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- PDB-5ulp: Structure of the NS5 methyltransferase from Zika bound to MS2042 -

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Basic information

Entry
Database: PDB / ID: 5ulp
TitleStructure of the NS5 methyltransferase from Zika bound to MS2042
ComponentsMRNA cap 0-1 NS5-type methyltransferase
KeywordsHYDROLASE / Zika / Flavivirus / NS5 / methyltransferase / MS2042 / SAM analog
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / molecular adaptor activity / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / centrosome / lipid binding / viral envelope / host cell nucleus / virion attachment to host cell / GTP binding / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / : / Flavivirus NS3 helicase, C-terminal helical domain / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Vaccinia Virus protein VP39 / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Chem-KB1 / UREA / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsJain, R. / Aggarwal, A.K.
CitationJournal: Sci Rep / Year: 2017
Title: Development of a S-adenosylmethionine analog that intrudes the RNA-cap binding site of Zika methyltransferase.
Authors: Jain, R. / Butler, K.V. / Coloma, J. / Jin, J. / Aggarwal, A.K.
History
DepositionJan 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MRNA cap 0-1 NS5-type methyltransferase
B: MRNA cap 0-1 NS5-type methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,84119
Polymers59,1622
Non-polymers1,67917
Water10,827601
1
A: MRNA cap 0-1 NS5-type methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,42610
Polymers29,5811
Non-polymers8459
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MRNA cap 0-1 NS5-type methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4159
Polymers29,5811
Non-polymers8348
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.989, 111.231, 77.400
Angle α, β, γ (deg.)90.00, 93.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein MRNA cap 0-1 NS5-type methyltransferase


Mass: 29580.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766 / Production host: Escherichia coli (E. coli) / References: UniProt: B3U3M3, UniProt: A0A024B7W1*PLUS

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Non-polymers , 6 types, 618 molecules

#2: Chemical ChemComp-KB1 / 5'-{[(3S)-3-amino-3-carboxypropyl][(4-fluorophenyl)methyl]amino}-5'-deoxyadenosine


Mass: 475.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H26FN7O5
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH4N2O
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.095 M Sodium sodium citrate tribasic dihydrate, pH 5.6, 19 % v/v 2-Propanol, 19 % w/v PEG 4K, 5 % v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03324 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 95052 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rsym value: 0.063 / Net I/σ(I): 23.1
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 4622 / Num. unique obs: 14622 / Rsym value: 0.6 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KQS

5kqs


Resolution: 1.55→35.724 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4
RfactorNum. reflection% reflection
Rfree0.1992 4620 4.86 %
Rwork0.1731 --
obs0.1744 95009 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→35.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 110 601 4694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064385
X-RAY DIFFRACTIONf_angle_d0.8455952
X-RAY DIFFRACTIONf_dihedral_angle_d16.8732674
X-RAY DIFFRACTIONf_chiral_restr0.052635
X-RAY DIFFRACTIONf_plane_restr0.005763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5493-1.56690.25251420.26322813X-RAY DIFFRACTION93
1.5669-1.58530.25831310.24582950X-RAY DIFFRACTION99
1.5853-1.60470.28411330.23713033X-RAY DIFFRACTION100
1.6047-1.6250.27011490.22653066X-RAY DIFFRACTION100
1.625-1.64640.22351480.2222987X-RAY DIFFRACTION100
1.6464-1.66890.25881830.21532944X-RAY DIFFRACTION100
1.6689-1.69280.25381600.21663087X-RAY DIFFRACTION100
1.6928-1.7180.25691430.21643010X-RAY DIFFRACTION100
1.718-1.74490.21451330.21243004X-RAY DIFFRACTION100
1.7449-1.77350.24881490.21283054X-RAY DIFFRACTION100
1.7735-1.80410.23081530.20252998X-RAY DIFFRACTION100
1.8041-1.83690.19511690.19483009X-RAY DIFFRACTION100
1.8369-1.87220.21051770.20152991X-RAY DIFFRACTION100
1.8722-1.91040.2491590.19782971X-RAY DIFFRACTION100
1.9104-1.9520.2161660.20073053X-RAY DIFFRACTION100
1.952-1.99740.23051270.19143033X-RAY DIFFRACTION100
1.9974-2.04730.21371270.19313071X-RAY DIFFRACTION100
2.0473-2.10260.23551470.19242989X-RAY DIFFRACTION100
2.1026-2.16450.19711630.18563042X-RAY DIFFRACTION100
2.1645-2.23440.2121520.18692983X-RAY DIFFRACTION100
2.2344-2.31420.24091550.18553032X-RAY DIFFRACTION100
2.3142-2.40690.17931720.17713032X-RAY DIFFRACTION100
2.4069-2.51640.19051620.18092977X-RAY DIFFRACTION100
2.5164-2.6490.23341560.18783040X-RAY DIFFRACTION100
2.649-2.81490.22171600.17963006X-RAY DIFFRACTION100
2.8149-3.03210.21011740.17483030X-RAY DIFFRACTION100
3.0321-3.33710.18231660.16622998X-RAY DIFFRACTION100
3.3371-3.81950.18511480.14393054X-RAY DIFFRACTION100
3.8195-4.81030.15771360.12893080X-RAY DIFFRACTION100
4.8103-35.73390.1611800.15673052X-RAY DIFFRACTION100

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