7UCG

Structure of the DU422 SOSIP.664 trimer in complex with neutralizing antibody Fab fragments 10-1074 and BG24


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A naturally arising broad and potent CD4-binding site antibody with low somatic mutation.

Barnes, C.O.Schoofs, T.Gnanapragasam, P.N.P.Golijanin, J.Huey-Tubman, K.E.Gruell, H.Schommers, P.Suh-Toma, N.Lee, Y.E.Cetrulo Lorenzi, J.C.Piechocka-Trocha, A.Scheid, J.F.West Jr., A.P.Walker, B.D.Seaman, M.S.Klein, F.Nussenzweig, M.C.Bjorkman, P.J.

(2022) Sci Adv 8: eabp8155-eabp8155

  • DOI: https://doi.org/10.1126/sciadv.abp8155
  • Primary Citation of Related Structures:  
    7UCE, 7UCF, 7UCG

  • PubMed Abstract: 

    The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, including insertions and deletions, which make their induction challenging. VRC01-class bNAbs not only exhibit extraordinary breadth and potency but also rank among the most highly somatically mutated bNAbs. Here, we describe a VRC01-class antibody isolated from a viremic controller, BG24, that is much less mutated than most relatives of its class while achieving comparable breadth and potency. A 3.8-Å x-ray crystal structure of a BG24-BG505 Env trimer complex revealed conserved contacts at the gp120 interface characteristic of the VRC01-class Abs, despite lacking common CDR3 sequence motifs. The existence of moderately mutated CD4-binding site (CD4bs) bNAbs such as BG24 provides a simpler blueprint for CD4bs antibody induction by a vaccine, raising the prospect that such an induction might be feasible with a germline-targeting approach.


  • Organizational Affiliation

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41A [auth B],
G [auth A],
M
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q202J5 (Human immunodeficiency virus 1)
Explore Q202J5 
Go to UniProtKB:  Q202J5
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ202J5
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BG24 CDRH2-v2 Fab heavy chainB [auth D],
H [auth C],
N
234Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
BG24 light chainC [auth E],
I [auth F],
O
205Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160D [auth G],
J [auth I],
P
507Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q202J5 (Human immunodeficiency virus 1)
Explore Q202J5 
Go to UniProtKB:  Q202J5
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UniProt GroupQ202J5
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
10-1074 Fab heavy chainE [auth H],
K [auth J],
Q
243Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
10-1074 light chainF [auth L],
L [auth K],
R
216Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 8
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-glucopyranoseFA [auth f],
NA [auth n],
X
5N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 9
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-glucopyranoseBA [auth b],
JA [auth j],
RA [auth r]
7N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G07617FP
GlyCosmos:  G07617FP
GlyGen:  G07617FP
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth I]
BB [auth I]
CB [auth I]
DB [auth I]
EB [auth I]
AB [auth I],
BB [auth I],
CB [auth I],
DB [auth I],
EB [auth I],
FB [auth I],
GB [auth I],
HB [auth P],
IB [auth P],
JB [auth P],
KB [auth P],
LB [auth P],
MB [auth P],
NB [auth P],
TA [auth G],
UA [auth G],
VA [auth G],
WA [auth G],
XA [auth G],
YA [auth G],
ZA [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.19

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 StatesP01 AI100148
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP50 AI150464
Bill & Melinda Gates FoundationUnited StatesOPP1124068

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-17
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references
  • Version 1.2: 2022-09-07
    Changes: Structure summary