8VYM

Soluble ectodomain of human cytomegalovirus (HCMV) glycoprotein B (gB) in the postfusion conformation in complex with 1G2 and 7H3 Fabs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Structure-based design of a soluble human cytomegalovirus glycoprotein B antigen stabilized in a prefusion-like conformation.

Sponholtz, M.R.Byrne, P.O.Lee, A.G.Ramamohan, A.R.Goldsmith, J.A.McCool, R.S.Zhou, L.Johnson, N.V.Hsieh, C.L.Connors, M.Karthigeyan, K.P.Crooks, C.M.Fuller, A.S.Campbell, J.D.Permar, S.R.Maynard, J.A.Yu, D.Bottomley, M.J.McLellan, J.S.

(2024) Proc Natl Acad Sci U S A 121: e2404250121-e2404250121

  • DOI: https://doi.org/10.1073/pnas.2404250121
  • Primary Citation of Related Structures:  
    8VYM, 8VYN

  • PubMed Abstract: 

    Human cytomegalovirus (HCMV) glycoprotein B (gB) is a class III membrane fusion protein required for viral entry. HCMV vaccine candidates containing gB have demonstrated moderate clinical efficacy, but no HCMV vaccine has been approved. Here, we used structure-based design to identify and characterize amino acid substitutions that stabilize gB in its metastable prefusion conformation. One variant containing two engineered interprotomer disulfide bonds and two cavity-filling substitutions (gB-C7), displayed increased expression and thermostability. A 2.8 Å resolution cryoelectron microscopy structure shows that gB-C7 adopts a prefusion-like conformation, revealing additional structural elements at the membrane-distal apex. Unlike previous observations for several class I viral fusion proteins, mice immunized with postfusion or prefusion-stabilized forms of soluble gB protein displayed similar neutralizing antibody titers, here specifically against an HCMV laboratory strain on fibroblasts. Collectively, these results identify initial strategies to stabilize class III viral fusion proteins and provide tools to probe gB-directed antibody responses.


  • Organizational Affiliation

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein B
A, B, C
786Human betaherpesvirus 5Mutation(s): 0 
Gene Names: gBUL55
UniProt
Find proteins for P13201 (Human cytomegalovirus (strain Towne))
Explore P13201 
Go to UniProtKB:  P13201
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13201
Glycosylation
Glycosylation Sites: 9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
1G2 Fab Heavy Chain
D, G, J
224Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
1G2 Fab Light Chain
E, F, I
214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
7H3 Fab Light Chain216Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
7H3 Fab Heavy Chain234Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Oligosaccharides

Help

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],
L,
M,
N,
O,
AA [auth a],
L,
M,
N,
O,
P,
Q,
S,
T,
U,
X,
Y,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
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
R, V, W
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
FA [auth B]
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth C],
KA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.0
MODEL REFINEMENTCoot
MODEL REFINEMENTISOLDE

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Structure summary