7X01 | pdb_00007x01

Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with inhibitor FHA

PDB DOI: https://doi.org/10.2210/pdb7X01/pdb
EM Map EMD-32914: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Chikungunya virus strain S27-African prototype
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-02-20 Released: 2022-08-10
Deposition Author(s): Zhang, K., Law, M.C.Y., Nguyen, T.M., Tan, Y.B., Wirawan, M., Law, Y.S., Luo, D.H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.62 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

Molecular basis of specific viral RNA recognition and 5'-end capping by the Chikungunya virus nsP1.

Zhang, K., Law, M.C.Y., Nguyen, T.M., Tan, Y.B., Wirawan, M., Law, Y.S., Jeong, L.S., Luo, D.

(2022) Cell Rep 40: 111133-111133

PubMed: 35905713 Search on PubMed
DOI: https://doi.org/10.1016/j.celrep.2022.111133
Primary Citation Related Structures:
7FGG, 7FGH, 7FGI, 7X01

PubMed Abstract:
Many viruses encode RNA-modifying enzymes to edit the 5' end of viral RNA to mimic the cellular mRNA for effective protein translation, genome replication, and evasion of the host defense mechanisms. Alphavirus nsP1 synthesizes the 5' end Cap-0 structure of viral RNAs. However, the molecular basis of the capping process remains unclear. We determine high-resolution cryoelectron microscopy (cryo-EM) structures of Chikungunya virus nsP1 in complex with m7GTP/SAH, covalently attached m7GMP, and Cap-0 viral RNA. These structures reveal details of viral-RNA-capping reactions and uncover a sequence-specific virus RNA-recognition pattern that, in turn, regulates viral-RNA-capping efficiency to ensure optimal genome replication and subgenomic RNA transcription. This sequence-specific enzyme-RNA pairing is conserved across all alphaviruses.

Organizational Affiliation

Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.

Macromolecule Content

Total Structure Weight: 749.03 kDa
Atom Count: 39,732
Modeled Residue Count: 5,052
Deposited Residue Count: 6,624
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA-capping enzyme nsP1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	552	Chikungunya virus strain S27-African prototype	Mutation(s): 0 EC: 2.1.1 (PDB Primary Data), 2.7.7 (PDB Primary Data)
UniProt
Find proteins for Q8JUX6 (Chikungunya virus (strain S27-African prototype)) Explore Q8JUX6 Go to UniProtKB: Q8JUX6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8JUX6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7XQ (Subject of Investigation/LOI) Query on 7XQ Download:Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain DA [auth I] SDF format, chain FA [auth J] SDF format, chain HA [auth K] SDF format, chain JA [auth L] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain Z [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain DA [auth I] MOL2 format, chain FA [auth J] MOL2 format, chain HA [auth K] MOL2 format, chain JA [auth L] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Z [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain DA [auth I] mmCIF format, chain FA [auth J] mmCIF format, chain HA [auth K] mmCIF format, chain JA [auth L] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Z [auth G]	BA [auth H] DA [auth I] FA [auth J] HA [auth K] JA [auth L] BA [auth H], DA [auth I], FA [auth J], HA [auth K], JA [auth L], N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]	(1R,2S,3S,4R,5R)-3-(6-aminopurin-9-yl)-4-fluoranyl-5-(2-hydroxyethyl)cyclopentane-1,2-diol C₁₂ H₁₆ F N₅ O₃ BHBYBYPYUGVDDF-LUTUWXHWSA-N		Interactions Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain CA [auth I] SDF format, chain EA [auth J] SDF format, chain GA [auth K] SDF format, chain IA [auth L] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain Y [auth G] MOL2 format, chain AA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain EA [auth J] MOL2 format, chain GA [auth K] MOL2 format, chain IA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth G] mmCIF format, chain AA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain EA [auth J] mmCIF format, chain GA [auth K] mmCIF format, chain IA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth G]	AA [auth H] CA [auth I] EA [auth J] GA [auth K] IA [auth L] AA [auth H], CA [auth I], EA [auth J], GA [auth K], IA [auth L], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G]