7SQ1 | pdb_00007sq1

BG505.MD39TS Env trimer in complex with Fab from antibody C05


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7SQ1

This is version 1.2 of the entry. See complete history

Literature

Induction of tier-2 neutralizing antibodies in mice with a DNA-encoded HIV envelope native like trimer.

Xu, Z.Walker, S.Wise, M.C.Chokkalingam, N.Purwar, M.Moore, A.Tello-Ruiz, E.Wu, Y.Majumdar, S.Konrath, K.M.Kulkarni, A.Tursi, N.J.Zaidi, F.I.Reuschel, E.L.Patel, I.Obeirne, A.Du, J.Schultheis, K.Gites, L.Smith, T.Mendoza, J.Broderick, K.E.Humeau, L.Pallesen, J.Weiner, D.B.Kulp, D.W.

(2022) Nat Commun 13: 695-695

  • DOI: https://doi.org/10.1038/s41467-022-28363-z
  • Primary Citation Related Structures: 
    7SQ1

  • PubMed Abstract: 

    HIV Envelope (Env) is the main vaccine target for induction of neutralizing antibodies. Stabilizing Env into native-like trimer (NLT) conformations is required for recombinant protein immunogens to induce autologous neutralizing antibodies(nAbs) against difficult to neutralize HIV strains (tier-2) in rabbits and non-human primates. Immunizations of mice with NLTs have generally failed to induce tier-2 nAbs. Here, we show that DNA-encoded NLTs fold properly in vivo and induce autologous tier-2 nAbs in mice. DNA-encoded NLTs also uniquely induce both CD4 + and CD8 + T-cell responses as compared to corresponding protein immunizations. Murine neutralizing antibodies are identified with an advanced sequencing technology. The structure of an Env-Ab (C05) complex, as determined by cryo-EM, identifies a previously undescribed neutralizing Env C3/V5 epitope. Beyond potential functional immunity gains, DNA vaccines permit in vivo folding of structured antigens and provide significant cost and speed advantages for enabling rapid evaluation of new HIV vaccines.


  • Organizational Affiliation
    • Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA.

Macromolecule Content 

  • Total Structure Weight: 282.51 kDa 
  • Atom Count: 18,340 
  • Modeled Residue Count: 2,157 
  • Deposited Residue Count: 2,341 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transmembrane protein gp41A [auth B],
C [auth D],
G [auth F]
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160B [auth C],
D [auth E],
H [auth G]
472Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 19
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
C05 Fab Light chainE [auth L],
I
111Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
C05 Fab heavy chainF [auth H],
J [auth A]
122Mus musculusMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose
O
2N/A
Glycosylation Resources
GlyTouCan: G07696MJ
GlyCosmos: G07696MJ
GlyGen: G07696MJ
Entity ID: 7
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-glucopyranoseFA [auth f],
GA [auth g],
U
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 8
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-glucopyranose
V
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AB [auth D]
BB [auth D]
CB [auth E]
DB [auth E]
EB [auth E]
AB [auth D],
BB [auth D],
CB [auth E],
DB [auth E],
EB [auth E],
FB [auth E],
GB [auth E],
HB [auth E],
IB [auth E],
JB [auth E],
KA [auth B],
KB [auth E],
LA [auth B],
LB [auth F],
MA [auth B],
MB [auth F],
NA [auth B],
NB [auth F],
OA [auth C],
OB [auth G],
PA [auth C],
PB [auth G],
QA [auth C],
QB [auth G],
RA [auth C],
RB [auth G],
SA [auth C],
SB [auth G],
TA [auth C],
TB [auth G],
UA [auth C],
UB [auth G],
VA [auth C],
VB [auth G],
WA [auth C],
WB [auth G],
XA [auth C],
XB [auth G],
YA [auth D],
YB [auth G],
ZA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTRosetta

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 Al109646-04

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary