6NF2

Cryo-EM structure of vaccine-elicited antibody 0PV-c.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization.

Kong, R.Duan, H.Sheng, Z.Xu, K.Acharya, P.Chen, X.Cheng, C.Dingens, A.S.Gorman, J.Sastry, M.Shen, C.H.Zhang, B.Zhou, T.Chuang, G.Y.Chao, C.W.Gu, Y.Jafari, A.J.Louder, M.K.O'Dell, S.Rowshan, A.P.Viox, E.G.Wang, Y.Choi, C.W.Corcoran, M.M.Corrigan, A.R.Dandey, V.P.Eng, E.T.Geng, H.Foulds, K.E.Guo, Y.Kwon, Y.D.Lin, B.Liu, K.Mason, R.D.Nason, M.C.Ohr, T.Y.Ou, L.Rawi, R.Sarfo, E.K.Schon, A.Todd, J.P.Wang, S.Wei, H.Wu, W.Mullikin, J.C.Bailer, R.T.Doria-Rose, N.A.Karlsson Hedestam, G.B.Scorpio, D.G.Overbaugh, J.Bloom, J.D.Carragher, B.Potter, C.S.Shapiro, L.Kwong, P.D.Mascola, J.R.

(2019) Cell 178: 567-584.e19

  • DOI: 10.1016/j.cell.2019.06.030
  • Primary Citation of Related Structures:  
    6OSY, 6OT1, 6NF2, 6N16, 6N1V, 6N1W, 6MPH, 6MPG, 6MQS, 6MQR, 6MQM, 6MQC, 6MQE

  • PubMed Abstract: 
  • The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time ...

    The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time. Genetic and structural analyses revealed two of these lineages to belong to a reproducible class capable of neutralizing up to 59% of 208 diverse viral strains. B cell analysis indicated each of the five lineages to have been initiated and expanded by FP-carrier priming, with envelope (Env)-trimer boosts inducing cross-reactive neutralization. These Abs had binding-energy hotspots focused on FP, whereas several FP-directed Abs induced by immunization with Env trimer-only were less FP-focused and less broadly neutralizing. Priming with a conserved subregion, such as FP, can thus induce Abs with binding-energy hotspots coincident with the target subregion and capable of broad neutralization.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA. Electronic address: jmascola@nih.gov.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp120A, G, Q480Human immunodeficiency virus 1Mutation(s): 7 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp41B, I, R153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
VRC03 Heavy ChainC, N, V235Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
VRC03 Light ChainD, M, U209Homo sapiensMutation(s): 0 
Protein Feature View
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
PGT122 Heavy ChainE, J, S235Homo sapiensMutation(s): 0 
Protein Feature View
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
PGT122 Light ChainF, K, T213Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
0PV-c.01 Heavy ChainH, O, W229Homo sapiensMutation(s): 0 
Protein Feature View
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
0PV-c.01 Light ChainL, P, X219Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 9
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AB [auth 0], EB [auth 4], FB [auth 5], GA [auth g], HA [auth h], KA [auth k], MB [auth CA], NB [auth DA]
AB [auth 0], EB [auth 4], FB [auth 5], GA [auth g], HA [auth h], KA [auth k], MB [auth CA], NB [auth DA], OA [auth o], PA [auth p], QB [auth GA], WA [auth w], XA [auth x], Y, Z
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 10
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseAA [auth a], DB [auth 3], GB [auth 6], NA [auth n], QA [auth q], TB [auth JA]4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 11
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseBA [auth b], HB [auth 7], JA [auth j], PB [auth FA], RA [auth r], ZA [auth z]5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 12
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
CA [auth c], CB [auth 2], EA [auth e], IA [auth i], IB [auth 8], KB [auth AA], MA [auth m], OB [auth EA]
CA [auth c], CB [auth 2], EA [auth e], IA [auth i], IB [auth 8], KB [auth AA], MA [auth m], OB [auth EA], SA [auth s], SB [auth IA], UA [auth u], YA [auth y]
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 13
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseDA [auth d], JB [auth 9], TA [auth t]4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 14
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseFA [auth f], LB [auth BA], VA [auth v]6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 15
MoleculeChainsChain Length2D DiagramGlycosylation3D 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)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseBB [auth 1], LA [auth l], RB [auth HA]9N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G68668TB
GlyCosmos:  G68668TB
GlyGen:  G68668TB
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AC [auth Q] , BC [auth R] , CC [auth R] , UB [auth A] , VB [auth B] , WB [auth B] , XB [auth G] , YB [auth I] , 
AC [auth Q],  BC [auth R],  CC [auth R],  UB [auth A],  VB [auth B],  WB [auth B],  XB [auth G],  YB [auth I],  ZB [auth I]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary