9MRZ | pdb_00009mrz

Structure of HCV broadly neutralizing antibody RM1-73

PDB DOI: https://doi.org/10.2210/pdb9MRZ/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., Stanfield, R.L., Wilson, I.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.196 (Depositor), 0.197 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

PubMed: 42009696 Search on PubMed Search on PubMed Central
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: 96.31 kDa
Atom Count: 7,431
Modeled Residue Count: 887
Deposited Residue Count: 894
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RM1-73 Fab light chain	A [auth l], D [auth L]	212	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RM1-73 Fab heavy chain	B [auth h], C [auth H]	235	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NHE (Subject of Investigation/LOI) Query on NHE Download:Ideal Coordinates CCD File SDF format, chain G [auth h] SDF format, chain I [auth H] MOL2 format, chain G [auth h] MOL2 format, chain I [auth H] mmCIF format, chain G [auth h] mmCIF format, chain I [auth H]	G [auth h], I [auth H]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain G [auth h] Focus chain I [auth H] Interactions & Density Focus chain G [auth h] Focus chain I [auth H]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth l] SDF format, chain F [auth l] SDF format, chain H [auth h] SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain L SDF format, chain M [auth L] SDF format, chain N [auth L] MOL2 format, chain E [auth l] MOL2 format, chain F [auth l] MOL2 format, chain H [auth h] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain L MOL2 format, chain M [auth L] MOL2 format, chain N [auth L] mmCIF format, chain E [auth l] mmCIF format, chain F [auth l] mmCIF format, chain H [auth h] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain L mmCIF format, chain M [auth L] mmCIF format, chain N [auth L]	E [auth l] F [auth l] H [auth h] J [auth H] K [auth H] E [auth l], F [auth l], H [auth h], J [auth H], K [auth H], L, M [auth L], N [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth l] Focus chain F [auth l] Focus chain H [auth h] Focus chain J [auth H] Focus chain K [auth H] Focus chain L Focus chain M [auth L] Focus chain N [auth L] Interactions & Density Focus chain E [auth l] Focus chain F [auth l] Focus chain H [auth h] Focus chain J [auth H] Focus chain K [auth H] Focus chain L Focus chain M [auth L] Focus chain N [auth L]