[English] 日本語
Yorodumi
- EMDB-4943: In situ structure of a pentameric IgM complex bound to complement... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4943
TitleIn situ structure of a pentameric IgM complex bound to complement components C1 and one molecule of C4b
Map dataPentameric IgM with C1 and one copy of C4b
Sample
  • Complex: pentameric IgM-C1-C4b1
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 25.6 Å
AuthorsSharp TH
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
European Research Council759517 Netherlands
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Insights into IgM-mediated complement activation based on in situ structures of IgM-C1-C4b.
Authors: Thomas H Sharp / Aimee L Boyle / Christoph A Diebolder / Alexander Kros / Abraham J Koster / Piet Gros /
Abstract: Antigen binding by serum Ig-M (IgM) protects against microbial infections and helps to prevent autoimmunity, but causes life-threatening diseases when mistargeted. How antigen-bound IgM activates ...Antigen binding by serum Ig-M (IgM) protects against microbial infections and helps to prevent autoimmunity, but causes life-threatening diseases when mistargeted. How antigen-bound IgM activates complement-immune responses remains unclear. We present cryoelectron tomography structures of IgM, C1, and C4b complexes formed on antigen-bearing lipid membranes by normal human serum at 4 °C. The IgM-C1-C4b complexes revealed C4b product release as the temperature-limiting step in complement activation. Both IgM hexamers and pentamers adopted hexagonal, dome-shaped structures with Fab pairs, dimerized by hinge domains, bound to surface antigens that support a platform of Fc regions. C1 binds IgM through widely spread C1q-collagen helices, with C1r proteases pointing outward and C1s bending downward and interacting with surface-attached C4b, which further interacts with the adjacent IgM-Fab and globular C1q-recognition unit. Based on these data, we present mechanistic models for antibody-mediated, C1q-transmitted activation of C1 and for C4b deposition, while further conformational rearrangements are required to form C3 convertases.
History
DepositionMay 8, 2019-
Header (metadata) releaseJun 12, 2019-
Map releaseJun 12, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4943.png

Downloads & links

-
Map

FileDownload / File: emd_4943.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPentameric IgM with C1 and one copy of C4b
Voxel sizeX=Y=Z: 4.3 Å
Density
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-1.2587223 - 2.720759
Average (Standard dev.)0.016073983 (±0.13479042)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 688.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.34.34.3
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z688.000688.000688.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-1.2592.7210.016

-
Supplemental data

-
Mask #1

Fileemd_4943_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : pentameric IgM-C1-C4b1

EntireName: pentameric IgM-C1-C4b1
Components
  • Complex: pentameric IgM-C1-C4b1

-
Supramolecule #1: pentameric IgM-C1-C4b1

SupramoleculeName: pentameric IgM-C1-C4b1 / type: complex / ID: 1 / Parent: 0
Details: Map contains a complex of pentameric IgM, complement component C1 and one molecule of complement component C4b
Source (natural)Organism: Homo sapiens (human) / Organ: Human serum
Molecular weightTheoretical: 1.931 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Component - Formula: PBS / Component - Name: PBS
VitrificationCryogen name: ETHANE / Chamber temperature: 277.15 K / Instrument: LEICA EM GP
DetailsAntigenic liposomes + IgM + Normal human serum

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 33000
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 2.4 sec. / Average electron dose: 1.48 e/Å2
Details: Exposures of 2.4 sec were dose-fractionated into 6 movie frames per tilt angle. The total dose for each tilt series was 80 e-/A^2. Focusing to -300 nm was performed before each image ...Details: Exposures of 2.4 sec were dose-fractionated into 6 movie frames per tilt angle. The total dose for each tilt series was 80 e-/A^2. Focusing to -300 nm was performed before each image acquisition using a low-dose routine
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 54 / Number images used: 1522 / Software - Name: EMAN2 (ver. 2.2)
Final 3D classificationNumber classes: 3 / Software - Name: Dynamo
Final angle assignmentType: NOT APPLICABLE / Software - Name: Dynamo
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 305
DetailsRaw frames were aligned using alignframes and tomograms were reconstructed using weighted back-projection from the software program IMOD.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model(PDB ID:

1dee

,

4jvu

,

4ba8

,

4jvw

,

1pk6

,

6f1c

,

1gpz

,

4j1y

,

5jtw

)
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