7SD3

Cytoplasmic tail deleted HIV-1 Env bound with three 4E10 Fabs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.67 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

Dynamic HIV-1 spike motion creates vulnerability for its membrane-bound tripod to antibody attack.

Yang, S.Hiotis, G.Wang, Y.Chen, J.Wang, J.H.Kim, M.Reinherz, E.L.Walz, T.

(2022) Nat Commun 13: 6393-6393

  • DOI: https://doi.org/10.1038/s41467-022-34008-y
  • Primary Citation of Related Structures:  
    7SC5, 7SD3

  • PubMed Abstract: 

    Vaccines targeting HIV-1's gp160 spike protein are stymied by high viral mutation rates and structural chicanery. gp160's membrane-proximal external region (MPER) is the target of naturally arising broadly neutralizing antibodies (bnAbs), yet MPER-based vaccines fail to generate bnAbs. Here, nanodisc-embedded spike protein was investigated by cryo-electron microscopy and molecular-dynamics simulations, revealing spontaneous ectodomain tilting that creates vulnerability for HIV-1. While each MPER protomer radiates centrally towards the three-fold axis contributing to a membrane-associated tripod structure that is occluded in the upright spike, tilting provides access to the opposing MPER. Structures of spike proteins with bound 4E10 bnAb Fabs reveal that the antibody binds exposed MPER, thereby altering MPER dynamics, modifying average ectodomain tilt, and imposing strain on the viral membrane and the spike's transmembrane segments, resulting in the abrogation of membrane fusion and informing future vaccine development.


  • Organizational Affiliation

    Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4E10 Fab light chainA [auth H],
C [auth N],
E [auth M]
214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
4E10 Fab heavy chainB [auth G],
D [auth K],
F [auth I]
230Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120G [auth A],
I [auth C],
K [auth E]
481HIV whole-genome vector AA1305#18Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
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UniProt GroupQ2N0S6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein gp41H [auth B],
J [auth D],
L [auth F]
173HIV whole-genome vector AA1305#18Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
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
M [auth J],
O,
P,
R,
S,
M [auth J],
O,
P,
R,
S,
U
3N/AO-Glycosylation, N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseN [auth L],
Q,
T
2N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth E]
BA [auth A]
BB [auth E]
CA [auth A]
AA [auth A],
AB [auth E],
BA [auth A],
BB [auth E],
CA [auth A],
CB [auth F],
DA [auth A],
DB [auth F],
EA [auth B],
EB [auth F],
FA [auth B],
GA [auth B],
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C],
PA [auth C],
QA [auth D],
RA [auth D],
SA [auth D],
TA [auth E],
UA [auth E],
V [auth A],
VA [auth E],
W [auth A],
WA [auth E],
X [auth A],
XA [auth E],
Y [auth A],
YA [auth E],
Z [auth A],
ZA [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: 3.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references