6DCQ

Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design.

Rantalainen, K.Berndsen, Z.T.Murrell, S.Cao, L.Omorodion, O.Torres, J.L.Wu, M.Umotoy, J.Copps, J.Poignard, P.Landais, E.Paulson, J.C.Wilson, I.A.Ward, A.B.

(2018) Cell Rep 23: 3249-3261

  • DOI: 10.1016/j.celrep.2018.05.046
  • Primary Citation of Related Structures:  
    6CA6, 6CA7, 6CA9, 6DCQ

  • PubMed Abstract: 
  • Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system ...

    Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes. Additionally, we observed differences in site-specific glycosylation between soluble and full-length Env constructs, which may be important for tuning optimal immunogenicity in soluble Env trimers. These studies therefore provide important guideposts for design of immunogens that prime and mature nAb responses to the Env V2-apex.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: andrew@scripps.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp160A, C, E480Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for A0A2H4K974 (Human immunodeficiency virus 1)
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Go to UniProtKB:  A0A2H4K974
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp160B, D, F352Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for A0A2H4K974 (Human immunodeficiency virus 1)
Explore A0A2H4K974 
Go to UniProtKB:  A0A2H4K974
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Immunoglobulin G PGT151 Fab, Heavy chainG [auth H], I [auth M]240Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6B291 (Homo sapiens)
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Go to UniProtKB:  S6B291
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Immunoglobulin G PGT151 Fab, Light chainH [auth L], J [auth N]219Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q8TCD0 (Homo sapiens)
Explore Q8TCD0 
Go to UniProtKB:  Q8TCD0
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth G]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D 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], HA [auth h], IA [auth i], JA [auth j], L [auth I]
AA [auth a], BA [auth b], DA [auth d], EA [auth e], HA [auth h], IA [auth i], JA [auth j], L [auth I], LA [auth l], M [auth J], MA [auth m], N [auth K], NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, T, U, W, X, Y, Z
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
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-glucopyranoseS6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseV3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 9
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-glucopyranoseCA [auth c]5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 10
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseFA [auth f]10N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07695ZT
GlyCosmos:  G07695ZT
GlyGen:  G07695ZT
Entity ID: 11
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseGA [auth g], RA [auth r]9N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G61207RZ
GlyCosmos:  G61207RZ
GlyGen:  G61207RZ
Entity ID: 12
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-glucopyranoseKA [auth k]7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07617FP
GlyCosmos:  G07617FP
GlyGen:  G07617FP
Entity ID: 13
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseSA [auth s]9N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G80237PG
GlyCosmos:  G80237PG
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth C] , BB [auth C] , CB [auth C] , DB [auth C] , EB [auth C] , FB [auth D] , GB [auth D] , HB [auth E] , 
AB [auth C],  BB [auth C],  CB [auth C],  DB [auth C],  EB [auth C],  FB [auth D],  GB [auth D],  HB [auth E],  IB [auth E],  JB [auth E],  KB [auth E],  LB [auth E],  MB [auth F],  NB [auth F],  TA [auth A],  UA [auth A],  VA [auth A],  WA [auth A],  XA [auth B],  YA [auth B],  ZA [auth B]
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: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-05-08 
  • Released Date: 2018-06-27 
  • Deposition Author(s): Rantalainen, K.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesUM1 AI100663
International AIDS Vaccine InitiativeUnited StatesOPP1084519
Bill & Melinda Gates FoundationUnited StatesOPP1115782

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary