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: https://doi.org/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  = 0.048 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; Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, 50931 Cologne, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence 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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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS6B2B6
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
1-18 Fab Light ChainD [auth E],
E [auth O],
F [auth I]
234Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6PIL8 (Homo sapiens)
Explore Q6PIL8 
Go to UniProtKB:  Q6PIL8
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UniProt GroupQ6PIL8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
10-1074 Fab Light ChainG [auth B],
I [auth L],
K [auth R]
214Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q8N355 (Homo sapiens)
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UniProt GroupQ8N355
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
1-18 Fab Heavy ChainH [auth D],
J [auth N],
L [auth H]
480Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41M [auth C],
O [auth M],
Q [auth F]
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
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UniProt GroupQ2N0S6
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Entity ID: 6
MoleculeChains Sequence 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)
Explore Q2N0S6 
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UniProt GroupQ2N0S6
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranose
S, T, U
9N-Glycosylation
Glycosylation Resources
GlyTouCan:  G68668TB
GlyCosmos:  G68668TB
GlyGen:  G68668TB
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranose
IA [auth i],
KB [auth AA],
LA [auth l],
WA [auth w],
X,
IA [auth i],
KB [auth AA],
LA [auth l],
WA [auth w],
X,
ZA [auth z]
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranose
BB [auth 1],
DA [auth d],
FB [auth 5],
NA [auth n],
RA [auth r],
BB [auth 1],
DA [auth d],
FB [auth 5],
NA [auth n],
RA [auth r],
Z
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D 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
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D 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],
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
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
LB [auth C]
MB [auth C]
NB [auth C]
OB [auth G]
PB [auth G]
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot

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