6VPX

Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and three 10E8 Fabs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 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

HIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies.

Rantalainen, K.Berndsen, Z.T.Antanasijevic, A.Schiffner, T.Zhang, X.Lee, W.H.Torres, J.L.Zhang, L.Irimia, A.Copps, J.Zhou, K.H.Kwon, Y.D.Law, W.H.Schramm, C.A.Verardi, R.Krebs, S.J.Kwong, P.D.Doria-Rose, N.A.Wilson, I.A.Zwick, M.B.Yates 3rd, J.R.Schief, W.R.Ward, A.B.

(2020) Cell Rep 31: 107583-107583

  • DOI: 10.1016/j.celrep.2020.107583
  • Primary Citation of Related Structures:  
    6VPX

  • PubMed Abstract: 
  • Structural and functional studies of HIV envelope glycoprotein (Env) as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the membrane-embedded hydrophobic regions. Here, we present approaches for incorporating full-length, wild-type HIV-1 Env, as well as C-terminally truncated and stabilized versions, into lipid assemblies, providing a modular platform for Env structural studies by single particle electron microscopy ...

    Structural and functional studies of HIV envelope glycoprotein (Env) as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the membrane-embedded hydrophobic regions. Here, we present approaches for incorporating full-length, wild-type HIV-1 Env, as well as C-terminally truncated and stabilized versions, into lipid assemblies, providing a modular platform for Env structural studies by single particle electron microscopy. We reconstitute a full-length Env clone into a nanodisc, complex it with a membrane-proximal external region (MPER) targeting antibody 10E8, and structurally define the full quaternary epitope of 10E8 consisting of lipid, MPER, and ectodomain contacts. By aligning this and other Env-MPER antibody complex reconstructions with the lipid bilayer, we observe evidence of Env tilting as part of the neutralization mechanism for MPER-targeting antibodies. We also adapt the platform toward vaccine design purposes by introducing stabilizing mutations that allow purification of unliganded Env with a peptidisc scaffold.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, 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 gp120A, C, B [auth E]465Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for B9V6B3 (Human immunodeficiency virus 1)
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Go to UniProtKB:  B9V6B3
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp41E [auth B], D, F153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for B0FAM5 (Human immunodeficiency virus 1)
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Go to UniProtKB:  B0FAM5
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody 10E8 Fab heavy chainG [auth H], J [auth K], M129Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody 10E8 Fab light chainH [auth L], K [auth N], N [auth O]108Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
MPER peptideI [auth G], L [auth I], O [auth J]17Homo sapiensMutation(s): 0 
UniProt
Find proteins for P05880 (Human immunodeficiency virus type 1 group M subtype B (isolate WMJ22))
Explore P05880 
Go to UniProtKB:  P05880
Protein Feature View
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody PGT151 Fab heavy chainP134Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody PGT151 Fab light chainQ109Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 8
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], FA [auth f], IA [auth i], R, T
AA [auth a], BA [auth b], DA [auth d], EA [auth e], FA [auth f], IA [auth i], R, T, U, V, X, Z
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 9
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseS2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G35932AR
GlyCosmos:  G35932AR
GlyGen:  G35932AR
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-glucopyranoseW4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 11
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseCA [auth c], Y3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 12
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-glucopyranoseGA [auth g]5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 13
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseHA [auth h], NA [auth n]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 14
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseJA [auth j], KA [auth k]3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 15
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[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-glucopyranoseLA [auth l]9N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42672MA
GlyCosmos:  G42672MA
GlyGen:  G42672MA
Entity ID: 16
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseMA [auth m]8N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G04744XB
GlyCosmos:  G04744XB
GlyGen:  G04744XB
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
44E (Subject of Investigation/LOI)
Query on 44E

Download Ideal Coordinates CCD File 
FC [auth L], GC [auth N], HC [auth O](2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate
C15 H29 O8 P
SFZZRGHNPILUOD-CYBMUJFWSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth E] , AC [auth D] , BB [auth E] , BC [auth F] , CB [auth E] , CC [auth F] , DB [auth E] , DC [auth F] , 
AB [auth E],  AC [auth D],  BB [auth E],  BC [auth F],  CB [auth E],  CC [auth F],  DB [auth E],  DC [auth F],  EB [auth E],  EC [auth F],  FB [auth E],  GB [auth E],  HB [auth E],  IB [auth E],  JB [auth E],  KB [auth E],  LB [auth E],  MB [auth E],  NB [auth C],  OA [auth A],  OB [auth C],  PA [auth A],  PB [auth C],  QA [auth A],  QB [auth C],  RA [auth A],  RB [auth C],  SA [auth A],  SB [auth C],  TA [auth A],  TB [auth C],  UA [auth A],  UB [auth C],  VA [auth A],  VB [auth C],  WA [auth A],  WB [auth C],  XA [auth E],  XB [auth C],  YA [auth E],  YB [auth C],  ZA [auth E],  ZB [auth C]
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: 5.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesUM1AI100663
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1AI144462
Bill & Melinda Gates FoundationUnited StatesOPP1115782

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary