6M6H | pdb_00006m6h

Structure of HSV2 C-capsid portal vertex

• PDB DOI: https://doi.org/10.2210/pdb6M6H/pdb
• EM Map EMD-30124: EMDB EMDataResource

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


• Deposited: 2020-03-14 Released: 2021-03-24 
• Deposition Author(s): Wang, X.X., Wang, N.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 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 of Related Structures:  
  6M6G, 6M6H, 6M6I

---

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 100-mer - A30B30C10D10E10F5G5 Pseudo Symmetry: Cyclic - C5  (Explore in 3D)
Pseudo Stoichiometry: Hetero 100-mer - A30B30C10D10E5F5G5H5 

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

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 1,951.56 kDa 
• Atom Count: 77,884 
• Modeled Residue Count: 10,426 
• Deposited Residue Count: 18,134 
• Unique protein chains: 7

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
Capsid vertex component 1	G	702	Human alphaherpesvirus 2	Mutation(s): 0
UniProt
Find proteins for P89440 (Human herpesvirus 2 (strain HG52)) Explore P89440  Go to UniProtKB:  P89440

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid vertex component 2	H, I	585	Human alphaherpesvirus 2	Mutation(s): 0
UniProt
Find proteins for P89448 (Human herpesvirus 2 (strain HG52)) Explore P89448  Go to UniProtKB:  P89448

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Small capsomere-interacting protein	J, K, L, M, N, O	112	Human alphaherpesvirus 2	Mutation(s): 0
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
Large tegument protein deneddylase	P, Q	3,122	Human alphaherpesvirus 2	Mutation(s): 0  EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P89459 (Human herpesvirus 2 (strain HG52)) Explore P89459  Go to UniProtKB:  P89459

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Triplex capsid protein 2	R, S	318	Human alphaherpesvirus 2	Mutation(s): 0
UniProt
Find proteins for P89441 (Human herpesvirus 2 (strain HG52)) Explore P89441  Go to UniProtKB:  P89441

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Triplex capsid protein 1	T	466	Human alphaherpesvirus 2	Mutation(s): 0
UniProt
Find proteins for P22486 (Human herpesvirus 2 (strain G)) Explore P22486  Go to UniProtKB:  P22486

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-24 
Deposition Author(s): Wang, X.X., Wang, N.

Revision History  

• Version 1.0: 2021-03-24
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary