[English] 日本語
Yorodumi
- EMDB-53111: Cryo-EM reconstruction of the Coronin-1B-decorated actin filament... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53111
TitleCryo-EM reconstruction of the Coronin-1B-decorated actin filament bound by two Cofilin-1 molecules (crosslinked)
Map dataMain, unsharpened cryo-EM density map of the Coronin-1B-decorated actin filament bound by two Cofilin-1 molecules (crosslinked)
Sample
  • Complex: Cryo-EM structure of the Coronin-1B-decorated actin filament bound by two Cofilin-1 molecules (crosslinked)
    • Complex: Actin filament
      • Protein or peptide: Cytoplasmic beta actin
    • Complex: Coronin-1B
      • Protein or peptide: Coronin-1B
    • Complex: Cofilin-1
      • Protein or peptide: Cofilin-1
Keywordsactin / coronin / cofilin / filament / cytoskeleton / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.43 Å
AuthorsOosterheert W / Boiero Sanders M / Hofnagel O / Bieling P / Raunser S
Funding support Germany, European Union, 4 items
OrganizationGrant numberCountry
Max Planck Society Germany
Alexander von Humboldt Foundation Germany
German Research Foundation (DFG)BI 1998/2-1 Germany
European Research Council (ERC)856118European Union
CitationJournal: To Be Published
Title: Choreography of rapid actin filament disassembly by coronin, cofilin and AIP1
Authors: Oosterheert W / Boiero Sanders M / Hofnagel O / Bieling P / Raunser S
History
DepositionMar 11, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53111.png

Downloads & links

-
Map

FileDownload / File: emd_53111.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain, unsharpened cryo-EM density map of the Coronin-1B-decorated actin filament bound by two Cofilin-1 molecules (crosslinked)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 600 pix.
= 408. Å		0.68 Å/pix.
x 600 pix.
= 408. Å		0.68 Å/pix.
x 600 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.145
Minimum - Maximum-0.10810867 - 0.47198388
Average (Standard dev.)0.0016916585 (±0.027568147)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_53111_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Additional sharpened map of the Coronin-1B-decorated actin filament...

Fileemd_53111_additional_1.map
AnnotationAdditional sharpened map of the Coronin-1B-decorated actin filament bound by two Cofilin-1 molecules (crosslinked)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B of the Coronin-1B-decorated actin filament...

Fileemd_53111_half_map_1.map
AnnotationHalf map B of the Coronin-1B-decorated actin filament bound by two Cofilin-1 molecules (crosslinked)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A of the Coronin-1B-decorated actin filament...

Fileemd_53111_half_map_2.map
AnnotationHalf map A of the Coronin-1B-decorated actin filament bound by two Cofilin-1 molecules (crosslinked)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of the Coronin-1B-decorated actin filament boun...

EntireName: Cryo-EM structure of the Coronin-1B-decorated actin filament bound by two Cofilin-1 molecules (crosslinked)
Components
  • Complex: Cryo-EM structure of the Coronin-1B-decorated actin filament bound by two Cofilin-1 molecules (crosslinked)
    • Complex: Actin filament
      • Protein or peptide: Cytoplasmic beta actin
    • Complex: Coronin-1B
      • Protein or peptide: Coronin-1B
    • Complex: Cofilin-1
      • Protein or peptide: Cofilin-1

-
Supramolecule #1: Cryo-EM structure of the Coronin-1B-decorated actin filament boun...

SupramoleculeName: Cryo-EM structure of the Coronin-1B-decorated actin filament bound by two Cofilin-1 molecules (crosslinked)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #2: Actin filament

SupramoleculeName: Actin filament / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: Assembled as a double stranded helix of beta-actin subunits.
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: Coronin-1B

SupramoleculeName: Coronin-1B / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #4: Cofilin-1

SupramoleculeName: Cofilin-1 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Cytoplasmic beta actin

