[English] 日本語
Yorodumi
- EMDB-1471: The Structural Basis of Membrane Invagination by F-BAR Domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1471
TitleThe Structural Basis of Membrane Invagination by F-BAR Domains
Map data3D reconstruction of a membrane tubule coated by a helical lattice of dimeric F-BAR modules from the human protein CIP4.
Sample
  • Sample: membrane tubule coated with a helical lattice of dimer F-BAR modules from the human protein CIP4
  • Protein or peptide: CIP4
KeywordsF-BAR / FCH / PCH / CIP4 / FBP17 / Toca / Membrane Tubule. Human Protein.
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsFrost A / Perera R / Roux A / Spasov K / Egelman E / De Camilli P / Unger V
CitationJournal: Cell / Year: 2008
Title: Structural basis of membrane invagination by F-BAR domains.
Authors: Adam Frost / Rushika Perera / Aurélien Roux / Krasimir Spasov / Olivier Destaing / Edward H Egelman / Pietro De Camilli / Vinzenz M Unger /
Abstract: BAR superfamily domains shape membranes through poorly understood mechanisms. We solved structures of F-BAR modules bound to flat and curved bilayers using electron (cryo)microscopy. We show that ...BAR superfamily domains shape membranes through poorly understood mechanisms. We solved structures of F-BAR modules bound to flat and curved bilayers using electron (cryo)microscopy. We show that membrane tubules form when F-BARs polymerize into helical coats that are held together by lateral and tip-to-tip interactions. On gel-state membranes or after mutation of residues along the lateral interaction surface, F-BARs adsorb onto bilayers via surfaces other than their concave face. We conclude that membrane binding is separable from membrane bending, and that imposition of the module's concave surface forces fluid-phase bilayers to bend locally. Furthermore, exposure of the domain's lateral interaction surface through a change in orientation serves as the crucial trigger for assembly of the helical coat and propagation of bilayer bending. The geometric constraints and sequential assembly of the helical lattice explain how F-BAR and classical BAR domains segregate into distinct microdomains, and provide insight into the spatial regulation of membrane invagination.
History
DepositionFeb 14, 2008-
Header (metadata) releaseFeb 19, 2008-
Map releaseMar 31, 2009-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Close-up
  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1471.gif

Downloads & links

-
Map

FileDownload / File: emd_1471.map.gz / Format: CCP4 / Size: 238.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of a membrane tubule coated by a helical lattice of dimeric F-BAR modules from the human protein CIP4.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.28 Å/pix.
x 400 pix.
= 912. Å		2.28 Å/pix.
x 400 pix.
= 912. Å		2.28 Å/pix.
x 400 pix.
= 912. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.28 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.12 / Movie #1: 0.07
Minimum - Maximum-0.223295 - 0.396232
Average (Standard dev.)0.0129856 (±0.0502637)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 912 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.282.282.28
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z912.000912.000912.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2230.3960.013

-
Supplemental data

-
Sample components

-
Entire : membrane tubule coated with a helical lattice of dimer F-BAR modu...

EntireName: membrane tubule coated with a helical lattice of dimer F-BAR modules from the human protein CIP4
Components
  • Sample: membrane tubule coated with a helical lattice of dimer F-BAR modules from the human protein CIP4
  • Protein or peptide: CIP4

-
Supramolecule #1000: membrane tubule coated with a helical lattice of dimer F-BAR modu...

SupramoleculeName: membrane tubule coated with a helical lattice of dimer F-BAR modules from the human protein CIP4
type: sample / ID: 1000
Details: membrane composed of phospholipids and cholesterol. recombinant protein
Number unique components: 2

-
Macromolecule #1: CIP4

MacromoleculeName: CIP4 / type: protein_or_peptide / ID: 1 / Name.synonym: CIP4 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: plasmsa membrane and cytoplasm
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pGEX

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI F20
DateJan 3, 2006
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: eucentric, single tilt / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: SPIDER, MRC, IHRSR
CTF correctionDetails: ACE, image

-
Atomic model buiding 1

Initial model(PDB ID:

2efk

,

2efl

)
SoftwareName: CHIMERA,SITUS
RefinementSpace: REAL

+
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