5W1K

JUNV GP1 CR1-10 Fab CR1-28 Fab complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.99 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Vaccine-elicited receptor-binding site antibodies neutralize two New World hemorrhagic fever arenaviruses.

Clark, L.E.Mahmutovic, S.Raymond, D.D.Dilanyan, T.Koma, T.Manning, J.T.Shankar, S.Levis, S.C.Briggiler, A.M.Enria, D.A.Wucherpfennig, K.W.Paessler, S.Abraham, J.

(2018) Nat Commun 9: 1884-1884

  • DOI: https://doi.org/10.1038/s41467-018-04271-z
  • Primary Citation of Related Structures:  
    5W1G, 5W1K, 5W1M

  • PubMed Abstract: 

    While five arenaviruses cause human hemorrhagic fevers in the Western Hemisphere, only Junin virus (JUNV) has a vaccine. The GP1 subunit of their envelope glycoprotein binds transferrin receptor 1 (TfR1) using a surface that substantially varies in sequence among the viruses. As such, receptor-mimicking antibodies described to date are type-specific and lack the usual breadth associated with this mode of neutralization. Here we isolate, from the blood of a recipient of the live attenuated JUNV vaccine, two antibodies that cross-neutralize Machupo virus with varying efficiency. Structures of GP1-Fab complexes explain the basis for efficient cross-neutralization, which involves avoiding receptor mimicry and targeting a conserved epitope within the receptor-binding site (RBS). The viral RBS, despite its extensive sequence diversity, is therefore a target for cross-reactive antibodies with activity against New World arenaviruses of public health concern.


  • Organizational Affiliation

    Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CR1-28 Fab light chain
A, F, K, S
206Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX7 (Homo sapiens)
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UniProt GroupP0DOX7
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CR1-28 Fab heavy chain
B, G, L, T
226Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6C4R2 (Homo sapiens)
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UniProt GroupS6C4R2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CR1-10 Fab light chain
C, H, M, N
213Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6PIL8 (Homo sapiens)
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UniProt GroupQ6PIL8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CR1-10 Fab heavy chain
D, I, O, Q
225Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6B2B6 (Homo sapiens)
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UniProt GroupS6B2B6
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-glycoprotein polyprotein GP complex
E, J, P, R
142Mammarenavirus juninenseMutation(s): 0 
Gene Names: GPCGP-C
UniProt
Find proteins for P26313 (Junin mammarenavirus)
Explore P26313 
Go to UniProtKB:  P26313
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UniProt GroupP26313
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Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
U, W, X
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
V
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
Y [auth P]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.99 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.84α = 90
b = 132.23β = 92.47
c = 167.42γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesDP5OD023084
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI007061
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI109740
Other privateUnited StatesBurroughs Wellcome Fund
Other privateUnited StatesWilliam Randolph Hearst Foundation and Brigham and Womens Hospital
Other privateUnited StatesHarvard Medical School DICP

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary