[English] 日本語
Yorodumi
- EMDB-1991: Structure of complement component complex, sC5b9. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1991
TitleStructure of complement component complex, sC5b9.
Map dataThis is an image of a surface rendered view of the sC5b9 complex
Sample
  • Sample: sC5b9
  • Protein or peptide: C5b
  • Protein or peptide: C6
  • Protein or peptide: C7
  • Protein or peptide: C8
  • Protein or peptide: C9
  • Protein or peptide: Clusterin
  • Protein or peptide: vibronectin
Keywordscomplement terminal pathway / humoral immune pore / MACPF domain
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 24.0 Å
AuthorsBubeck D / Roversi P / Hakabyan S / Morgan BP / Lea SM / Llorca O
CitationJournal: Cell Rep / Year: 2012
Title: Assembly and regulation of the membrane attack complex based on structures of C5b6 and sC5b9.
Authors: Michael A Hadders / Doryen Bubeck / Pietro Roversi / Svetlana Hakobyan / Federico Forneris / B Paul Morgan / Michael K Pangburn / Oscar Llorca / Susan M Lea / Piet Gros /
Abstract: Activation of the complement system results in formation of membrane attack complexes (MACs), pores that disrupt lipid bilayers and lyse bacteria and other pathogens. Here, we present the crystal ...Activation of the complement system results in formation of membrane attack complexes (MACs), pores that disrupt lipid bilayers and lyse bacteria and other pathogens. Here, we present the crystal structure of the first assembly intermediate, C5b6, together with a cryo-electron microscopy reconstruction of a soluble, regulated form of the pore, sC5b9. Cleavage of C5 to C5b results in marked conformational changes, distinct from those observed in the homologous C3-to-C3b transition. C6 captures this conformation, which is preserved in the larger sC5b9 assembly. Together with antibody labeling, these structures reveal that complement components associate through sideways alignment of the central MAC-perforin (MACPF) domains, resulting in a C5b6-C7-C8β-C8α-C9 arc. Soluble regulatory proteins below the arc indicate a potential dual mechanism in protection from pore formation. These results provide a structural framework for understanding MAC pore formation and regulation, processes important for fighting infections and preventing complement-mediated tissue damage.
History
DepositionNov 17, 2011-
Header (metadata) releaseJan 27, 2012-
Map releaseFeb 24, 2012-
UpdateAug 29, 2012-
Current statusAug 29, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0122
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0122
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1991.png

Downloads & links

-
Map

FileDownload / File: emd_1991.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered view of the sC5b9 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.76 Å/pix.
x 150 pix.
= 414. Å		2.76 Å/pix.
x 150 pix.
= 414. Å		2.76 Å/pix.
x 150 pix.
= 414. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0122 / Movie #1: 0.0122
Minimum - Maximum-0.02482872 - 0.09138546
Average (Standard dev.)0.00034994 (±0.00500717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 414.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z414.000414.000414.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.0250.0910.000

-
Supplemental data

-
Sample components

-
Entire : sC5b9

EntireName: sC5b9
Components
  • Sample: sC5b9
  • Protein or peptide: C5b
  • Protein or peptide: C6
  • Protein or peptide: C7
  • Protein or peptide: C8
  • Protein or peptide: C9
  • Protein or peptide: Clusterin
  • Protein or peptide: vibronectin

-
Supramolecule #1000: sC5b9

SupramoleculeName: sC5b9 / type: sample / ID: 1000 / Details: The sample was monodisperse
Oligomeric state: 7, C8, and C9. In addition it contains clusterin and vitronectin with an unknown stoichiometry.
Number unique components: 7

-
Macromolecule #1: C5b

MacromoleculeName: C5b / type: protein_or_peptide / ID: 1 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

-
Macromolecule #2: C6

MacromoleculeName: C6 / type: protein_or_peptide / ID: 2 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

-
Macromolecule #3: C7

MacromoleculeName: C7 / type: protein_or_peptide / ID: 3 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

-
Macromolecule #4: C8

MacromoleculeName: C8 / type: protein_or_peptide / ID: 4 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

-
Macromolecule #5: C9

MacromoleculeName: C9 / type: protein_or_peptide / ID: 5 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

-
Macromolecule #6: Clusterin

MacromoleculeName: Clusterin / type: protein_or_peptide / ID: 6 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

-
Macromolecule #7: vibronectin

MacromoleculeName: vibronectin / type: protein_or_peptide / ID: 7 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 150mM NaCl, 50mM Tris, 1mM CaCl2, and 1mM MgCl2
GridDetails: quantifoil holey carbon grids
VitrificationCryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot

-
Electron microscopy

MicroscopeJEOL 2200FS
Specialist opticsEnergy filter - Name: OMEGA
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 405 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 54400
Sample stageSpecimen holder: single-tilt cryo holder / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

CTF correctionDetails: Bsoft, phase flip on each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2, XMIPP / Number images used: 18983

-
Atomic model buiding 1

Initial modelPDB ID:

3ojy


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C
SoftwareName: Chimera
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation Coefficient

+
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