8D53 | pdb_00008d53

Crystal Structure of Mosaic HIV-1 Envelope (MosM3.3) in Complex with antibodies PGT124 and 35O22 at 3.25 Angstrom

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 
    0.331 (Depositor), 0.308 (DCC) 
  • R-Value Work: 
    0.317 (Depositor), 0.317 (DCC) 
  • R-Value Observed: 
    0.318 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history. 

Literature

Structural and Antigenic Characterization of B Cell Mosaic Env Trimers

Xian, Y., Wilson, I.A.

To be published.

Macromolecule Content 

  • Total Structure Weight: 147.71 kDa 
  • Atom Count: 10,333 
  • Modeled Residue Count: 1,243 
  • Deposited Residue Count: 1,243 
  • Unique protein chains: 6

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120A [auth G]446Human immunodeficiency virus 1Mutation(s): 0 
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41132Human immunodeficiency virus 1Mutation(s): 0 
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT124 Fab Light ChainC [auth L]212Homo sapiensMutation(s): 0 
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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT124 Fab Heavy ChainD [auth H]229Homo sapiensMutation(s): 0 
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|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
35O22scFV Heavy chain variableE [auth D]117Homo sapiensMutation(s): 0 
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|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
35O22scFv Light Chain VariableF [auth E]107Homo sapiensMutation(s): 0 

Oligosaccharides

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Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G [auth A],
H [auth C],
L [auth K],
M,
Q,
G [auth A],
H [auth C],
L [auth K],
M,
Q,
R
2N/AN-Glycosylation
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth F]9N/AN-Glycosylation
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth I],
P,
S		3N/AN-Glycosylation
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth J]4N/AN-Glycosylation
Entity ID: 11
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(5-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N
6N/AN-Glycosylation
Entity ID: 12
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(6-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
O
5N/AN-Glycosylation

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free:  0.331 (Depositor), 0.308 (DCC) 
  • R-Value Work:  0.317 (Depositor), 0.317 (DCC) 
  • R-Value Observed: 0.318 (Depositor) 
Space Group: P 3 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.266α = 90
b = 139.266β = 90
c = 320.332γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
International AIDS Vaccine InitiativeUnited StatesINV-008352/OPP1153692
Consortia for HIV/AIDS Vaccine DevelopmentUnited StatesCHAVD 1UM1 AI144462
Other private2 P01 AI110657

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Structure summary
  • Version 1.2: 2026-03-04
    Changes: Refinement description