2PX8

Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH and 7M-GTP

PDB DOI: https://doi.org/10.2210/pdb2PX8/pdb

Classification: TRANSFERASE
Organism(s): Murray valley encephalitis virus (strain MVE-1-51)
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-05-14 Released: 2007-05-29
Deposition Author(s): Assenberg, R., Ren, J., Verma, A., Walter, T.S., Alderton, D., Hurrelbrink, R.J., Fuller, S.D., Owens, R.J., Stuart, D.I., Grimes, J.M., Oxford Protein Production Facility (OPPF)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.217
R-Value Work: 0.166
R-Value Observed: 0.169

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the Murray Valley encephalitis virus NS5 methyltransferase domain in complex with cap analogues.

Assenberg, R., Ren, J., Verma, A., Walter, T.S., Alderton, D., Hurrelbrink, R.J., Fuller, S.D., Bressanelli, S., Owens, R.J., Stuart, D.I., Grimes, J.M.

(2007) J Gen Virol 88: 2228-2236

PubMed: 17622627 Search on PubMed
DOI: https://doi.org/10.1099/vir.0.82757-0
Primary Citation of Related Structures:
2PX2, 2PX4, 2PX5, 2PX8, 2PXA, 2PXC

PubMed Abstract:
We have determined the high resolution crystal structure of the methyltransferase domain of the NS5 polypeptide from the Murray Valley encephalitis virus. This domain is unusual in having both the N7 and 2'-O methyltransferase activity required for Cap 1 synthesis. We have also determined structures for complexes of this domain with nucleotides and cap analogues providing information on cap binding, based on which we suggest a model of how the sequential methylation of the N7 and 2'-O groups of the cap may be coordinated.

Organizational Affiliation

Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK.

Macromolecule Content

Total Structure Weight: 63.95 kDa
Atom Count: 4,823
Modelled Residue Count: 529
Deposited Residue Count: 538
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein [Contains: Capsid protein C (Core protein); Envelope protein M (Matrix protein); Major envelope protein E; Non-structural protein 1 (NS1); Non-structural protein 2A (NS2A); Flavivirin protease NS2B regulatory subunit; Flavivirin protease NS3 catalytic subunit; Non-structural protein 4A (NS4A); Non-structural protein 4B (NS4B); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5)]	A, B	269	Murray valley encephalitis virus (strain MVE-1-51)	Mutation(s): 4 Gene Names: NS5 EC: 2.7.7.48
UniProt
Find proteins for P05769 (Murray valley encephalitis virus (strain MVE-1-51)) Explore P05769 Go to UniProtKB: P05769
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05769
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGT Query on MGT Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B], I [auth B]	7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE C₁₁ H₂₀ N₅ O₁₄ P₃ BUJQMJUTTBGELS-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B]
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	E [auth A], K [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
3PO Query on 3PO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	TRIPHOSPHATE H₅ O₁₀ P₃ UNXRWKVEANCORM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B]	F [auth A], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A, B	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.217
R-Value Work: 0.166
R-Value Observed: 0.169
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.579	α = 90
b = 87.445	β = 90
c = 100.914	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-05-29

Deposition Author(s):

Oxford Protein Production Facility (OPPF)

Revision History (Full details and data files)

Version 1.0: 2007-05-29
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description