[English] 日本語
Yorodumi
- EMDB-0401: MERS-CoV complex with human neutralizing LCA60 antibody Fab fragm... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 0401
TitleMERS-CoV complex with human neutralizing LCA60 antibody Fab fragment (state 1)
Map dataMERS-CoV complex with human neutralizing LCA60 antibody Fab fragment (state 1), primary map
SampleMERS-CoV complex with human neutralizing LCA60 antibody Fab fragment (state 1):
Spike glycoprotein / LCA60 light chain / LCA60 heavy chain / (ligand) x 3
Function / homologyCoronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike receptor binding domain superfamily / Coronavirus S2 glycoprotein / Spike receptor binding domain / membrane fusion / receptor-mediated virion attachment to host cell / viral envelope / integral component of membrane / Spike glycoprotein
Function and homology information
SourceMiddle East respiratory syndrome coronavirus / Middle East respiratory syndrome-related coronavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsWalls AC / Xiong X / Park YJ / Tortorici MA / Snijder S / Quispe J / Cameroni E / Gopal R / Mian D / Lanzavecchia A / Zambon M / Rey FA / Corti D / Veesler D / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Cell / Year: 2019
Title: Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion.
Authors: Alexandra C Walls / Xiaoli Xiong / Young-Jun Park / M Alejandra Tortorici / Joost Snijder / Joel Quispe / Elisabetta Cameroni / Robin Gopal / Mian Dai / Antonio Lanzavecchia / Maria Zambon / Félix A Rey / Davide Corti / David Veesler
Abstract: Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways ...Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways to combat these viruses. The trimeric spike transmembrane glycoprotein S mediates entry into host cells and is the major target of neutralizing antibodies. To understand the humoral immune response elicited upon natural infections with coronaviruses, we structurally characterized the SARS-CoV and MERS-CoV S glycoproteins in complex with neutralizing antibodies isolated from human survivors. Although the two antibodies studied blocked attachment to the host cell receptor, only the anti-SARS-CoV S antibody triggered fusogenic conformational changes via receptor functional mimicry. These results provide a structural framework for understanding coronavirus neutralization by human antibodies and shed light on activation of coronavirus membrane fusion, which takes place through a receptor-driven ratcheting mechanism.
Validation ReportPDB-ID: 6nb3

SummaryFull reportAbout validation report
DateDeposition: Dec 6, 2018 / Header (metadata) release: Jan 16, 2019 / Map release: Feb 6, 2019 / Last update: Feb 6, 2019

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Map surface with fitted models
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_0401.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.37 Å/pix.
= 526.08 Å
384 pix
1.37 Å/pix.
= 526.08 Å
384 pix
1.37 Å/pix.
= 526.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density
Contour Level:0.7 (by author), 0.7 (movie #1):
Minimum - Maximum-2.9722195 - 5.1119576
Average (Standard dev.)0.0023687242 (0.06053859)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin0.00.00.0
Limit383.0383.0383.0
Spacing384384384
CellA=B=C: 526.08 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z526.080526.080526.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-16-63-38
NX/NY/NZ727975
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-2.9725.1120.002

-
Supplemental data

-
Sample components

+
Entire MERS-CoV complex with human neutralizing LCA60 antibody Fab fragm...

EntireName: MERS-CoV complex with human neutralizing LCA60 antibody Fab fragment (state 1)
Number of components: 7

+
Component #1: protein, MERS-CoV complex with human neutralizing LCA60 antibody ...

ProteinName: MERS-CoV complex with human neutralizing LCA60 antibody Fab fragment (state 1)
Recombinant expression: No
MassExperimental: 572 MDa
SourceSpecies: Middle East respiratory syndrome coronavirus
Source (engineered)Expression System: Homo sapiens (human)

+
Component #2: protein, Spike glycoprotein

ProteinName: Spike glycoprotein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 149.172062 kDa
SourceSpecies: Middle East respiratory syndrome-related coronavirus
Source (engineered)Expression System: Homo sapiens (human)

+
Component #3: protein, LCA60 light chain

ProteinName: LCA60 light chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.25939 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #4: protein, LCA60 heavy chain

ProteinName: LCA60 heavy chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.920568 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #5: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 93 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

+
Component #6: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 30 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

+
Component #7: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 37 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
Support filmunspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 54071
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement space: REAL
Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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