6P65 | pdb_00006p65

HIV Env 16055 NFL TD 2CC+ in complex with antibody 1C2 fragment antigen binding


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6P65

This is version 2.1 of the entry. See complete history

Literature

Vaccination with Glycan-Modified HIV NFL Envelope Trimer-Liposomes Elicits Broadly Neutralizing Antibodies to Multiple Sites of Vulnerability.

Dubrovskaya, V.Tran, K.Ozorowski, G.Guenaga, J.Wilson, R.Bale, S.Cottrell, C.A.Turner, H.L.Seabright, G.O'Dell, S.Torres, J.L.Yang, L.Feng, Y.Leaman, D.P.Vazquez Bernat, N.Liban, T.Louder, M.McKee, K.Bailer, R.T.Movsesyan, A.Doria-Rose, N.A.Pancera, M.Karlsson Hedestam, G.B.Zwick, M.B.Crispin, M.Mascola, J.R.Ward, A.B.Wyatt, R.T.

(2019) Immunity 51: 915-929.e7

  • DOI: https://doi.org/10.1016/j.immuni.2019.10.008
  • Primary Citation Related Structures: 
    6P62, 6P65, 6PEH

  • PubMed Abstract: 

    The elicitation of broadly neutralizing antibodies (bNAbs) against the HIV-1 envelope glycoprotein (Env) trimer remains a major vaccine challenge. Most cross-conserved protein determinants are occluded by self-N-glycan shielding, limiting B cell recognition of the underlying polypeptide surface. The exceptions to the contiguous glycan shield include the conserved receptor CD4 binding site (CD4bs) and glycoprotein (gp)41 elements proximal to the furin cleavage site. Accordingly, we performed heterologous trimer-liposome prime:boosting in rabbits to drive B cells specific for cross-conserved sites. To preferentially expose the CD4bs to B cells, we eliminated proximal N-glycans while maintaining the native-like state of the cleavage-independent NFL trimers, followed by gradual N-glycan restoration coupled with heterologous boosting. This approach successfully elicited CD4bs-directed, cross-neutralizing Abs, including one targeting a unique glycan-protein epitope and a bNAb (87% breadth) directed to the gp120:gp41 interface, both resolved by high-resolution cryoelectron microscopy. This study provides proof-of-principle immunogenicity toward eliciting bNAbs by vaccination.


  • Organizational Affiliation
    • Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 412.03 kDa 
  • Atom Count: 20,319 
  • Modeled Residue Count: 2,379 
  • Deposited Residue Count: 3,522 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV Env 16055 NFL TD 2CC+A,
D [auth B],
G [auth E]
680Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for A1EAI1 (Human immunodeficiency virus type 1)
Explore A1EAI1 
Go to UniProtKB:  A1EAI1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1EAI1
Glycosylation
Glycosylation Sites: 22
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Rabbit antibody 1C2 heavy chain fragment antigen bindingB [auth H],
E [auth C],
H [auth F]
259Oryctolagus cuniculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Rabbit antibody 1C2 kappa chainC [auth L],
F [auth D],
I [auth G]
235Oryctolagus cuniculusMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
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-glucopyranose
FA [auth f],
J [auth I],
NA [auth n],
Q,
UA [auth u],
FA [auth f],
J [auth I],
NA [auth n],
Q,
UA [auth u],
Y
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
AB [auth 0],
BA [auth b],
CA [auth c],
DA [auth d],
AA [auth a],
AB [auth 0],
BA [auth b],
CA [auth c],
DA [auth d],
EA [auth e],
GA [auth g],
IA [auth i],
JA [auth j],
K [auth J],
KA [auth k],
L [auth K],
LA [auth l],
M,
N,
O,
OA [auth o],
P,
PA [auth p],
QA [auth q],
R,
RA [auth r],
SA [auth s],
T,
TA [auth t],
U,
V,
VA [auth v],
W,
XA [auth x],
YA [auth y],
Z,
ZA [auth z]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 6
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-glucopyranoseHA [auth h],
S,
WA [auth w]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseBB [auth 1],
MA [auth m],
X
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
CB [auth A]
DB [auth A]
EB [auth A]
FB [auth A]
GB [auth A]
CB [auth A],
DB [auth A],
EB [auth A],
FB [auth A],
GB [auth A],
HB [auth A],
IB [auth A],
JB [auth B],
KB [auth B],
LB [auth B],
MB [auth B],
NB [auth B],
OB [auth B],
PB [auth B],
QB [auth E],
RB [auth E],
SB [auth E],
TB [auth E],
UB [auth E],
VB [auth E],
WB [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta3.10
RECONSTRUCTIONRELION3.0

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)United StatesUM AI100663
Bill & Melinda Gates FoundationUnited StatesOPP1115782
Bill & Melinda Gates FoundationUnited StatesOPP1084519
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI136621

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2020-04-01
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary