain in the structure of the CARMIL dimer... -

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Basic information

Entry
Database: EMDB / ID: EMD-47896
TitleFocused map of the PH domain in the structure of the CARMIL dimer bound to Capping Protein
Map data
Sample
  • Complex: Complex of the CARMIL dimer bound to Capping Protein
    • Protein or peptide: CARMIL
    • Protein or peptide: CapZ alpha
    • Protein or peptide: CapZ beta
Keywordscytoskeleton / membrane / cell motility / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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_47896.png

Downloads & links

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Map

FileDownload / File: emd_47896.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.004
Minimum - Maximum-0.004968855 - 0.013431722
Average (Standard dev.)0.00001386929 (±0.0003694658)
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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Mask #1

Fileemd_47896_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47896_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47896_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: CARMIL
    • Protein or peptide: CapZ alpha
    • Protein or peptide: CapZ 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
Molecular weightTheoretical: 370 KDa

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Macromolecule #1: CARMIL

MacromoleculeName: CARMIL / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHGMT EESSDVPREL IESIKDVIGR KIKISVKKKV KLEVKGDKVE NKVLVLTSCR AFLVTARIPT KLELTFSYLE IHGVVCSKSA QMIVETEKCS ISMKMASPED VSEVLAHIGT CLRKIFPGLS PVRIMKKVSM EPSERLASLQ ALWDSQTVAE QGPCGGFSQM ...String:
MHHHHHHGMT EESSDVPREL IESIKDVIGR KIKISVKKKV KLEVKGDKVE NKVLVLTSCR AFLVTARIPT KLELTFSYLE IHGVVCSKSA QMIVETEKCS ISMKMASPED VSEVLAHIGT CLRKIFPGLS PVRIMKKVSM EPSERLASLQ ALWDSQTVAE QGPCGGFSQM YACVCDWLGF SYREEVQWDV DTIYLTQDTR ELNLQDFSHL DHRDLIPIIA ALEYNQWFTK LSSKDLKLST DVCEQILRVV SRSNRLEELV LENAGLRTDF AQKLASALAH NPNSGLHTIN LAGNPLEDRG VSSLSIQFAK LPKGLKHLNL SKTSLSPKGV NSLSQSLSAN PLTASTLVHL DLSGNVLRGD DLSHMYNFLA QPNAIVHLDL SNTECSLDMV CGALLRGCLQ YLAVLNLSRT VFSHRKGKEV PPSFKQFFSS SLALMHINLS GTKLSPEPLK ALLLGLACNH NLKGVSLDLS NCELRSGGAQ VLEGCIAEIH NITSLDISDN GLESDLSTLI VWLSKNRSIQ HLALGKNFNN MKSKNLTPVL DNLVQMIQDE ESPLQSLSLA DSKLKTEVTI IINALGSNTS LTKVDISGNG MGDMGAKMLA KALQINTKLR TVIWDKNNIT AQGFQDIAVA MEKNYTLRFM PIPMYDASQA LKTNPEKTED ALQKIENYLL RNHETRKYLQ EQAYRLQQGI VTSTTQQMID RICVKVQDHL NSLRNCGGDA IQEDLKSAER LMRDAKNSKT LLPNLYHVGG ASWAGASGLL SSPIQETLES MAGEVTRVVD EQLKALLESM VDAAENLCPN VMKKAHIRQD LIHASTEKIS IPRTFVKNVL LEQSGIDILN KISEVKLTVA SFLSDRIVDE ILDALSHCHH KLADHFSRRG KTLPQQESLE IELAEEKPVK RSIITVEELT EIERLEDLDT CMMTPKSKRK SIHSRMLRPV SRAFEMEFDL DKALEEVPIH IEDPPFPSLR QEKRSSGFIS ELPSEEGKKL EHFTKLRPKR NKKQQPTQAA VCAANIVSQD GEQNGLMGRV DEGVDEFFTK KVTKMDSKKW STRGWSHPQF EK

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Macromolecule #2: CapZ alpha

MacromoleculeName: CapZ alpha / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADFDDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY EDQVLITEHG DLGNSRFLDP RNKISFKFDH LRKEASDPQP EEADGGLKSW RESCDSALRA YVKDHYSNGF CTVYAKTIDG QQTIIACIES HQFQPKNFWN ...String:
MADFDDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY EDQVLITEHG DLGNSRFLDP RNKISFKFDH LRKEASDPQP EEADGGLKSW RESCDSALRA YVKDHYSNGF CTVYAKTIDG QQTIIACIES HQFQPKNFWN GRWRSEWKFT ITPPTAQVVG VLKIQVHYYE DGNVQLVSHK DVQDSLTVSN EAQTAKEFIK IIENAENEYQ TAISENYQTM SDTTFKALRR QLPVTRTKID WNKILSYKIG KEMQNA

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Macromolecule #3: CapZ beta

MacromoleculeName: CapZ beta / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDQQLDCALD LMRRLPPQQI EKNLSDLIDL VPSLCEDLLS SVDQPLKIAR DKVVGKDYLL CDYNRDGDSY RSPWSNKYDP PLEDGAMPSA RLRKLEVEAN NAFDQYRDLY FEGGVSSVYL WDLDHGFAGV ILIKKAGDGS KKIKGCWDSI HVVEVQEKSS GRTAHYKLTS ...String:
SDQQLDCALD LMRRLPPQQI EKNLSDLIDL VPSLCEDLLS SVDQPLKIAR DKVVGKDYLL CDYNRDGDSY RSPWSNKYDP PLEDGAMPSA RLRKLEVEAN NAFDQYRDLY FEGGVSSVYL WDLDHGFAGV ILIKKAGDGS KKIKGCWDSI HVVEVQEKSS GRTAHYKLTS TVMLWLQTNK SGSGTMNLGG SLTRQMEKDE TVSDCSPHIA NIGRLVEDME NKIRSTLNEI YFGKTKDIVN GLRSIDAIPD NQKFKQLQRE LSQVLTQRQI YIQPDN

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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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135195
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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