3MLR | pdb_00003mlr

Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a NY5 V3 peptide

• PDB DOI: https://doi.org/10.2210/pdb3MLR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
• Mutation(s): No 


• Deposited: 2010-04-18 Released: 2010-07-14 
• Deposition Author(s): Kong, X.-P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 

Literature

Conserved structural elements in the V3 crown of HIV-1 gp120.

Jiang, X., Burke, V., Totrov, M., Williams, C., Cardozo, T., Gorny, M.K., Zolla-Pazner, S., Kong, X.P.

(2010) Nat Struct Mol Biol 17: 955-961

• PubMed: 20622876 
• DOI: https://doi.org/10.1038/nsmb.1861
• Primary Citation Related Structures: 
  3GO1, 3MLR, 3MLS, 3MLT, 3MLU, 3MLV, 3MLW, 3MLX, 3MLY, 3MLZ


• PubMed Abstract: 
  

  Binding of the third variable region (V3) of the HIV-1 envelope glycoprotein gp120 to the cell-surface coreceptors CCR5 or CXCR4 during viral entry suggests that there are conserved structural elements in this sequence-variable region. These conserved elements could serve as epitopes to be targeted by a vaccine against HIV-1. Here we perform a systematic structural analysis of representative human anti-V3 monoclonal antibodies in complex with V3 peptides, revealing that the crown of V3 has four conserved structural elements: an arch, a band, a hydrophobic core and the peptide backbone. These are either unaffected by or are subject to minimal sequence variation. As these regions are targeted by cross-clade neutralizing human antibodies, they provide a blueprint for the design of vaccine immunogens that could elicit broadly cross-reactive protective antibodies.

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Organizational Affiliation: 
• Department of Biochemistry, New York University School of Medicine, New York, New York, 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.72 kDa 
• Atom Count: 3,927 
• Modeled Residue Count: 459 
• Deposited Residue Count: 465 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain	A [auth L]	219	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain	B [auth H]	226	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 gp120 third variable region (V3) crown	C [auth P]	20	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	Mutation(s): 0
UniProt
Find proteins for P12490 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12490  Go to UniProtKB:  P12490

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.414	α = 87.86
b = 43.076	β = 85.5
c = 58.212	γ = 85.82

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-14 
Deposition Author(s): Kong, X.-P.

Revision History  

• Version 1.0: 2010-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary