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- EMDB-0402: MERS-CoV S complex with human neutralizing LCA60 antibody Fab fra... -

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Basic information

Entry
Database: EMDB / ID: EMD-0402
TitleMERS-CoV S complex with human neutralizing LCA60 antibody Fab fragment (state 2)
Map data
SampleMERS-CoV complex with human neutralizing LCA60 antibody Fab fragment (state 2):
Spike glycoprotein / LCA60 heavy chain / LCA60 light chain / (ligand) x 3
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / pathogenesis / integral component of membrane
Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike receptor binding domain superfamily / Spike glycoprotein
Spike glycoprotein
Biological speciesMiddle East respiratory syndrome coronavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
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)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120553 United States
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 / ...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: 6nb4

SummaryFull reportAbout validation report
History
DepositionDec 6, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseFeb 6, 2019-
UpdateJan 8, 2020-
Current statusJan 8, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6nb4
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0402.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 384 pix.
= 526.08 Å
1.37 Å/pix.
x 384 pix.
= 526.08 Å
1.37 Å/pix.
x 384 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 LevelBy AUTHOR: 0.55 / Movie #1: 0.55
Minimum - Maximum-0.82948273 - 2.0453196
Average (Standard dev.)-0.001160151 (±0.04857579)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 526.08 Å
α=β=γ: 90.0 °

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-2.6924.3920.002

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Supplemental data

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Additional map: Unsharpened map

Fileemd_0402_additional.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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

EntireName: MERS-CoV complex with human neutralizing LCA60 antibody Fab fragment (state 2)
Number of components: 7

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

ProteinName: MERS-CoV complex with human neutralizing LCA60 antibody Fab fragment (state 2)
Recombinant expression: No
MassExperimental: 570 kDa
SourceSpecies: Middle East respiratory syndrome coronavirus
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Spike glycoprotein

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

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Component #3: protein, LCA60 heavy chain

ProteinName: LCA60 heavy chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.920568 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, LCA60 light chain

ProteinName: LCA60 light chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.25939 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 85 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #6: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 11 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #7: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 17 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Experimental details

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Sample preparation

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

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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)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 78719
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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