7RDW | pdb_00007rdw

Crystal Structure of FH1 Fab bound to HXb2 HIV-1 gp120 core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 
    0.295 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.260 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 
    0.262 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Characterization of a vaccine-elicited human antibody with sequence homology to VRC01-class antibodies that binds the C1C2 gp120 domain.

Gray, M.D.Feng, J.Weidle, C.E.Cohen, K.W.Ballweber-Fleming, L.MacCamy, A.J.Huynh, C.N.Trichka, J.J.Montefiori, D.Ferrari, G.Pancera, M.McElrath, M.J.Stamatatos, L.

(2022) Sci Adv 8: eabm3948-eabm3948

  • DOI: https://doi.org/10.1126/sciadv.abm3948
  • Primary Citation Related Structures: 
    7RDW

  • PubMed Abstract: 

    Broadly HIV-1-neutralizing VRC01-class antibodies bind the CD4-binding site of Env and contain V H 1-2*02-derived heavy chains paired with light chains expressing five-amino acid-long CDRL3s. Their unmutated germline forms do not recognize HIV-1 Env, and their lack of elicitation in human clinical trials could be due to the absence of activation of the corresponding naïve B cells by the vaccine immunogens. To address this point, we examined Env-specific B cell receptor sequences from participants in the HVTN 100 clinical trial. Of all the sequences analyzed, only one displayed homology to VRC01-class antibodies, but the corresponding antibody (FH1) recognized the C1C2 gp120 domain. For FH1 to switch epitope recognition to the CD4-binding site, alterations in the CDRH3 and CDRL3 were necessary. Only germ line-targeting Env immunogens efficiently activated VRC01 B cells, even in the presence of FH1 B cells. Our findings support the use of these immunogens to activate VRC01 B cells in humans.


  • Organizational Affiliation
    • Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

Macromolecule Content 

  • Total Structure Weight: 365.29 kDa 
  • Atom Count: 21,960 
  • Modeled Residue Count: 2,973 
  • Deposited Residue Count: 3,236 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoprotein 120A [auth C],
B [auth D],
G [auth M],
H [auth N]
373Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04578 
Go to UniProtKB:  P04578
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04578
Glycosylation
Glycosylation Sites: 11
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
FH1 Fab Heavy ChainC [auth G],
K [auth U]
225Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
FH1 Fab Heavy ChainD [auth H],
I [auth Q]
225Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
FH1 Fab Light ChainE [auth I],
F [auth L],
J [auth R],
L [auth V]
211Homo sapiensMutation(s): 0 

Oligosaccharides

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Entity ID: 5
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-glucopyranoseM [auth O],
N [auth c],
O [auth m],
P [auth y]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AB [auth N]
BB [auth N]
CA [auth D]
CB [auth N]
DA [auth D]
AB [auth N],
BB [auth N],
CA [auth D],
CB [auth N],
DA [auth D],
DB [auth N],
EA [auth D],
FA [auth D],
GA [auth D],
NA [auth M],
OA [auth M],
PA [auth M],
Q [auth C],
QA [auth M],
R [auth C],
RA [auth M],
S [auth C],
SA [auth M],
T [auth C],
U [auth C],
UA [auth N],
V [auth C],
VA [auth N],
W [auth C],
WA [auth N],
XA [auth N],
YA [auth N],
ZA [auth N]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
BA [auth C],
JA [auth D],
TA [auth M]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth C]
EB [auth N]
IA [auth D]
KA [auth H]
LA [auth H]
AA [auth C],
EB [auth N],
IA [auth D],
KA [auth H],
LA [auth H],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NH4

Query on NH4



Download:Ideal Coordinates CCD File
HA [auth D],
MA [auth I],
X [auth C],
Y [auth C]
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
C [auth G],
K [auth U]
L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free:  0.295 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.260 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 0.262 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.361α = 67.566
b = 106.266β = 76.674
c = 113.219γ = 60.987
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary