7RFC

Crystal structure of broadly neutralizing antibody mAb1382 in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Analysis of antibodies from HCV elite neutralizers identifies genetic determinants of broad neutralization.

Weber, T.Potthoff, J.Bizu, S.Labuhn, M.Dold, L.Schoofs, T.Horning, M.Ercanoglu, M.S.Kreer, C.Gieselmann, L.Vanshylla, K.Langhans, B.Janicki, H.Stroh, L.J.Knops, E.Nierhoff, D.Spengler, U.Kaiser, R.Bjorkman, P.J.Krey, T.Bankwitz, D.Pfeifer, N.Pietschmann, T.Flyak, A.I.Klein, F.

(2022) Immunity 55: 341-354.e7

  • DOI: https://doi.org/10.1016/j.immuni.2021.12.003
  • Primary Citation of Related Structures:  
    7RFB, 7RFC

  • PubMed Abstract: 

    The high genetic diversity of hepatitis C virus (HCV) complicates effective vaccine development. We screened a cohort of 435 HCV-infected individuals and found that 2%-5% demonstrated outstanding HCV-neutralizing activity. From four of these patients, we isolated 310 HCV antibodies, including neutralizing antibodies with exceptional breadth and potency. High neutralizing activity was enabled by the use of the VH1-69 heavy-chain gene segment, somatic mutations within CDRH1, and CDRH2 hydrophobicity. Structural and mutational analyses revealed an important role for mutations replacing the serines at positions 30 and 31, as well as the presence of neutral and hydrophobic residues at the tip of the CDRH3. Based on these characteristics, we computationally created a de novo antibody with a fully synthetic VH1-69 heavy chain that efficiently neutralized multiple HCV genotypes. Our findings provide a deep understanding of the generation of broadly HCV-neutralizing antibodies that can guide the design of effective vaccine candidates.


  • Organizational Affiliation

    Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mAb1382 Heavy ChainA,
E [auth H]
236Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
mAb1382 Light ChainB,
F [auth L]
216Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
envelope glycoprotein E2
C, D
262Hepacivirus hominisMutation(s): 0 
UniProt
Find proteins for A0A2P0NE26 (Hepacivirus hominis)
Explore A0A2P0NE26 
Go to UniProtKB:  A0A2P0NE26
Entity Groups  
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UniProt GroupA0A2P0NE26
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G [auth E],
H [auth F],
J [auth I],
K [auth J],
L [auth K],
G [auth E],
H [auth F],
J [auth I],
K [auth J],
L [auth K],
M,
O
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
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-glucopyranoseI [auth G]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D 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
N
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.291α = 90
b = 140.184β = 90
c = 142.8γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI127469
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesK99 AI153465

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references
  • Version 1.2: 2022-02-23
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description