8FIS | pdb_00008fis

Structure of Bispecific CAP256V2LS-J3 Fab in complex with BG505 DS-SOSIP.664

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8FIS

This is version 1.2 of the entry. See complete history. 

Literature

Bispecific antibody CAP256.J3LS targets V2-apex and CD4-binding sites with high breadth and potency.

Zhang, B., Gorman, J., Kwon, Y.D., Pegu, A., Chao, C.W., Liu, T., Asokan, M., Bender, M.F., Bylund, T., Damron, L., Gollapudi, D., Lei, P., Li, Y., Liu, C., Louder, M.K., McKee, K., Olia, A.S., Rawi, R., Schon, A., Wang, S., Yang, E.S., Yang, Y., Carlton, K., Doria-Rose, N.A., Shapiro, L., Seaman, M.S., Mascola, J.R., Kwong, P.D.

(2023) MAbs 15: 2165390-2165390

  • DOI: https://doi.org/10.1080/19420862.2023.2165390
  • Primary Citation Related Structures: 
    8FIS

  • PubMed Abstract: 

    Antibody CAP256-VRC26.25 targets the second hypervariable region (V2) at the apex of the HIV envelope (Env) trimer with extraordinary neutralization potency, although less than optimal breadth. To improve breadth, we linked the light chain of CAP256V2LS, an optimized version of CAP256-VRC26.25 currently under clinical evaluation, to the llama nanobody J3, which has broad CD4-binding site-directed neutralization. The J3-linked bispecific antibody exhibited improved breadth and potency over both J3 and CAP256V2LS, indicative of synergistic neutralization. The cryo-EM structure of the bispecific antibody in complex with a prefusion-closed Env trimer revealed simultaneous binding of J3 and CAP256V2LS. We further optimized the pharmacokinetics of the bispecific antibody by reducing the net positive charge of J3. The optimized bispecific antibody, which we named CAP256.J3LS, had a half-life similar to CAP256V2LS in human FcRn knock-in mice and exhibited suitable auto-reactivity, manufacturability, and biophysical risk. CAP256.J3LS neutralized over 97% of a multiclade 208-strain panel (geometric mean concentration for 80% inhibition (IC 80 ) 0.079 μg/ml) and 100% of a 100-virus clade C panel (geometric mean IC 80 of 0.05 μg/ml), suggesting its anti-HIV utility especially in regions where clade C dominates.

    • Organizational Affiliation: 
    • Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA.

Macromolecule Content 

  • Total Structure Weight: 381.23 kDa 
  • Atom Count: 20,356 
  • Modeled Residue Count: 2,357 
  • Deposited Residue Count: 3,208 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41A,
B,
D [auth E]		153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120C,
E [auth F],
F [auth G]		481Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 19
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
J3-VRC26.25 LightG [auth J],
H [auth I],
J [auth L]		353Lama glamaMutation(s): 0 
Find similar proteins by:
|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
VRC26.25 HeavyI [auth H]247Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
K [auth D],
KA [auth k],
MA [auth m],
NA [auth n],
AA [auth a],
K [auth D],
KA [auth k],
MA [auth m],
NA [auth n],
V,
XA [auth x],
Z
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
DA [auth d],
FA [auth f],
GA [auth g],
HA [auth h],
BA [auth b],
DA [auth d],
FA [auth f],
GA [auth g],
HA [auth h],
IA [auth i],
JA [auth j],
L [auth K],
LA [auth l],
N,
OA [auth o],
P,
Q,
QA [auth q],
R,
S,
SA [auth s],
TA [auth t],
U,
UA [auth u],
VA [auth v],
W
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseCA [auth c],
M,
PA [auth p]		4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseEA [auth e],
O,
RA [auth r]		4N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC
GlyCosmos: G22573RC
GlyGen: G22573RC
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseT,
WA [auth w],
X,
Y,
YA [auth y]		5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG


Download:Ideal Coordinates CCD File
AB [auth A]
BB [auth A]
CB [auth B]
DB [auth B]
EB [auth B]
AB [auth A],
BB [auth A],
CB [auth B],
DB [auth B],
EB [auth B],
FB [auth C],
GB [auth C],
HB [auth C],
IB [auth C],
JB [auth E],
KB [auth E],
LB [auth E],
MB [auth F],
NB [auth F],
OB [auth F],
PB [auth F],
QB [auth F],
RB [auth G],
SB [auth G],
TB [auth G],
UB [auth G],
VB [auth G],
WB [auth G],
XB [auth G],
ZA [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS		I [auth H]L-PEPTIDE LINKINGC9 H11 N O6 STYR

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC3

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310
Other privateSimons Foundation (SF349247)

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary