7Y38

Molecular architecture of the chikungunya virus replication complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Molecular architecture of the Chikungunya virus replication complex.

Tan, Y.B.Chmielewski, D.Law, M.C.Y.Zhang, K.He, Y.Chen, M.Jin, J.Luo, D.

(2022) Sci Adv 8: eadd2536-eadd2536

  • DOI: https://doi.org/10.1126/sciadv.add2536
  • Primary Citation of Related Structures:  
    7Y38

  • PubMed Abstract: 

    To better understand how positive-strand (+) RNA viruses assemble membrane-associated replication complexes (RCs) to synthesize, process, and transport viral RNA in virus-infected cells, we determined both the high-resolution structure of the core RNA replicase of chikungunya virus and the native RC architecture in its cellular context at subnanometer resolution, using in vitro reconstitution and in situ electron cryotomography, respectively. Within the core RNA replicase, the viral polymerase nsP4, which is in complex with nsP2 helicase-protease, sits in the central pore of the membrane-anchored nsP1 RNA-capping ring. The addition of a large cytoplasmic ring next to the C terminus of nsP1 forms the holo-RNA-RC as observed at the neck of spherules formed in virus-infected cells. These results represent a major conceptual advance in elucidating the molecular mechanisms of RNA virus replication and the principles underlying the molecular architecture of RCs, likely to be shared with many pathogenic (+) RNA viruses.


  • Organizational Affiliation

    Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA-capping enzyme nsP1,affinity-tag (strepII-3XFLAG)
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
573Chikungunya virus strain S27-African prototypesynthetic constructMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JUX6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase nsP4M [auth X]611Onyong-nyong virusMutation(s): 0 
Gene Names: nsP4
EC: 2.7.7.19 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for O90368 (O'nyong-nyong virus (strain SG650))
Explore O90368 
Go to UniProtKB:  O90368
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO90368
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protease nsP2N [auth Y]798Chikungunya virus strain S27-African prototypeMutation(s): 0 
EC: 3.1.3.33 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for Q8JUX6 (Chikungunya virus (strain S27-African prototype))
Explore Q8JUX6 
Go to UniProtKB:  Q8JUX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JUX6
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(P*CP*CP*A)-3')O [auth Z]3in vitro transcription vector pT7-TP(deltai)
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
CA [auth E]
FA [auth F]
JA [auth G]
MA [auth H]
PA [auth I]
CA [auth E],
FA [auth F],
JA [auth G],
MA [auth H],
PA [auth I],
R [auth A],
RA [auth J],
T [auth B],
VA [auth K],
W [auth C],
YA [auth L],
Z [auth D]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth D]
DA [auth E]
GA [auth F]
IA [auth G]
LA [auth H]
AA [auth D],
DA [auth E],
GA [auth F],
IA [auth G],
LA [auth H],
OA [auth I],
Q [auth A],
SA [auth J],
U [auth B],
UA [auth K],
X [auth C],
XA [auth L]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth E]
EA [auth F]
HA [auth G]
KA [auth H]
NA [auth I]
BA [auth E],
EA [auth F],
HA [auth G],
KA [auth H],
NA [auth I],
P [auth A],
QA [auth J],
S [auth B],
TA [auth K],
V [auth C],
WA [auth L],
Y [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTPHENIX1.2
MODEL REFINEMENTCoot0.9.5

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)SingaporeT2EP30220-0020, 2021-T1-002-021

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection, Refinement description