8E1P | pdb_00008e1p

Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex with gl-PGV20 and PGT124 Fabs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.82 Å
  • R-Value Free: 
    0.301 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.271 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.272 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Germline-targeting HIV-1 Env vaccination induces VRC01-class antibodies with rare insertions.

Caniels, T.G.Medina-Ramirez, M.Zhang, J.Sarkar, A.Kumar, S.LaBranche, A.Derking, R.Allen, J.D.Snitselaar, J.L.Capella-Pujol, J.Sanchez, I.D.M.Yasmeen, A.Diaz, M.Aldon, Y.Bijl, T.P.L.Venkatayogi, S.Martin Beem, J.S.Newman, A.Jiang, C.Lee, W.H.Pater, M.Burger, J.A.van Breemen, M.J.de Taeye, S.W.Rantalainen, K.LaBranche, C.Saunders, K.O.Montefiori, D.Ozorowski, G.Ward, A.B.Crispin, M.Moore, J.P.Klasse, P.J.Haynes, B.F.Wilson, I.A.Wiehe, K.Verkoczy, L.Sanders, R.W.

(2023) Cell Rep Med 4: 101003-101003

  • DOI: https://doi.org/10.1016/j.xcrm.2023.101003
  • Primary Citation Related Structures: 
    8E1P

  • PubMed Abstract: 

    Targeting germline (gl-) precursors of broadly neutralizing antibodies (bNAbs) is acknowledged as an important strategy for HIV-1 vaccines. The VRC01-class of bNAbs is attractive because of its distinct genetic signature. However, VRC01-class bNAbs often require extensive somatic hypermutation, including rare insertions and deletions. We describe a BG505 SOSIP trimer, termed GT1.2, to optimize binding to gl-CH31, the unmutated common precursor of the CH30-34 bNAb lineage that acquired a large CDRH1 insertion. The GT1.2 trimer activates gl-CH31 naive B cells in knock-in mice, and B cell responses could be matured by selected boosting immunogens to generate cross-reactive Ab responses. Next-generation B cell sequencing reveals selection for VRC01-class mutations, including insertions in CDRH1 and FWR3 at positions identical to VRC01-class bNAbs, as well as CDRL1 deletions and/or glycine substitutions to accommodate the N276 glycan. These results provide proof of concept for vaccine-induced affinity maturation of B cell lineages that require rare insertions and deletions.


  • Organizational Affiliation
    • Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands.

Macromolecule Content 

  • Total Structure Weight: 514.28 kDa 
  • Atom Count: 34,410 
  • Modeled Residue Count: 4,320 
  • Deposited Residue Count: 4,536 
  • Unique protein chains: 7

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
germline PGV20 heavy chainA [auth F],
B [auth H],
E [auth N]
225Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
germline PGV20 light chainC [auth I]210Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
germline PGV20 light chainD [auth L],
F [auth O]
210Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT124 Fab Light ChainG [auth A],
H [auth C],
K [auth J]
214Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
BG505-SOSIP.v4.1-GT1.2gp120I [auth E],
J [auth G],
L [auth M]
474Human immunodeficiency virus 1Mutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT124 Fab Heavy ChainM [auth B],
N [auth D],
O [auth K]
236Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41P [auth Y],
Q [auth X],
R [auth Z]
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: 2
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 8
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-glucopyranoseCA [auth c],
EA [auth e],
S [auth P],
X [auth U]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
DA [auth d],
FA [auth f],
IA [auth i],
T [auth Q],
BA [auth b],
DA [auth d],
FA [auth f],
IA [auth i],
T [auth Q],
V [auth S],
W [auth T],
Y [auth V],
Z [auth W]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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-glucopyranoseU [auth R]7N-Glycosylation
Glycosylation Resources
GlyTouCan: G46836GH
GlyCosmos: G46836GH
GlyGen: G46836GH
Entity ID: 11
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseAA [auth a]9N-Glycosylation
Entity ID: 12
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-glucopyranoseGA [auth g]6N-Glycosylation
Glycosylation Resources
GlyTouCan: G94106MV
GlyCosmos: G94106MV
GlyGen: G94106MV
Entity ID: 13
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranoseHA [auth h]3N/A
Glycosylation Resources
GlyTouCan: G25559RS
GlyCosmos: G25559RS
GlyGen: G25559RS

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
AB [auth M]
BB [auth M]
CB [auth M]
DB [auth M]
EB [auth M]
AB [auth M],
BB [auth M],
CB [auth M],
DB [auth M],
EB [auth M],
FB [auth M],
GB [auth Y],
HB [auth Y],
IB [auth Y],
JA [auth E],
JB [auth X],
KA [auth E],
KB [auth X],
LA [auth E],
LB [auth Z],
MA [auth E],
MB [auth Z],
NA [auth E],
OA [auth E],
PA [auth E],
QA [auth E],
RA [auth G],
SA [auth G],
TA [auth G],
UA [auth G],
VA [auth G],
WA [auth G],
XA [auth G],
YA [auth M],
ZA [auth M]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.82 Å
  • R-Value Free:  0.301 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.271 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 0.272 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.057α = 90
b = 157.666β = 102.973
c = 158.558γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction
Cootmodel building
PHENIXphasing
Aimlessdata scaling

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: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary