9MS9 | pdb_00009ms9

Structure of HCV neutralizing antibody RM5-16

• PDB DOI: https://doi.org/10.2210/pdb9MS9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Macaca mulatta
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-01-09 Released: 2026-01-14 
• Deposition Author(s): Nguyen, T.K.Y., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.175 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: in silico

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 

• PubMed: 42009696 
• 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.

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Organizational Affiliation: 
• Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
Southwest National Primate Research Centre (SNPRC) at Texas Biomedical Research Institute, San Antonio, TX, USA.
PKD Foundation, Kansas City, MO, USA.
Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Hebrew University of Jerusalem, Jerusalem, Israel.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. [e-mail].
Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA. [e-mail].
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA. [e-mail].
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.16 kDa 
• Atom Count: 3,739 
• Modeled Residue Count: 432 
• Deposited Residue Count: 440 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RM5-16 Fab light chain	A [auth L]	216	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RM5-16 Fab heavy chain	B [auth H]	224	Macaca mulatta	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	C [auth L], D [auth L], E [auth L], F [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	B [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.175 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.072	α = 90
b = 70.168	β = 90
c = 161.068	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-14 
Deposition Author(s): Nguyen, T.K.Y., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI106005

Revision History  

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