5ZZ8 | pdb_00005zz8

Structure of the Herpes simplex virus type 2 C-capsid with capsid-vertex-specific component

• PDB DOI: https://doi.org/10.2210/pdb5ZZ8/pdb
• EM Map EMD-6976: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Human alphaherpesvirus 2
• Expression System: Chlorocebus sabaeus
• Mutation(s): No 


• Deposited: 2018-05-31 Released: 2018-10-10 
• Deposition Author(s): Wang, J.L., Yuan, S., Zhu, D.J., Tang, H., Wang, N., Chen, W.Y., Gao, Q., Li, Y.H., Wang, J.Z., Liu, H.R., Zhang, X.Z., Rao, Z.H., Wang, X.X.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the herpes simplex virus type 2 C-capsid with capsid-vertex-specific component.

Wang, J., Yuan, S., Zhu, D., Tang, H., Wang, N., Chen, W., Gao, Q., Li, Y., Wang, J., Liu, H., Zhang, X., Rao, Z., Wang, X.

(2018) Nat Commun 9: 3668-3668

• PubMed: 30201968 
• DOI: https://doi.org/10.1038/s41467-018-06078-4
• Primary Citation Related Structures: 
  5ZZ8


• PubMed Abstract: 
  

  Herpes simplex viruses (HSVs) cause human oral and genital ulcer diseases. Patients with HSV-2 have a higher risk of acquiring a human immunodeficiency virus infection. HSV-2 is a member of the α-herpesvirinae subfamily that together with the β- and γ-herpesvirinae subfamilies forms the Herpesviridae family. Here, we report the cryo-electron microscopy structure of the HSV-2 C-capsid with capsid-vertex-specific component (CVSC) that was determined at 3.75 Å using a block-based reconstruction strategy. We present atomic models of multiple conformers for the capsid proteins (VP5, VP23, VP19C, and VP26) and CVSC. Comparison of the HSV-2 homologs yields information about structural similarities and differences between the three herpesviruses sub-families and we identify α-herpesvirus-specific structural features. The hetero-pentameric CVSC, consisting of a UL17 monomer, a UL25 dimer and a UL36 dimer, is bound tightly by a five-helix bundle that forms extensive networks of subunit contacts with surrounding capsid proteins, which reinforce capsid stability.

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Organizational Affiliation: 
• National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
College of Physics and Information Science, Synergetic Innovation Center for Quantum Effects and Applications, Key Laboratory of Low-dimensional Quantum Structures, and Quantum Control of the Ministry of Education, Hunan Normal University, Changsha, 410008, China.
Sinovac Biotech Co., Ltd, Beijing, 100085, China.
National Institutes for Food and Drug Control, No. 2, Tiantanxili, Beijing, 100050, China.
College of Physics and Information Science, Synergetic Innovation Center for Quantum Effects and Applications, Key Laboratory of Low-dimensional Quantum Structures, and Quantum Control of the Ministry of Education, Hunan Normal University, Changsha, 410008, China. [e-mail].
National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].
National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].
Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China. [e-mail].
State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300353, China. [e-mail].
Laboratory of Structural Biology, Tsinghua University, Beijing, 100084, China. [e-mail].
National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 3060-mer - A960B900C600D300E120F120G60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 3060-mer - A960B900C600D300E120F60G60H60 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 4,032.16 kDa 
• Atom Count: 218,714 
• Modeled Residue Count: 28,735 
• Deposited Residue Count: 37,290 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP19C	A [auth Q], D [auth T], G [auth W], J [auth 1], M [auth w]	466	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: UL38, TRX1
UniProt
Find proteins for G9I260 (Human herpesvirus 2) Explore G9I260  Go to UniProtKB:  G9I260

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP23	B [auth R], C [auth S], E [auth U], F [auth V], H [auth X], I [auth Y], K [auth 3], L [auth 2], N [auth x], O [auth y]	318	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: TRX2, UL18
UniProt
Find proteins for P89441 (Human herpesvirus 2 (strain HG52)) Explore P89441  Go to UniProtKB:  P89441

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	FA [auth N], GA [auth O], HA [auth P], IA [auth B], JA [auth C], KA [auth D], MA [auth E], OA [auth F], P [auth I], Q [auth J], QA [auth G], R [auth K], S [auth L], T [auth M], U [auth A], V [auth H]	1,374	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: UL19, MCP
UniProt
Find proteins for A0A0E3U2U0 (Human herpesvirus 2) Explore A0A0E3U2U0  Go to UniProtKB:  A0A0E3U2U0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VP26	AA [auth l], BA [auth m], CA [auth n], DA [auth o], EA [auth p], SA [auth b], TA [auth c], UA [auth d], VA [auth e], W [auth h], WA [auth f], X [auth i], XA [auth g], Y [auth j], Z [auth k]	112	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: SCP, UL35
UniProt
Find proteins for P89458 (Human herpesvirus 2 (strain HG52)) Explore P89458  Go to UniProtKB:  P89458

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
UL17	LA [auth q]	702	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: UL17, CVC1
UniProt
Find proteins for G9I238 (Human herpesvirus 2) Explore G9I238  Go to UniProtKB:  G9I238

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
UL25	NA [auth r], PA [auth s]	585	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: UL25, CVC2
UniProt
Find proteins for D6PUY5 (Human herpesvirus 2) Explore D6PUY5  Go to UniProtKB:  D6PUY5

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
UL36	RA [auth t], YA [auth u]	3,122	Human alphaherpesvirus 2	Mutation(s): 0  Gene Names: UL36
UniProt
Find proteins for A0A1U9ZLV0 (Human herpesvirus 2) Explore A0A1U9ZLV0  Go to UniProtKB:  A0A1U9ZLV0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Wang, J.L., Yuan, S., Zhu, D.J., Tang, H., Wang, N., Chen, W.Y., Gao, Q., Li, Y.H., Wang, J.Z., Liu, H.R., Zhang, X.Z., Rao, Z.H., Wang, X.X.

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2019-11-06
  Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary