6NFC

BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precursor HMP42 fragmentantigen binding and base-binding RM20A3 fragment antigen binding


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses.

Steichen, J.M.Lin, Y.C.Havenar-Daughton, C.Pecetta, S.Ozorowski, G.Willis, J.R.Toy, L.Sok, D.Liguori, A.Kratochvil, S.Torres, J.L.Kalyuzhniy, O.Melzi, E.Kulp, D.W.Raemisch, S.Hu, X.Bernard, S.M.Georgeson, E.Phelps, N.Adachi, Y.Kubitz, M.Landais, E.Umotoy, J.Robinson, A.Briney, B.Wilson, I.A.Burton, D.R.Ward, A.B.Crotty, S.Batista, F.D.Schief, W.R.

(2019) Science 366

  • DOI: https://doi.org/10.1126/science.aax4380
  • Primary Citation of Related Structures:  
    6DFG, 6DFH, 6NF5, 6NFC, 6OC7

  • PubMed Abstract: 

    Vaccine induction of broadly neutralizing antibodies (bnAbs) to HIV remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for most bnAbs, a strong dependence on antibody heavy chain complementarity-determining region 3 (HCDR3) is a major barrier. Exploiting ultradeep human antibody sequencing data, we identified a diverse set of potential antibody precursors for a bnAb with dominant HCDR3 contacts. We then developed HIV envelope trimer-based immunogens that primed responses from rare bnAb-precursor B cells in a mouse model and bound a range of potential bnAb-precursor human naïve B cells in ex vivo screens. Our repertoire-guided germline-targeting approach provides a framework for priming the induction of many HIV bnAbs and could be applied to most HCDR3-dominant antibodies from other pathogens.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
base-binding RM20A3 fragment antigen binding heavy chainA [auth C],
G [auth J],
M [auth K]
125Macaca mulattaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
base-binding RM20A3 fragment antigen binding light chainB [auth D],
H [auth M],
N
128Macaca mulattaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 Env BG505 MD64 N332-GT5 SOSIP gp120C [auth A],
I [auth E],
K [auth F]
481Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
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Go to UniProtKB:  Q2N0S6
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UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 15
Sequence Annotations
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 Env BG505 MD64 N332-GT5 SOSIP gp41D [auth B],
J [auth G],
L [auth I]
162Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
BG18-like precursor HMP42 fragment antigen binding heavy chainE [auth H]128Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
BG18-like precursor HMP42 fragment antigen binding light chainF [auth L]108Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BA [auth b],
DA [auth d],
EA [auth e],
FA [auth f],
AA [auth a],
BA [auth b],
DA [auth d],
EA [auth e],
FA [auth f],
O,
P,
R,
S,
T,
U,
V,
X,
Y,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranoseCA [auth c],
Q,
W
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 E]
BB [auth E]
CB [auth E]
DB [auth G]
EB [auth G]
AB [auth E],
BB [auth E],
CB [auth E],
DB [auth G],
EB [auth G],
FB [auth G],
GA [auth A],
GB [auth F],
HA [auth A],
HB [auth F],
IA [auth A],
IB [auth F],
JA [auth A],
JB [auth F],
KA [auth A],
KB [auth F],
LA [auth A],
LB [auth F],
MA [auth A],
MB [auth F],
NA [auth A],
NB [auth F],
OA [auth A],
OB [auth F],
PA [auth A],
PB [auth F],
QA [auth B],
QB [auth I],
RA [auth B],
RB [auth I],
SA [auth B],
SB [auth I],
TA [auth E],
UA [auth E],
VA [auth E],
WA [auth E],
XA [auth E],
YA [auth E],
ZA [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: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTRosetta3.10

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 StatesUM1 AI100663
Bill & Melinda Gates FoundationUnited StatesOPP1115782
Bill & Melinda Gates FoundationUnited StatesOPP1084519

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary