1NAK | pdb_00001nak

IGG1 FAB FRAGMENT (83.1) COMPLEX WITH 16-RESIDUE PEPTIDE (RESIDUES 304-321 OF HIV-1 GP120 (MN ISOLATE))

• PDB DOI: https://doi.org/10.2210/pdb1NAK/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Human immunodeficiency virus type 1 group M subtype B (isolate MN)
• Mutation(s): No 


• Deposited: 2002-11-27 Released: 2003-11-18 
• Deposition Author(s): Stanfield, R.L., Ghiara, J.B., Saphire, E.O., Profy, A.T., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.326 (Depositor), 0.329 (DCC) 
• R-Value Work: 
  0.288 (Depositor), 0.290 (DCC) 

Starting Model: experimental

Literature

Recurring conformation of the human immunodeficiency virus type 1 gp120 V3 loop.

Stanfield, R.L., Ghiara, J.B., Ollmann Saphire, E., Profy, A.T., Wilson, I.A.

(2003) Virology 315: 159-173

• PubMed: 14592768 
• DOI: https://doi.org/10.1016/s0042-6822(03)00525-7
• Primary Citation Related Structures: 
  1NAK


• PubMed Abstract: 
  

  The crystal structure of the human immunodeficiency virus type 1 (HIV-1) neutralizing, murine Fab 83.1 in complex with an HIV-1 gp120 V3 peptide has been determined to 2.57 A resolution. The conformation of the V3 loop peptide in complex with Fab 83.1 is very similar to V3 conformations seen previously with two other neutralizing Fabs, 50.1 and 59.1. The repeated identification of this same V3 conformation in complex with three very different, neutralizing antibodies indicates that it is a highly preferred structure for V3 loops on some strains of the HIV-1 virus.

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Organizational Affiliation: 
• Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 98.15 kDa 
• Atom Count: 6,877 
• Modeled Residue Count: 882 
• Deposited Residue Count: 898 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 83.1 - light chain	A [auth L], D [auth M]	219	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 83.1 - heavy chain	B [auth H], E [auth I]	214	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide MP1	C [auth P], F [auth Q]	16	N/A	Mutation(s): 0
UniProt
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B (isolate MN)) Explore P05877  Go to UniProtKB:  P05877

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.326 (Depositor), 0.329 (DCC) 
• R-Value Work:  0.288 (Depositor), 0.290 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.511	α = 90
b = 122.597	β = 108.54
c = 69.464	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-18 
Deposition Author(s): Stanfield, R.L., Ghiara, J.B., Saphire, E.O., Profy, A.T., Wilson, I.A.

Revision History  

• Version 1.0: 2003-11-18
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-09-03
  Changes: Structure summary
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary