7SSC | pdb_00007ssc

TRL345 lineage ancestor I8 Fab bound to an HCMV gB-derived peptide

• PDB DOI: https://doi.org/10.2210/pdb7SSC/pdb

• Classification: IMMUNE SYSTEM/VIRAL PROTEIN
• Organism(s): Homo sapiens, Human betaherpesvirus 5
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-11-10 Released: 2022-10-19 
• Deposition Author(s): Sponholtz, M.R., McLellan, J.S.
• Funding Organization(s): Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.174 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Models: experimental

Literature

A single, improbable B cell receptor mutation confers potent neutralization against cytomegalovirus.

Jenks, J.A., Amin, S., Sponholtz, M.R., Kumar, A., Wrapp, D., Venkatayogi, S., Tu, J.J., Karthigeyan, K., Valencia, S.M., Connors, M., Harnois, M.J., Hora, B., Rochat, E., McLellan, J.S., Wiehe, K., Permar, S.R.

(2023) PLoS Pathog 19: e1011107-e1011107

• PubMed: 36662906 
• DOI: https://doi.org/10.1371/journal.ppat.1011107
• Primary Citation Related Structures: 
  7SSC


• PubMed Abstract: 
  

  Cytomegalovirus (CMV) is a leading cause of infant hearing loss and neurodevelopmental delay, but there are no clinically licensed vaccines to prevent infection, in part due to challenges eliciting neutralizing antibodies. One of the most well-studied targets for CMV vaccines is the viral fusogen glycoprotein B (gB), which is required for viral entry into host cells. Within gB, antigenic domain 2 site 1 (AD-2S1) is a target of potently neutralizing antibodies, but gB-based candidate vaccines have yet to elicit robust responses against this region. We mapped the genealogy of B cells encoding potently neutralizing anti-gB AD-2S1 antibodies from their inferred unmutated common ancestor (UCA) and characterized the binding and function of early lineage ancestors. Surprisingly, we found that a single amino acid heavy chain mutation A33N, which was an improbable mutation rarely generated by somatic hypermutation machinery, conferred broad CMV neutralization to the non-neutralizing UCA antibody. Structural studies revealed that this mutation mediated key contacts with the gB AD-2S1 epitope. Collectively, these results provide insight into potently neutralizing gB-directed antibody evolution in a single donor and lay a foundation for using this B cell-lineage directed approach for the design of next-generation CMV vaccines.

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Organizational Affiliation: 
• Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America.
Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America.
Department of Pediatrics, Weill Cornell Medicine, New York, New York, United States of America.
Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 48.76 kDa 
• Atom Count: 4,090 
• Modeled Residue Count: 444 
• Deposited Residue Count: 452 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRL345-I8 Fab heavy chain	A [auth H]	223	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TRL345-I8 Fab light chain	B [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein B peptide	C [auth P]	15	Human betaherpesvirus 5	Mutation(s): 0
UniProt
Find proteins for P06473 (Human cytomegalovirus (strain AD169)) Explore P06473  Go to UniProtKB:  P06473

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.174 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.879	α = 90
b = 74.669	β = 90
c = 104.88	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-19 
Deposition Author(s): Sponholtz, M.R., McLellan, J.S.

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Funding Organization	Location	Grant Number
Welch Foundation	United States	F-0003-19620604

Revision History  

• Version 1.0: 2022-10-19
  Type: Initial release
  
• Version 1.1: 2023-02-01
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary