2GTI | pdb_00002gti

mutation of MHV coronavirus non-structural protein nsp15 (F307L)

PDB DOI: https://doi.org/10.2210/pdb2GTI/pdb

Classification: VIRAL PROTEIN
Organism(s): Murine hepatitis virus strain A59
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-04-28 Released: 2006-08-15
Deposition Author(s): Xu, X., Zhai, Y., Sun, F., Lou, Z., Su, D., Rao, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.248 (Depositor), 0.256 (DCC)
R-Value Work:
0.229 (Depositor), 0.222 (DCC)
R-Value Observed:
0.231 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

New Antiviral Target Revealed by the Hexameric Structure of Mouse Hepatitis Virus Nonstructural Protein nsp15

Xu, X., Zhai, Y., Sun, F., Lou, Z., Su, D., Xu, Y., Zhang, R., Joachimiak, A., Zhang, X.C., Bartlam, M., Rao, Z.

(2006) J Virol 80: 7909-7917

PubMed: 16873248 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/JVI.00525-06
Primary Citation Related Structures:
2GTH, 2GTI

PubMed Abstract:
The unique coronavirus transcription/replication machinery comprised of multiple virus-encoded nonstructural proteins (nsp) plays a vital role during initial and intermediate phases of the viral life cycle. The crystal structure of mouse hepatitis virus strain A59 (MHV-A59) nsp15 is reported at 2.15-A resolution. nsp15 is an XendoU endoribonuclease and is the first one from this family to have its structure unveiled. The MHV-A59 nsp15 monomer structure has a novel protein fold. Two nsp15 trimers form a back-to-back hexamer that is believed to be the functional unit. The structure reveals the catalytic site including the highly conserved residues His262, His277, and Lys317, which is supported by mutagenesis analysis. Gel filtration and enzyme activity assays confirmed that the hexamer is the active form for nsp15 and demonstrate the specificity of nsp15 for uridylate. The high sequence conservation of nsp15 in coronaviruses, including that of severe acute respiratory syndrome, suggests that this protein may provide a new target for the design of antiviral therapeutics.

Organizational Affiliation

Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China.

Macromolecule Content

Total Structure Weight: 42.85 kDa
Atom Count: 3,077
Modeled Residue Count: 348
Deposited Residue Count: 370
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A	370	Murine hepatitis virus strain A59	Mutation(s): 6
UniProt
Find proteins for P0C6X9 (Murine coronavirus (strain A59)) Explore P0C6X9 Go to UniProtKB: P0C6X9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C6X9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.248 (Depositor), 0.256 (DCC)
R-Value Work: 0.229 (Depositor), 0.222 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.356	α = 90
b = 86.356	β = 90
c = 221.103	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
HKL-2000	data reduction
SOLVE	phasing
CNS	refinement
CrystalClear	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-08-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-08-15
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2024-10-23
Changes: Data collection, Structure summary