6M6I | pdb_00006m6i

Structure of HSV2 B-capsid portal vertex

• PDB DOI: https://doi.org/10.2210/pdb6M6I/pdb
• EM Map EMD-30125: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Human alphaherpesvirus 2
• Mutation(s): No 


• Deposited: 2020-03-14 Released: 2021-03-10 
• Deposition Author(s): Wang, X.X., Wang, N.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.05 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures of the portal vertex reveal essential protein-protein interactions for Herpesvirus assembly and maturation.

Wang, N., Chen, W., Zhu, L., Zhu, D., Feng, R., Wang, J., Zhu, B., Zhang, X., Chen, X., Liu, X., Yan, R., Ni, D., Zhou, G.G., Liu, H., Rao, Z., Wang, X.

(2020) Protein Cell 11: 366-373

• PubMed: 32285350 
• DOI: https://doi.org/10.1007/s13238-020-00711-z
• Primary Citation Related Structures: 
  6M6G, 6M6H, 6M6I

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Organizational Affiliation: 
• CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, 410081, China.
ImmVira Co., Ltd, Silver Star Hi-tech Industrial Park, Longhua District, Shenzhen, 518116, China.
Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, 410081, China. [e-mail].
CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
Laboratory of Structural Biology, Tsinghua University, Beijing, 100084, China. [e-mail].
State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300353, China. [e-mail].
CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Hetero 85-mer - A30B30C10D10E5 Pseudo Symmetry: Cyclic - C5  (Explore in 3D)
Pseudo Stoichiometry: Hetero 85-mer - A30B30C10D5E5F5 

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

Macromolecule Content 

• Total Structure Weight: 1,102.59 kDa 
• Atom Count: 72,384 
• Modeled Residue Count: 9,791 
• Deposited Residue Count: 10,182 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A, B, C, D, E, F	1,374	Human alphaherpesvirus 2	Mutation(s): 0
UniProt
Find proteins for P89442 (Human herpesvirus 2 (strain HG52)) Explore P89442  Go to UniProtKB:  P89442

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coiled coils chain 1	G	81	Human alphaherpesvirus 2	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Coiled coils chain 2	H	83	Human alphaherpesvirus 2	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Triplex capsid protein 2	I, J	318	Human alphaherpesvirus 2	Mutation(s): 0
UniProt
Find proteins for G9I239 (Human herpesvirus 2) Explore G9I239  Go to UniProtKB:  G9I239

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Triplex capsid protein 1	K	466	Human alphaherpesvirus 2	Mutation(s): 0
UniProt
Find proteins for P22486 (Human herpesvirus 2 (strain G)) Explore P22486  Go to UniProtKB:  P22486

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Small capsomere-interacting protein	L, M, N, O, P, Q	112	Human alphaherpesvirus 2	Mutation(s): 0
UniProt
Find proteins for G9I257 (Human herpesvirus 2) Explore G9I257  Go to UniProtKB:  G9I257

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.05 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-10 
Deposition Author(s): Wang, X.X., Wang, N.

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary