8YQQ | pdb_00008yqq

Structure of HKU1B RBD with TMPRSS2

PDB DOI: https://doi.org/10.2210/pdb8YQQ/pdb
EM Map EMD-39502: EMDB EMDataResource

Classification: VIRAL PROTEIN/HYDROLASE
Organism(s): Candidatus Accumulibacter adiacens, Homo sapiens
Expression System: Baculovirus expression vector pFastBac1-HM
Mutation(s): No

Deposited: 2024-03-19 Released: 2024-08-28
Deposition Author(s): Gao, X., Cui, S., Ding, W., Zhu, K., Shang, K., Zhu, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.95 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for the interaction between human coronavirus HKU1 spike receptor binding domain and its receptor TMPRSS2.

Gao, X., Zhu, K., Wang, L., Shang, K., Hua, L., Qin, B., Zhu, H., Ding, W., Cui, S.

(2024) Cell Discov 10: 84-84

PubMed: 39112468 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-024-00717-5
Primary Citation of Related Structures:
8YOY, 8YQQ

Organizational Affiliation

NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. gaoxiaopan@pumc.edu.cn.

Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. gaoxiaopan@pumc.edu.cn.

State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. gaoxiaopan@pumc.edu.cn.

NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.

Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.

Songshan Lake Materials Laboratory, Dongguan, Guangdong, China.

Medical School, Yan'an University, Yan'an, Shaanxi, China.

Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China. hongtao.zhu@iphy.ac.cn.

Songshan Lake Materials Laboratory, Dongguan, Guangdong, China. hongtao.zhu@iphy.ac.cn.

University of Chinese Academy of Sciences, Beijing, China. hongtao.zhu@iphy.ac.cn.

Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China. dingwei@iphy.ac.cn.

Songshan Lake Materials Laboratory, Dongguan, Guangdong, China. dingwei@iphy.ac.cn.

University of Chinese Academy of Sciences, Beijing, China. dingwei@iphy.ac.cn.

NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. cui.sheng@ipb.pumc.edu.cn.

Macromolecule Content

Total Structure Weight: 75.41 kDa
Atom Count: 5,141
Modeled Residue Count: 649
Deposited Residue Count: 669
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	285	Candidatus Accumulibacter adiacens	Mutation(s): 0 Gene Names: S, 3
UniProt
Find proteins for Q0ZME7 (Human coronavirus HKU1 (isolate N5)) Explore Q0ZME7 Go to UniProtKB: Q0ZME7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0ZME7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 2	B	384	Homo sapiens	Mutation(s): 0 Gene Names: TMPRSS2, PRSS10 EC: 3.4.21.122
UniProt & NIH Common Fund Data Resources
Find proteins for O15393 (Homo sapiens) Explore O15393 Go to UniProtKB: O15393
PHAROS: O15393 GTEx: ENSG00000184012
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15393
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth B] C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B]