7TI6 | pdb_00007ti6

Crystal structure of the wild-type least mutated common ancestor (LMCA) of the HIV-targeting PCT64 antibody lineage

• PDB DOI: https://doi.org/10.2210/pdb7TI6/pdb

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


• Deposited: 2022-01-12 Released: 2022-10-05 
• Deposition Author(s): Omorodion, O., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.229 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Human immunoglobulin repertoire analysis guides design of vaccine priming immunogens targeting HIV V2-apex broadly neutralizing antibody precursors.

Willis, J.R., Berndsen, Z.T., Ma, K.M., Steichen, J.M., Schiffner, T., Landais, E., Liguori, A., Kalyuzhniy, O., Allen, J.D., Baboo, S., Omorodion, O., Diedrich, J.K., Hu, X., Georgeson, E., Phelps, N., Eskandarzadeh, S., Groschel, B., Kubitz, M., Adachi, Y., Mullin, T.M., Alavi, N.B., Falcone, S., Himansu, S., Carfi, A., Wilson, I.A., Yates 3rd, J.R., Paulson, J.C., Crispin, M., Ward, A.B., Schief, W.R.

(2022) Immunity 55: 2149-2167.e9

• PubMed: 36179689 
• DOI: https://doi.org/10.1016/j.immuni.2022.09.001
• Primary Citation Related Structures: 
  7T73, 7T74, 7T75, 7T76, 7T77, 7TI6


• PubMed Abstract: 
  

  Broadly neutralizing antibodies (bnAbs) to the HIV envelope (Env) V2-apex region are important leads for HIV vaccine design. Most V2-apex bnAbs engage Env with an uncommonly long heavy-chain complementarity-determining region 3 (HCDR3), suggesting that the rarity of bnAb precursors poses a challenge for vaccine priming. We created precursor sequence definitions for V2-apex HCDR3-dependent bnAbs and searched for related precursors in human antibody heavy-chain ultradeep sequencing data from 14 HIV-unexposed donors. We found potential precursors in a majority of donors for only two long-HCDR3 V2-apex bnAbs, PCT64 and PG9, identifying these bnAbs as priority vaccine targets. We then engineered ApexGT Env trimers that bound inferred germlines for PCT64 and PG9 and had higher affinities for bnAbs, determined cryo-EM structures of ApexGT trimers complexed with inferred-germline and bnAb forms of PCT64 and PG9, and developed an mRNA-encoded cell-surface ApexGT trimer. These methods and immunogens have promise to assist HIV vaccine development.

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Organizational Affiliation: 
• Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.
Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
Moderna Inc., Cambridge, MA 02139, USA.
Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: mass spectrometry, gel filtration

Macromolecule Content 

• Total Structure Weight: 49.35 kDa 
• Atom Count: 3,428 
• Modeled Residue Count: 446 
• Deposited Residue Count: 454 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PCT64_LMCA Fab heavy chain	A [auth H]	238	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PCT64_LMCA light chain (wild type)	B [auth L]	216	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth L]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.229 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.083	α = 90
b = 64.317	β = 98.182
c = 76.324	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-05 
Deposition Author(s): Omorodion, O., 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	UM1 AI144462
Bill & Melinda Gates Foundation	United States	OPP119635

Revision History  

• Version 1.0: 2022-10-05
  Type: Initial release
  
• Version 1.1: 2022-10-12
  Changes: Database references
• Version 1.2: 2022-11-16
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary