7FGI | pdb_00007fgi

Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7Gppp-AU

PDB DOI: https://doi.org/10.2210/pdb7FGI/pdb
NAKB: 7FGI
EM Map EMD-31582: EMDB EMDataResource

Classification: VIRAL PROTEIN/RNA
Organism(s): Chikungunya virus strain S27-African prototype, synthetic construct
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2021-07-27 Released: 2022-07-27
Deposition Author(s): Zhang, K., Law, M.C.Y., Nguyen, T.M., Tan, Y.B., Wirawan, M., Law, Y.S., Luo, D.H.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.51 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 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: 766.07 kDa
Atom Count: 42,288
Modeled Residue Count: 5,280
Deposited Residue Count: 6,660
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 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): 1 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

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
m7Gppp-AU	M, N, O, P, Q M, N, O, P, Q, R, S, T, U, V, W, X	3	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain VA [auth L] SDF format, chain TA [auth K] SDF format, chain RA [auth J] SDF format, chain PA [auth I] SDF format, chain NA [auth H] SDF format, chain LA [auth G] SDF format, chain JA [auth F] SDF format, chain HA [auth E] SDF format, chain FA [auth D] SDF format, chain DA [auth C] SDF format, chain BA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain VA [auth L] MOL2 format, chain TA [auth K] MOL2 format, chain RA [auth J] MOL2 format, chain PA [auth I] MOL2 format, chain NA [auth H] MOL2 format, chain LA [auth G] MOL2 format, chain JA [auth F] MOL2 format, chain HA [auth E] MOL2 format, chain FA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain BA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain VA [auth L] mmCIF format, chain TA [auth K] mmCIF format, chain RA [auth J] mmCIF format, chain PA [auth I] mmCIF format, chain NA [auth H] mmCIF format, chain LA [auth G] mmCIF format, chain JA [auth F] mmCIF format, chain HA [auth E] mmCIF format, chain FA [auth D] mmCIF format, chain DA [auth C] mmCIF format, chain BA [auth B]	BA [auth B] DA [auth C] FA [auth D] HA [auth E] JA [auth F] BA [auth B], DA [auth C], FA [auth D], HA [auth E], JA [auth F], LA [auth G], NA [auth H], PA [auth I], RA [auth J], TA [auth K], VA [auth L], Z [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain BA [auth B] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain HA [auth E] Focus chain JA [auth F] Focus chain LA [auth G] Focus chain NA [auth H] Focus chain PA [auth I] Focus chain RA [auth J] Focus chain TA [auth K] Focus chain VA [auth L] Focus chain Z [auth A] Interactions & Density Focus chain BA [auth B] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain HA [auth E] Focus chain JA [auth F] Focus chain LA [auth G] Focus chain NA [auth H] Focus chain PA [auth I] Focus chain RA [auth J] Focus chain TA [auth K] Focus chain VA [auth L] Focus chain Z [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain UA [auth L] SDF format, chain SA [auth K] SDF format, chain QA [auth J] SDF format, chain OA [auth I] SDF format, chain MA [auth H] SDF format, chain KA [auth G] SDF format, chain IA [auth F] SDF format, chain GA [auth E] SDF format, chain EA [auth D] SDF format, chain CA [auth C] SDF format, chain AA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain UA [auth L] MOL2 format, chain SA [auth K] MOL2 format, chain QA [auth J] MOL2 format, chain OA [auth I] MOL2 format, chain MA [auth H] MOL2 format, chain KA [auth G] MOL2 format, chain IA [auth F] MOL2 format, chain GA [auth E] MOL2 format, chain EA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain UA [auth L] mmCIF format, chain SA [auth K] mmCIF format, chain QA [auth J] mmCIF format, chain OA [auth I] mmCIF format, chain MA [auth H] mmCIF format, chain KA [auth G] mmCIF format, chain IA [auth F] mmCIF format, chain GA [auth E] mmCIF format, chain EA [auth D] mmCIF format, chain CA [auth C] mmCIF format, chain AA [auth B]	AA [auth B] CA [auth C] EA [auth D] GA [auth E] IA [auth F] AA [auth B], CA [auth C], EA [auth D], GA [auth E], IA [auth F], KA [auth G], MA [auth H], OA [auth I], QA [auth J], SA [auth K], UA [auth L], Y [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain CA [auth C] Focus chain EA [auth D] Focus chain GA [auth E] Focus chain IA [auth F] Focus chain KA [auth G] Focus chain MA [auth H] Focus chain OA [auth I] Focus chain QA [auth J] Focus chain SA [auth K] Focus chain UA [auth L] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth C] Focus chain EA [auth D] Focus chain GA [auth E] Focus chain IA [auth F] Focus chain KA [auth G] Focus chain MA [auth H] Focus chain OA [auth I] Focus chain QA [auth J] Focus chain SA [auth K] Focus chain UA [auth L] Focus chain Y [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain ZA [auth P] SDF format, chain YA [auth O] SDF format, chain XA [auth N] SDF format, chain WA [auth M] SDF format, chain HB [auth X] SDF format, chain GB [auth W] SDF format, chain FB [auth V] SDF format, chain EB [auth U] SDF format, chain DB [auth T] SDF format, chain CB [auth S] SDF format, chain BB [auth R] SDF format, chain AB [auth Q] MOL2 format, chain ZA [auth P] MOL2 format, chain YA [auth O] MOL2 format, chain XA [auth N] MOL2 format, chain WA [auth M] MOL2 format, chain HB [auth X] MOL2 format, chain GB [auth W] MOL2 format, chain FB [auth V] MOL2 format, chain EB [auth U] MOL2 format, chain DB [auth T] MOL2 format, chain CB [auth S] MOL2 format, chain BB [auth R] MOL2 format, chain AB [auth Q] mmCIF format, chain ZA [auth P] mmCIF format, chain YA [auth O] mmCIF format, chain XA [auth N] mmCIF format, chain WA [auth M] mmCIF format, chain HB [auth X] mmCIF format, chain GB [auth W] mmCIF format, chain FB [auth V] mmCIF format, chain EB [auth U] mmCIF format, chain DB [auth T] mmCIF format, chain CB [auth S] mmCIF format, chain BB [auth R] mmCIF format, chain AB [auth Q]	AB [auth Q] BB [auth R] CB [auth S] DB [auth T] EB [auth U] AB [auth Q], BB [auth R], CB [auth S], DB [auth T], EB [auth U], FB [auth V], GB [auth W], HB [auth X], WA [auth M], XA [auth N], YA [auth O], ZA [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth Q] Focus chain BB [auth R] Focus chain CB [auth S] Focus chain DB [auth T] Focus chain EB [auth U] Focus chain FB [auth V] Focus chain GB [auth W] Focus chain HB [auth X] Focus chain WA [auth M] Focus chain XA [auth N] Focus chain YA [auth O] Focus chain ZA [auth P] Interactions & Density Focus chain AB [auth Q] Focus chain BB [auth R] Focus chain CB [auth S] Focus chain DB [auth T] Focus chain EB [auth U] Focus chain FB [auth V] Focus chain GB [auth W] Focus chain HB [auth X] Focus chain WA [auth M] Focus chain XA [auth N] Focus chain YA [auth O] Focus chain ZA [auth P]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.51 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History

Deposition Data

Released Date: 2022-07-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-07-27
Type: Initial release
Version 1.1: 2022-08-10
Changes: Database references
Version 2.0: 2024-06-05
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary