5VK2

Structural basis for antibody-mediated neutralization of Lassa virus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Literature

Structural basis for antibody-mediated neutralization of Lassa virus.

Hastie, K.M., Zandonatti, M.A., Kleinfelter, L.M., Heinrich, M.L., Rowland, M.M., Chandran, K., Branco, L.M., Robinson, J.E., Garry, R.F., Saphire, E.O.

(2017) Science 356: 923-928

  • DOI: https://doi.org/10.1126/science.aam7260
  • Primary Citation of Related Structures:  
    5VK2

  • PubMed Abstract: 

    • The arenavirus Lassa causes severe hemorrhagic fever and a significant disease burden in West Africa every year. The glycoprotein, GPC, is the sole antigen expressed on the viral surface and the critical target for antibody-mediated neutralization. Here we present the crystal structure of the trimeric, prefusion ectodomain of Lassa GP bound to a neutralizing antibody from a human survivor at 3 ...

    The arenavirus Lassa causes severe hemorrhagic fever and a significant disease burden in West Africa every year. The glycoprotein, GPC, is the sole antigen expressed on the viral surface and the critical target for antibody-mediated neutralization. Here we present the crystal structure of the trimeric, prefusion ectodomain of Lassa GP bound to a neutralizing antibody from a human survivor at 3.2-angstrom resolution. The antibody extensively anchors two monomers together at the base of the trimer, and biochemical analysis suggests that it neutralizes by inhibiting conformational changes required for entry. This work illuminates pH-driven conformational changes in both receptor-binding and fusion subunits of Lassa virus, illustrates the unique assembly of the arenavirus glycoprotein spike, and provides a much-needed template for vaccine design against these threats to global health.

    Organizational Affiliation: 

    Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-glycoprotein polyprotein GP complexA,
C [auth B],
E [auth C]		259Lassa virus JosiahMutation(s): 3 
Gene Names: GPC, GP-C
UniProt
Find proteins for P08669 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976))
Explore P08669 
Go to UniProtKB:  P08669
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08669
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-glycoprotein polyprotein GP complexB [auth a],
D [auth b],
F [auth c]		164Lassa virus JosiahMutation(s): 3 
Gene Names: GPC, GP-C
UniProt
Find proteins for P08669 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976))
Explore P08669 
Go to UniProtKB:  P08669
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UniProt GroupP08669
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab 37.7H heavy chainG [auth D],
I [auth F],
K [auth H]		229Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fab 37.7H light chainH [auth E],
J [auth G],
L		217Homo sapiensMutation(s): 0 
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Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseCA [auth Z],
M [auth I],
Y [auth V]		3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth X],
BA [auth Y],
EA [auth e],
N [auth J],
O [auth K],
AA [auth X],
BA [auth Y],
EA [auth e],
N [auth J],
O [auth K],
P [auth M],
R [auth O],
T [auth Q],
U [auth R],
V [auth S],
Z [auth W]
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
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-glucopyranoseDA [auth d],
Q [auth N],
W [auth T]		4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseFA [auth f],
S [auth P],
X [auth U]		3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.697α = 90
b = 152.697β = 90
c = 456.738γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1U19AI109762-01
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI116112
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM007491

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-14
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary