4R2G

Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural Evolution of Glycan Recognition by a Family of Potent HIV Antibodies.

Garces, F.Sok, D.Kong, L.McBride, R.Kim, H.J.Saye-Francisco, K.F.Julien, J.P.Hua, Y.Cupo, A.Moore, J.P.Paulson, J.C.Ward, A.B.Burton, D.R.Wilson, I.A.

(2014) Cell 159: 69-79

  • DOI: 10.1016/j.cell.2014.09.009
  • Primary Citation of Related Structures:  
    4R2G, 4R26

  • PubMed Abstract: 
  • The HIV envelope glycoprotein (Env) is densely covered with self-glycans that should help shield it from recognition by the human immune system. Here, we examine how a particularly potent family of broadly neutralizing antibodies (Abs) has evolved common and distinct structural features to counter the glycan shield and interact with both glycan and protein components of HIV Env ...

    The HIV envelope glycoprotein (Env) is densely covered with self-glycans that should help shield it from recognition by the human immune system. Here, we examine how a particularly potent family of broadly neutralizing antibodies (Abs) has evolved common and distinct structural features to counter the glycan shield and interact with both glycan and protein components of HIV Env. The inferred germline antibody already harbors potential binding pockets for a glycan and a short protein segment. Affinity maturation then leads to divergent evolutionary branches that either focus on a single glycan and protein segment (e.g., Ab PGT124) or engage multiple glycans (e.g., Abs PGT121-123). Furthermore, other surrounding glycans are avoided by selecting an appropriate initial antibody shape that prevents steric hindrance. Such molecular recognition lessons are important for engineering proteins that can recognize or accommodate glycans.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: wilson@scripps.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Surface protein gp160O [auth A], A [auth E], P [auth K], N [auth O]309Human immunodeficiency virus type 1 (JRCSF ISOLATE)Mutation(s): 0 
Gene Names: env
Find proteins for P20871 (Human immunodeficiency virus type 1 group M subtype B (isolate JRCSF))
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Go to UniProtKB:  P20871
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD4E [auth B], B [auth F], H, K [auth L]184Homo sapiensMutation(s): 0 
Gene Names: CD4
Find proteins for P01730 (Homo sapiens)
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Go to UniProtKB:  P01730
NIH Common Fund Data Resources
PHAROS:  P01730
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PGT124 Light ChainF [auth C], I, L [auth M], C [auth P]214Homo sapiensMutation(s): 0 
Gene Names: IGL@IGLC3
Find proteins for P0DOY3 (Homo sapiens)
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Go to UniProtKB:  P0DOY3
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PGT124 Heavy ChainG [auth D], J, M [auth N], D [auth Q]236Homo sapiensMutation(s): 0 
Gene Names: IGH@
Find proteins for P0DOX5 (Homo sapiens)
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Go to UniProtKB:  P0DOX5
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseQ [auth G], R, S, V10 N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseT, U2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth E] , AB [auth K] , BA [auth E] , BB [auth K] , CA [auth E] , CB [auth K] , DA [auth E] , JA [auth O] , 
AA [auth E],  AB [auth K],  BA [auth E],  BB [auth K],  CA [auth E],  CB [auth K],  DA [auth E],  JA [auth O],  KA [auth O],  LA [auth O],  MA [auth O],  NA [auth O],  OA [auth O],  PA [auth O],  RA [auth A],  SA [auth A],  TA [auth A],  UA [auth A],  VA [auth A],  W [auth E],  WA [auth A],  X [auth E],  Y [auth E],  YA [auth K],  Z [auth E],  ZA [auth K]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
FA [auth Q], GA [auth D], HA [auth J], IA [auth N]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
DB [auth K], EA [auth E], QA [auth O], XA [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.406α = 90
b = 165.438β = 90
c = 229.712γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Derived calculations
  • Version 1.2: 2017-06-21
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary