6UDJ

HIV-1 bNAb 1-18 in complex with BG505 SOSIP.664 and 10-1074


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 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

Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody.

Schommers, P.Gruell, H.Abernathy, M.E.Tran, M.K.Dingens, A.S.Gristick, H.B.Barnes, C.O.Schoofs, T.Schlotz, M.Vanshylla, K.Kreer, C.Weiland, D.Holtick, U.Scheid, C.Valter, M.M.van Gils, M.J.Sanders, R.W.Vehreschild, J.J.Cornely, O.A.Lehmann, C.Fatkenheuer, G.Seaman, M.S.Bloom, J.D.Bjorkman, P.J.Klein, F.

(2020) Cell 180: 471

  • DOI: 10.1016/j.cell.2020.01.010
  • Primary Citation of Related Structures:  
    6UDJ, 6UDK

  • PubMed Abstract: 
  • Broadly neutralizing antibodies (bNAbs) represent a promising approach to prevent and treat HIV-1 infection. However, viral escape through mutation of the HIV-1 envelope glycoprotein (Env) limits clinical applications. Here we describe 1-18, a new V H 1-46-encoded CD4 binding site (CD4bs) bNAb with outstanding breadth (97%) and potency (GeoMean IC 50  = 0 ...

    Broadly neutralizing antibodies (bNAbs) represent a promising approach to prevent and treat HIV-1 infection. However, viral escape through mutation of the HIV-1 envelope glycoprotein (Env) limits clinical applications. Here we describe 1-18, a new V H 1-46-encoded CD4 binding site (CD4bs) bNAb with outstanding breadth (97%) and potency (GeoMean IC 50  = 0.048 μg/mL). Notably, 1-18 is not susceptible to typical CD4bs escape mutations and effectively overcomes HIV-1 resistance to other CD4bs bNAbs. Moreover, mutational antigenic profiling uncovered restricted pathways of HIV-1 escape. Of most promise for therapeutic use, even 1-18 alone fully suppressed viremia in HIV-1-infected humanized mice without selecting for resistant viral variants. A 2.5-Å cryo-EM structure of a 1-18-BG505 SOSIP.664 Env complex revealed that these characteristics are likely facilitated by a heavy-chain insertion and increased inter-protomer contacts. The ability of 1-18 to effectively restrict HIV-1 escape pathways provides a new option to successfully prevent and treat HIV-1 infection.


    Organizational Affiliation

    Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany. Electronic address: florian.klein@uk-koeln.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
10-1074 Fab Heavy ChainA, B [auth K], C [auth Q]238Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6B2B6 (Homo sapiens)
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Go to UniProtKB:  S6B2B6
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
1-18 Fab Light ChainD [auth E], F [auth I], E [auth O]234Homo sapiensMutation(s): 0 
Gene Names: IGK@
UniProt
Find proteins for Q6PIL8 (Homo sapiens)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
10-1074 Fab Light ChainG [auth B], I [auth L], K [auth R]214Homo sapiensMutation(s): 0 
Gene Names: IGL@
UniProt
Find proteins for Q8N355 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
1-18 Fab Heavy ChainH [auth D], L [auth H], J [auth N]480Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp41M [auth C], Q [auth F], O [auth M]153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp120N [auth G], P [auth J], R [auth P]479Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
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  • Reference Sequence
Oligosaccharides

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Entity ID: 7
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-glucopyranoseS, T, U9N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G68668TB
GlyCosmos:  G68668TB
GlyGen:  G68668TB
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], AB [auth 0], CA [auth c], CB [auth 2], EB [auth 4], FA [auth f], HB [auth 7], JA [auth j]
AA [auth a], AB [auth 0], CA [auth c], CB [auth 2], EB [auth 4], FA [auth f], HB [auth 7], JA [auth j], KA [auth k], MA [auth m], OA [auth o], QA [auth q], TA [auth t], V, W, XA [auth x], Y, YA [auth y]
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
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-glucopyranoseIA [auth i], KB [auth AA], LA [auth l], WA [auth w], X, ZA [auth z]5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 10
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-glucopyranoseBB [auth 1], DA [auth d], FB [auth 5], NA [auth n], RA [auth r], Z4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 11
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-glucopyranoseBA [auth b], DB [auth 3], PA [auth p]6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
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
EA [auth e], GA [auth g], GB [auth 6], HA [auth h], IB [auth 8], JB [auth 9], SA [auth s], UA [auth u]
EA [auth e], GA [auth g], GB [auth 6], HA [auth h], IB [auth 8], JB [auth 9], SA [auth s], UA [auth u], VA [auth v]
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
LB [auth C] , MB [auth C] , NB [auth C] , OB [auth G] , PB [auth G] , QB [auth M] , RB [auth M] , SB [auth M] , 
LB [auth C],  MB [auth C],  NB [auth C],  OB [auth G],  PB [auth G],  QB [auth M],  RB [auth M],  SB [auth M],  TB [auth J],  UB [auth J],  VB [auth F],  WB [auth F],  XB [auth F],  YB [auth P],  ZB [auth P]
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: 2.50 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 StatesHIVRAD P01 AI100148
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP50 GM082545-06

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-12
    Changes: Data collection, Database references
  • Version 1.2: 2020-02-19
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary