3U7Y

Structure of NIH45-46 Fab in complex with gp120 of 93TH057 HIV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report



Literature

Increasing the Potency and Breadth of an HIV Antibody by Using Structure-Based Rational Design.

Diskin, R.Scheid, J.F.Marcovecchio, P.M.West, A.P.Klein, F.Gao, H.Gnanapragasam, P.N.Abadir, A.Seaman, M.S.Nussenzweig, M.C.Bjorkman, P.J.

(2011) Science 334: 1289-1293

  • DOI: 10.1126/science.1213782
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Antibodies against the CD4 binding site (CD4bs) on the HIV-1 spike protein gp120 can show exceptional potency and breadth. We determined structures of NIH45-46, a more potent clonal variant of VRC01, alone and bound to gp120. Comparisons with VRC01-g ...

    Antibodies against the CD4 binding site (CD4bs) on the HIV-1 spike protein gp120 can show exceptional potency and breadth. We determined structures of NIH45-46, a more potent clonal variant of VRC01, alone and bound to gp120. Comparisons with VRC01-gp120 revealed that a four-residue insertion in heavy chain complementarity-determining region 3 (CDRH3) contributed to increased interaction between NIH45-46 and the gp120 inner domain, which correlated with enhanced neutralization. We used structure-based design to create NIH45-46(G54W), a single substitution in CDRH2 that increases contact with the gp120 bridging sheet and improves breadth and potency, critical properties for potential clinical use, by an order of magnitude. Together with the NIH45-46-gp120 structure, these results indicate that gp120 inner domain and bridging sheet residues should be included in immunogens to elicit CD4bs antibodies.


    Organizational Affiliation

    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NIH45-46 heavy chain, Ig gamma-1 chain C region
H
229Homo sapiensMutation(s): 0 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Go to UniProtKB:  P01857
NIH Common Fund Data Resources
PHAROS  P01857

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
G
361Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: envpol
Find proteins for Q0ED31 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q0ED31

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NIH45-46 light chain, Ig kappa chain C region
L
210Homo sapiensMutation(s): 0 
Gene Names: IGKC
Find proteins for P01834 (Homo sapiens)
Go to UniProtKB:  P01834
NIH Common Fund Data Resources
PHAROS  P01834
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
G, L
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FLC
Query on FLC

Download CCD File 
H
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
G
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
H
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.13α = 90
b = 70.5β = 90
c = 217.74γ = 90
Software Package:
Software NamePurpose
Web-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-12-21
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence, Refinement description