5EWI | pdb_00005ewi

Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing Antibody Isolated from Donor N90

• PDB DOI: https://doi.org/10.2210/pdb5EWI/pdb

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


• Deposited: 2015-11-20 Released: 2016-11-23 
• Deposition Author(s): Gorman, J., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Virus-like Particles Identify an HIV V1V2 Apex-Binding Neutralizing Antibody that Lacks a Protruding Loop.

Cale, E.M., Gorman, J., Radakovich, N.A., Crooks, E.T., Osawa, K., Tong, T., Li, J., Nagarajan, R., Ozorowski, G., Ambrozak, D.R., Asokan, M., Bailer, R.T., Bennici, A.K., Chen, X., Doria-Rose, N.A., Druz, A., Feng, Y., Joyce, M.G., Louder, M.K., O'Dell, S., Oliver, C., Pancera, M., Connors, M., Hope, T.J., Kepler, T.B., Wyatt, R.T., Ward, A.B., Georgiev, I.S., Kwong, P.D., Mascola, J.R., Binley, J.M.

(2017) Immunity 46: 777-791.e10

• PubMed: 28514685 
• DOI: https://doi.org/10.1016/j.immuni.2017.04.011
• Primary Citation Related Structures: 
  5EWI, 5VGJ


• PubMed Abstract: 
  

  Most HIV-1-specific neutralizing antibodies isolated to date exhibit unusual characteristics that complicate their elicitation. Neutralizing antibodies that target the V1V2 apex of the HIV-1 envelope (Env) trimer feature unusually long protruding loops, which enable them to penetrate the HIV-1 glycan shield. As antibodies with loops of requisite length are created through uncommon recombination events, an alternative mode of apex binding has been sought. Here, we isolated a lineage of Env apex-directed neutralizing antibodies, N90-VRC38.01-11, by using virus-like particles and conformationally stabilized Env trimers as B cell probes. A crystal structure of N90-VRC38.01 with a scaffolded V1V2 revealed a binding mode involving side-chain-to-side-chain interactions that reduced the distance the antibody loop must traverse the glycan shield, thereby facilitating V1V2 binding via a non-protruding loop. The N90-VRC38 lineage thus identifies a solution for V1V2-apex binding that provides a more conventional B cell pathway for vaccine design.

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Organizational Affiliation: 
• Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
San Diego Biomedical Research Institute, San Diego, CA 92121, USA.
Sunway University, School of Science and Technology, Department of Biological Sciences, Jalan Universiti, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia.
Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.
HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Department of Cell and Molecular Biology, Feinberg Medical School, Northwestern University, Chicago, IL 60611, USA.
Boston University Department of Microbiology, Boston, MA 02118, USA.
Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: [e-mail].
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: [e-mail].
San Diego Biomedical Research Institute, San Diego, CA 92121, USA. Electronic address: [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)

Macromolecule Content 

• Total Structure Weight: 49.28 kDa 
• Atom Count: 3,935 
• Modeled Residue Count: 438 
• Deposited Residue Count: 456 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC38.01 Heavy Chain	A [auth H]	236	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q6N089 (Homo sapiens) Explore Q6N089  Go to UniProtKB:  Q6N089

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC38.01 Light Chain	B [auth L]	220	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens) Explore P01834  Go to UniProtKB:  P01834
PHAROS:  P01834

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.353	α = 90
b = 84.775	β = 90
c = 90.003	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-23 
Deposition Author(s): Gorman, J., Kwong, P.D.

Revision History  

• Version 1.0: 2016-11-23
  Type: Initial release
  
• Version 1.1: 2017-05-24
  Changes: Database references
• Version 1.2: 2017-05-31
  Changes: Database references
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary