9BER

Cryo-EM structure of the HIV-1 JR-FL IDL Env trimer in complex with PGT122 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Design of soluble HIV-1 envelope trimers free of covalent gp120-gp41 bonds with prevalent native-like conformation.

Zhang, P.Gorman, J.Tsybovsky, Y.Lu, M.Liu, Q.Gopan, V.Singh, M.Lin, Y.Miao, H.Seo, Y.Kwon, A.Olia, A.S.Chuang, G.Y.Geng, H.Lai, Y.T.Zhou, T.Mascola, J.R.Mothes, W.Kwong, P.D.Lusso, P.

(2024) Cell Rep 43: 114518-114518

  • DOI: https://doi.org/10.1016/j.celrep.2024.114518
  • Primary Citation of Related Structures:  
    9BER, 9BEW, 9BF6

  • PubMed Abstract: 

    Soluble HIV-1 envelope (Env) trimers may serve as effective vaccine immunogens. The widely utilized SOSIP trimers have been paramount for structural studies, but the disulfide bond they feature between gp120 and gp41 constrains intersubunit mobility and may alter antigenicity. Here, we report an alternative strategy to generate stabilized soluble Env trimers free of covalent gp120-gp41 bonds. Stabilization was achieved by introducing an intrasubunit disulfide bond between the inner and outer domains of gp120, defined as interdomain lock (IDL). Correctly folded IDL trimers displaying a native-like antigenic profile were produced for HIV-1 Envs of different clades. Importantly, the IDL design abrogated CD4 binding while not affecting recognition by potent neutralizing antibodies to the CD4-binding site. By cryoelectron microscopy, IDL trimers were shown to adopt a closed prefusion configuration, while single-molecule fluorescence resonance energy transfer documented a high prevalence of native-like conformation. Thus, IDL trimers may be promising candidates as vaccine immunogens.


  • Organizational Affiliation

    Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: zhangp@ihm.ac.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120A [auth G],
C [auth A],
E [auth F]
477Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q75760 (Human immunodeficiency virus 1)
Explore Q75760 
Go to UniProtKB:  Q75760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ75760
Glycosylation
Glycosylation Sites: 18
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41B,
D [auth C],
F [auth I]
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q6BC19 (Human immunodeficiency virus 1)
Explore Q6BC19 
Go to UniProtKB:  Q6BC19
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6BC19
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PGT122 heavy chainG [auth H],
I [auth D],
K [auth J]
132Homo sapiensMutation(s): 0 
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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
PGT122 light chainH [auth L],
J [auth E],
L [auth K]
105Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
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],
M,
N,
P,
BA [auth b],
CA [auth c],
M,
N,
P,
Q,
S,
T,
V,
W,
Y,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
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-glucopyranoseAA [auth a],
O,
U
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-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-glucopyranoseDA [auth d],
R,
X
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
Small Molecules
Ligands 2 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 A]
DB [auth A]
EA [auth G]
AB [auth A],
BB [auth A],
CB [auth A],
DB [auth A],
EA [auth G],
EB [auth A],
FA [auth G],
GA [auth G],
GB [auth C],
HA [auth G],
HB [auth C],
IA [auth G],
IB [auth C],
JA [auth G],
JB [auth C],
KA [auth G],
KB [auth F],
LA [auth G],
LB [auth F],
MA [auth G],
MB [auth F],
NA [auth G],
NB [auth F],
OA [auth G],
OB [auth F],
PA [auth G],
PB [auth F],
QA [auth B],
QB [auth F],
RA [auth B],
RB [auth F],
SA [auth B],
SB [auth F],
TA [auth A],
TB [auth F],
UA [auth A],
UB [auth F],
VA [auth A],
VB [auth I],
WA [auth A],
WB [auth I],
XA [auth A],
XB [auth I],
YA [auth A],
ZA [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
FB [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.14
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310
Simons FoundationUnited StatesSF349247

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release