6UDK

HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RC1 variant of HIV-1 Env glycoprotein gp120A [auth G],
B [auth K],
C [auth R]
481Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
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Go to UniProtKB:  Q2N0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
10-1074 Fab Heavy ChainD [auth A],
F,
H [auth O]
238Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6B2B6 (Homo sapiens)
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS6B2B6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
10-1074 Fab Light ChainE [auth B],
G [auth I],
I [auth P]
214Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q8N355 (Homo sapiens)
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UniProt GroupQ8N355
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
1-55 Fab Heavy ChainJ [auth M],
L [auth D],
N [auth H]
262Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6C4S0 (Homo sapiens)
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UniProt GroupS6C4S0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
1-55 Fab Light ChainK [auth N],
M [auth E],
O [auth L]
234Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6PJF2 (Homo sapiens)
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UniProt GroupQ6PJF2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RC1 variant of HIV-1 Env glycoprotein gp41P [auth C],
Q [auth J],
R [auth Q]
153Human immunodeficiency virus 1Mutation(s): 0 
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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
CA [auth c],
FA [auth f],
GA [auth g],
S,
BA [auth b],
CA [auth c],
FA [auth f],
GA [auth g],
S,
W,
X
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranoseDA [auth d],
T
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 9
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
U, Z
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranoseAA [auth a],
V
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80966KZ
GlyCosmos:  G80966KZ
GlyGen:  G80966KZ
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranose
Y
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07617FP
GlyCosmos:  G07617FP
GlyGen:  G07617FP
Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(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)-2-acetamido-2-deoxy-beta-D-glucopyranoseEA [auth e]6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G34442SS
GlyCosmos:  G34442SS
GlyGen:  G34442SS
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth R]
BB [auth R]
CB [auth R]
DB [auth R]
EB [auth R]
AB [auth R],
BB [auth R],
CB [auth R],
DB [auth R],
EB [auth R],
FB [auth R],
GB [auth R],
HA [auth G],
HB [auth R],
IA [auth G],
JA [auth G],
KA [auth G],
LA [auth G],
MA [auth G],
NA [auth G],
OA [auth G],
PA [auth G],
QA [auth K],
RA [auth K],
SA [auth K],
TA [auth K],
UA [auth K],
VA [auth K],
WA [auth K],
XA [auth K],
YA [auth K],
ZA [auth R]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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: Atomic model, Data collection, Derived calculations, Structure summary