6NB7

SARS-CoV complex with human neutralizing S230 antibody Fab fragment (state 2)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion.

Walls, A.C., Xiong, X., Park, Y.J., Tortorici, M.A., Snijder, J., Quispe, J., Cameroni, E., Gopal, R., Dai, M., Lanzavecchia, A., Zambon, M., Rey, F.A., Corti, D., Veesler, D.

(2019) Cell 176: 1026-1039.e15

  • DOI: https://doi.org/10.1016/j.cell.2018.12.028
  • Primary Citation of Related Structures:  
    6NB3, 6NB4, 6NB5, 6NB6, 6NB7, 6NB8

  • PubMed 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 to combat these viruses. The trimeric spike transmembrane glycoprotein S mediates entry into host cells and is the major target of neutralizing antibodies ...

    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.

    Organizational Affiliation: 

    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA. Electronic address: dveesler@uw.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,263Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: S, 2
UniProt
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus)
Explore P59594 
Go to UniProtKB:  P59594
Entity Groups  
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UniProt GroupP59594
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
S230 heavy chainD,
F [auth G],
G [auth H]		127Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
S230 light chainE,
H [auth I],
I [auth L]		112Homo sapiensMutation(s): 0 
Entity Groups  
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Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
CA [auth c],
EA [auth e],
HA [auth h],
J [auth F],
AA [auth a],
CA [auth c],
EA [auth e],
HA [auth h],
J [auth F],
JA [auth j],
K [auth J],
L [auth K],
LA [auth l],
M,
MA [auth m],
N,
NA [auth n],
O,
Q,
RA [auth r],
TA [auth t],
V,
X,
Y,
Z
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
DA [auth d],
P,
QA [auth q],
R,
S,
DA [auth d],
P,
QA [auth q],
R,
S,
U
5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseSA [auth s],
T		4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
IA [auth i],
KA [auth k],
OA [auth o],
PA [auth p],
BA [auth b],
IA [auth i],
KA [auth k],
OA [auth o],
PA [auth p],
W
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseFA [auth f],
GA [auth g]		4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM120553

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Database references, Other
  • Version 1.2: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary