3P30 | pdb_00003p30

crystal structure of the cluster II Fab 1281 in complex with HIV-1 gp41 ectodomain

• PDB DOI: https://doi.org/10.2210/pdb3P30/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Homo sapiens
• Mutation(s): No 


• Deposited: 2010-10-04 Released: 2010-11-17 
• Deposition Author(s): Frey, G., Chen, J., Rits-Volloch, S., Freeman, M.M., Zolla-Pazner, S., Chen, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.289 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.261 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

Literature

Distinct conformational states of HIV-1 gp41 are recognized by neutralizing and non-neutralizing antibodies.

Frey, G., Chen, J., Rits-Volloch, S., Freeman, M.M., Zolla-Pazner, S., Chen, B.

(2010) Nat Struct Mol Biol 17: 1486-1491

• PubMed: 21076402 
• DOI: https://doi.org/10.1038/nsmb.1950
• Primary Citation Related Structures: 
  3P30


• PubMed Abstract: 
  

  HIV-1 envelope glycoprotein gp41 undergoes large conformational changes to drive fusion of viral and target cell membranes, adopting at least three distinct conformations during the viral entry process. Neutralizing antibodies against gp41 block HIV-1 infection by targeting gp41's membrane-proximal external region in a fusion-intermediate state. Here we report biochemical and structural evidence that non-neutralizing antibodies, capable of binding with high affinity to an immunodominant segment adjacent to the neutralizing epitopes in the membrane-proximal region, recognize a gp41 conformation that exists only when membrane fusion is complete. We propose that these non-neutralizing antibodies are induced in HIV-1-infected individuals by gp41 in a triggered, postfusion form and contribute to production of ineffective humoral responses. These results have important implications for gp41-based vaccine design.

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Organizational Affiliation: 
• Division of Molecular Medicine, Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.78 kDa 
• Atom Count: 3,770 
• Modeled Residue Count: 521 
• Deposited Residue Count: 535 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 gp41	A	96	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: HIV-1 ENV

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1281 Fab light chain	B [auth L]	213	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
1281 Fab heavy chain	C [auth H]	226	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.289 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.261 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.83	α = 90
b = 115.83	β = 90
c = 119.544	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Frey, G., Chen, J., Rits-Volloch, S., Freeman, M.M., Zolla-Pazner, S., Chen, B.

Revision History  

• Version 1.0: 2010-11-17
  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