7T4G

The Envelope Glycoprotein SIVmac239.K180S SOSIP trimer in complex with 3 copies of the neutralizing antibody K11


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus.

Zhao, F.Berndsen, Z.T.Pedreno-Lopez, N.Burns, A.Allen, J.D.Barman, S.Lee, W.H.Chakraborty, S.Gnanakaran, S.Sewall, L.M.Ozorowski, G.Limbo, O.Song, G.Yong, P.Callaghan, S.Coppola, J.Weisgrau, K.L.Lifson, J.D.Nedellec, R.Voigt, T.B.Laurino, F.Louw, J.Rosen, B.C.Ricciardi, M.Crispin, M.Desrosiers, R.C.Rakasz, E.G.Watkins, D.I.Andrabi, R.Ward, A.B.Burton, D.R.Sok, D.

(2022) Nat Commun 13: 5236-5236

  • DOI: https://doi.org/10.1038/s41467-022-32783-2
  • Primary Citation of Related Structures:  
    7T2P, 7T4G

  • PubMed Abstract: 

    SIVmac239 infection of macaques is a favored model of human HIV infection. However, the SIVmac239 envelope (Env) trimer structure, glycan occupancy, and the targets and ability of neutralizing antibodies (nAbs) to protect against SIVmac239 remain unknown. Here, we report the isolation of SIVmac239 nAbs that recognize a glycan hole and the V1/V4 loop. A high-resolution structure of a SIVmac239 Env trimer-nAb complex shows many similarities to HIV and SIVcpz Envs, but with distinct V4 features and an extended V1 loop. Moreover, SIVmac239 Env has a higher glycan shield density than HIV Env that may contribute to poor or delayed nAb responses in SIVmac239-infected macaques. Passive transfer of a nAb protects macaques from repeated intravenous SIVmac239 challenge at serum titers comparable to those described for protection of humans against HIV infection. Our results provide structural insights for vaccine design and shed light on antibody-mediated protection in the SIV model.


  • Organizational Affiliation

    Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120A,
E [auth C],
I [auth E]
527Simian immunodeficiency virusMutation(s): 1 
Gene Names: env
UniProt
Find proteins for Q5QG95 (Simian immunodeficiency virus)
Explore Q5QG95 
Go to UniProtKB:  Q5QG95
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5QG95
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41B,
F [auth D],
J [auth F]
159Simian immunodeficiency virusMutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q5QG95 (Simian immunodeficiency virus)
Explore Q5QG95 
Go to UniProtKB:  Q5QG95
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5QG95
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
K11 IgG heavy chainC [auth H],
G,
K [auth J]
485Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
K11 IgG light chainD [auth L],
H [auth I],
L [auth K]
232Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-glucopyranoseM,
MA [auth m],
Z
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G34499SX
GlyCosmos:  G34499SX
GlyGen:  G34499SX
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
HA [auth h],
KA [auth k],
LA [auth l],
N,
AA [auth a],
HA [auth h],
KA [auth k],
LA [auth l],
N,
NA [auth n],
U,
UA [auth u],
X,
XA [auth x],
Y
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
CA [auth c],
DA [auth d],
IA [auth i],
O,
BA [auth b],
CA [auth c],
DA [auth d],
IA [auth i],
O,
OA [auth o],
P,
PA [auth p],
Q,
QA [auth q],
V,
VA [auth v]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseEA [auth e],
R,
RA [auth r]
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G46836GH
GlyCosmos:  G46836GH
GlyGen:  G46836GH
Entity ID: 9
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-glucopyranoseS,
SA [auth s]
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 10
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-glucopyranoseGA [auth g],
JA [auth j],
T,
W,
YA [auth y]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 11
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]5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranoseTA [auth t],
WA [auth w]
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth E]
BB [auth A]
BC [auth E]
CB [auth A]
AB [auth A],
AC [auth E],
BB [auth A],
BC [auth E],
CB [auth A],
CC [auth E],
DB [auth A],
DC [auth E],
EB [auth A],
EC [auth E],
FB [auth A],
FC [auth E],
GB [auth A],
GC [auth F],
HB [auth A],
HC [auth F],
IB [auth B],
IC [auth F],
JB [auth B],
KB [auth B],
LB [auth C],
MB [auth C],
NB [auth C],
OB [auth C],
PB [auth C],
QB [auth C],
RB [auth C],
SB [auth C],
TB [auth C],
UB [auth D],
VB [auth D],
WB [auth D],
XB [auth E],
YB [auth E],
ZA [auth A],
ZB [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta
RECONSTRUCTIONcryoSPARC

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 StatesUM1 AI144462
Bill & Melinda Gates FoundationUnited StatesOPP1196345/INV-008813

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Structure summary