9MNS | pdb_00009mns

Structure of Hepatitis C virus envelope glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody RM1-36


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 
    0.250 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structural and genetic signatures of two classes of HCV E2 neutralizing face antibodies from non-human primates immunized with a recombinant E1E2.

Nguyen, Y.T.K.Chen, F.Giang, E.Saha, S.Ueno, L.A.Chen, C.Watson, C.T.Tzarum, N.Wilson, I.A.Law, M.Stanfield, R.L.

(2026) NPJ Vaccines 

  • DOI: https://doi.org/10.1038/s41541-026-01449-1
  • Primary Citation Related Structures: 
    9MNQ, 9MNS, 9MNT, 9MNU, 9MRZ, 9MS9, 9MSC

  • PubMed Abstract: 

    Hepatitis C continues to be a significant public health problem despite advancements in antiviral therapeutics. To eliminate this disease, an effective vaccine against new infections and re-infections is needed. However, to date only one Hepatitis C virus (HCV) envelope protein (E1E2) immunogen, developed by Chiron Inc., has been tested in a Phase I clinical trial (ClinicalTrials.gov identifier NCT00500747). To establish a benchmark for elicitation of broadly neutralizing antibodies (bnAbs) by E1E2, we previously immunized non-human primates (NHPs) with this immunogen and isolated monoclonal nAbs that exhibit neutralization potency comparable to human nAbs. Here we show that NHP nAbs, encoded by germline genes IGHV1-138*01 and IGHV4-NL_5*01 (homologs of human IGHV1-69*10 and IGHV4-59*12, respectively), recognize a relatively conserved E2 region (neutralizing face) proximal to antigenic region 3 (AR3). These NHP AR3-targeting nAbs share highly similar binding modes to human AR3-targeting nAbs, suggesting a similarity in human and NHP immune responses to the same HCV immunogen.


  • Organizational Affiliation
    • Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 146.4 kDa 
  • Atom Count: 9,140 
  • Modeled Residue Count: 1,185 
  • Deposited Residue Count: 1,328 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RM1-36 Fab heavy chainA [auth H],
D [auth h]
222Macaca mulattaMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RM1-36 Fab light chainB [auth L],
C [auth l]
211Macaca mulattaMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein E2E,
F [auth B]
231Recombinant Hepatitis C virus HK6a/JFH-1Mutation(s): 0 
UniProt
Find proteins for B9V0E2 (Recombinant Hepatitis C virus HK6a/JFH-1)
Explore B9V0E2 
Go to UniProtKB:  B9V0E2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9V0E2
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free:  0.250 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.751α = 90
b = 223.545β = 93.58
c = 73.296γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

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 StatesAI106005
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI123861

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-14
    Type: Initial release
  • Version 1.1: 2026-08-05
    Changes: Database references