MacromoleculeName: Cytoplasmic beta actin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVTNWDD MEKIWHHTFY NELRVAPEEH PVLLTEAPLN PKANREKMTQ IMFETFNTPA MYVAIQAVLS LYASGRTTGI VMDSGDGVTH TVPIYEGYAL ...String:
DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVTNWDD MEKIWHHTFY NELRVAPEEH PVLLTEAPLN PKANREKMTQ IMFETFNTPA MYVAIQAVLS LYASGRTTGI VMDSGDGVTH TVPIYEGYAL PHAILRLDLA GRDLTDYLMK ILTERGYSFT TTAEREIVRD IKEKLCYVAL DFEQEMATAA SSSSLEKSYE LPDGQVITIG NERFRCPEAL FQPSFLGMES AGIHETTFNS IMKCDVDIRK DLYANTVLSG GTTMYPGIAD RMQKEITALA PSTMKIKIIA PPERKYSVWI GGSILASLST FQQMWISKQE YDESGPSIVH RKCF

-
Macromolecule #2: Coronin-1B

MacromoleculeName: Coronin-1B / type: protein_or_peptide / ID: 2 / Details: Coronin-1B with C-terminal SNAP-tag. / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GAMGSMSFRK VVRQSKFRHV FGQPVKNDQC YEDIRVSRVT WDSTFCAVNP KFLAVIVEAS GGGAFLVLPL SKTGRIDKAY PTVCGHTGPV LDIDWCPHND EVIASGSEDC TVMVWQIPEN GLTSPLTEPV VVLEGHTKRV GIIAWHPTAR NVLLSAGCDN VVLIWNVGTA ...String:
GAMGSMSFRK VVRQSKFRHV FGQPVKNDQC YEDIRVSRVT WDSTFCAVNP KFLAVIVEAS GGGAFLVLPL SKTGRIDKAY PTVCGHTGPV LDIDWCPHND EVIASGSEDC TVMVWQIPEN GLTSPLTEPV VVLEGHTKRV GIIAWHPTAR NVLLSAGCDN VVLIWNVGTA EELYRLDSLH PDLIYNVSWN HNGSLFCSAC KDKSVRIIDP RRGTLVAERE KAHEGARPMR AIFLADGKVF TTGFSRMSER QLALWDPENL EEPMALQELD SSNGALLPFY DPDTSVVYVC GKGDSSIRYF EITEEPPYIH FLNTFTSKEP QRGMGSMPKR GLEVSKCEIA RFYKLHERKC EPIVMTVPRK SDLFQDDLYP DTAGPEAALE AEEWVSGRDA DPILISLREA YVPSKQRDLK ISRRNVLSDS RPAMAPGSSH LGAPASTTTA ADATPSGSLA RAGEAGKLEE VMQELRALRA LVKEQGDRIC RLEEQLGRME NGDAGTGGGG SGGGGSMDKD CEMKRTTLDS PLGKLELSGC EQGLHEIKLL GKGTSAADAV EVPAPAAVLG GPEPLMQATA WLNAYFHQPE AIEEFPVPAL HHPVFQQESF TRQVLWKLLK VVKFGEVISY QQLAALAGNP AATAAVKTAL SGNPVPILIP CHRVVSSSGA VGGYEGGLAV KEWLLAHEGH RLGKPGLG

-
Macromolecule #3: Cofilin-1

MacromoleculeName: Cofilin-1 / type: protein_or_peptide / ID: 3 / Details: Cofilin-1 purified from E. Coli. / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MASGVAVSDG VIKVFNDMKV RKSSTPEEVK KRKKAVLFCL SEDKKNIILE EGKEILVGDV GQTVDDPYAT FVKMLPDKDC RYALYDATYE TKESKKEDLV FIFWAPESAP LKSKMIYASS KDAIKKKLTG IKHELQANCY EEVKDRCTLA EKLGGSAVIS LEGKPL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.1
Component:
ConcentrationNameFormula
10.0 mMHEPES
100.0 mMpotassium chlorideKCl
2.0 mMmagnesium chlorideMgCl2
1.0 mMEGTA
0.5 mMTCEP
0.02 % (v/v)Tween20

Details: 1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.02% Tween20).
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: The used Titan Krios G2 microscope contains an in-column Cs corrector.
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 22906 / Average electron dose: 62.3 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 / Cs: 0.01 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 8030748
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.1) / Software - details: Patch CTF / Details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

53105

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Software - details: Local Refinement / Number images used: 4245
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1) / Details: CryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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