5WB9 | pdb_00005wb9

Crystal structure of CD4 binding site antibody N60P23 in complex with HIV-1 clade A/E strain 93TH057 gp120 core

• PDB DOI: https://doi.org/10.2210/pdb5WB9/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2017-06-28 Released: 2018-05-23 
• Deposition Author(s): Gohain, N., Tolbert, W., Pazgier, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.258 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Identification of Near-Pan-neutralizing Antibodies against HIV-1 by Deconvolution of Plasma Humoral Responses.

Sajadi, M.M., Dashti, A., Rikhtegaran Tehrani, Z., Tolbert, W.D., Seaman, M.S., Ouyang, X., Gohain, N., Pazgier, M., Kim, D., Cavet, G., Yared, J., Redfield, R.R., Lewis, G.K., DeVico, A.L.

(2018) Cell 173: 1783-1795.e14

• PubMed: 29731169 
• DOI: https://doi.org/10.1016/j.cell.2018.03.061
• Primary Citation Related Structures: 
  5WB9, 6BCK


• PubMed Abstract: 
  

  Anti-HIV-1 envelope broadly neutralizing monoclonal antibodies (bNAbs) isolated from memory B cells may not fully represent HIV-1-neutralizing profiles measured in plasma. Accordingly, we characterized near-pan-neutralizing antibodies extracted directly from the plasma of two "elite neutralizers." Circulating anti-gp120 polyclonal antibodies were deconvoluted using proteomics to guide lineage analysis of bone marrow plasma cells. In both subjects, a single lineage of anti-CD4-binding site (CD4bs) antibodies explained the plasma-neutralizing activity. Importantly, members of these lineages potently neutralized 89%-100% of a multi-tier 117 pseudovirus panel, closely matching the specificity and breadth of the circulating antibodies. X-ray crystallographic analysis of one monoclonal, N49P7, suggested a unique ability to bypass the CD4bs Phe43 cavity, while reaching deep into highly conserved residues of Layer 3 of the gp120 inner domain, likely explaining its extreme potency and breadth. Further direct analyses of plasma anti-HIV-1 bNAbs should provide new insights for developing antibody-based antiviral agents and vaccines.

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Organizational Affiliation: 
• Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Medicine, Baltimore VA Medical Center, Baltimore, MD 21201, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA. Electronic address: [e-mail].
Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Virology Department, Pasteur Institute of Iran, Tehran, Iran.
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA.
Atreca, Inc., Redwood City, CA 94063, USA.
Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 88.84 kDa 
• Atom Count: 6,260 
• Modeled Residue Count: 760 
• Deposited Residue Count: 788 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
clade A/E 93TH057 HIV-1 gp120 core	A [auth G]	353	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: HIV-1 Env
UniProt
Find proteins for A0A0M3KKW9 (Human immunodeficiency virus type 1) Explore A0A0M3KKW9  Go to UniProtKB:  A0A0M3KKW9
Glycosylation
Glycosylation Sites: 8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N60P23 Fab heavy chain	B [auth H]	227	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N60P23 Fab light chain	C [auth L]	208	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth G], E [auth G], F [auth G], G, H [auth G], I [auth G], J [auth G], K [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MPO	M [auth G]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C7 H15 N O4 S DVLFYONBTKHTER-UHFFFAOYSA-N
MPD	L [auth G]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.258 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.562	α = 90
b = 68.567	β = 111.36
c = 119.356	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Gohain, N., Tolbert, W., Pazgier, M.

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2018-06-27
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-13
  Changes: Structure summary