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- PDB-4mtp: RdRp from Japanesese Encephalitis Virus -

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Basic information

Entry
Database: PDB / ID: 4mtp
TitleRdRp from Japanesese Encephalitis Virus
ComponentsRNA dependent RNA polymerase
KeywordsTRANSFERASE / RNA dependent RNA Polymerase / Nucleotidyltransferases / apo
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 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 / host cell surface / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / symbiont entry into host cell / induction by virus of host autophagy / serine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Flavivirus RNA-directed RNA polymerase, thumb domain / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Flavivirus RNA-directed RNA polymerase, thumb domain / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / 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, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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 / 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 / Alpha-Beta Plaits / 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 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesJapanese encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsSurana, P. / Nair, D.T.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state.
Authors: Surana, P. / Satchidanandam, V. / Nair, D.T.
History
DepositionSep 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA dependent RNA polymerase
B: RNA dependent RNA polymerase
C: RNA dependent RNA polymerase
D: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,41612
Polymers291,8924
Non-polymers5238
Water00
1
A: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1043
Polymers72,9731
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1043
Polymers72,9731
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1043
Polymers72,9731
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1043
Polymers72,9731
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.470, 174.010, 182.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
RNA dependent RNA polymerase


Mass: 72973.117 Da / Num. of mol.: 4 / Fragment: RdRp module of NS5 (UNP Residues 2799-3422)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Japanese encephalitis virus / Gene: NS5 / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3
References: UniProt: G3LHD9, UniProt: P27395*PLUS, RNA-directed RNA polymerase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10-15% PEG 5000 mono methyl ether, 100mM Tris-Cl pH 8.0, 200mM NaSCN, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.65→56.7838 Å / Num. all: 81766 / Num. obs: 81030 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.65→3.6929 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.569 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.65→56.777 Å / SU ML: 0.5 / σ(F): 1.04 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 4087 5.04 %Random R-free value of 0 was used for refinement
Rwork0.2263 ---
obs0.2287 81030 99.1 %-
all-81766 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.65→56.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18714 0 8 0 18722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319154
X-RAY DIFFRACTIONf_angle_d0.68225910
X-RAY DIFFRACTIONf_dihedral_angle_d11.5257099
X-RAY DIFFRACTIONf_chiral_restr0.0452755
X-RAY DIFFRACTIONf_plane_restr0.0033312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.65-3.69290.45611330.3812636X-RAY DIFFRACTION99
3.6929-3.7380.34331200.31372723X-RAY DIFFRACTION100
3.738-3.78530.32711480.28542658X-RAY DIFFRACTION100
3.7853-3.83510.31431640.25692691X-RAY DIFFRACTION100
3.8351-3.88760.34011120.30312652X-RAY DIFFRACTION99
3.8876-3.94310.33711520.29672623X-RAY DIFFRACTION99
3.9431-4.0020.29741190.25072690X-RAY DIFFRACTION100
4.002-4.06450.28571350.2562684X-RAY DIFFRACTION100
4.0645-4.13110.29481470.23832673X-RAY DIFFRACTION100
4.1311-4.20230.25771750.23172578X-RAY DIFFRACTION100
4.2023-4.27870.27461260.2192738X-RAY DIFFRACTION100
4.2787-4.3610.25831430.22242647X-RAY DIFFRACTION99
4.361-4.44990.21991450.21422636X-RAY DIFFRACTION99
4.4499-4.54670.28261500.20542663X-RAY DIFFRACTION100
4.5467-4.65240.22731600.20692652X-RAY DIFFRACTION99
4.6524-4.76870.2921280.20852661X-RAY DIFFRACTION99
4.7687-4.89750.29031350.22062658X-RAY DIFFRACTION99
4.8975-5.04160.29121400.22052662X-RAY DIFFRACTION99
5.0416-5.20420.27341650.20372631X-RAY DIFFRACTION99
5.2042-5.390.28471410.2182645X-RAY DIFFRACTION99
5.39-5.60570.23291290.20212661X-RAY DIFFRACTION99
5.6057-5.86060.26641140.21952684X-RAY DIFFRACTION99
5.8606-6.16920.271330.21592636X-RAY DIFFRACTION99
6.1692-6.55520.25191180.22162679X-RAY DIFFRACTION99
6.5552-7.06040.31171610.21952608X-RAY DIFFRACTION98
7.0604-7.76940.29071540.20392622X-RAY DIFFRACTION99
7.7694-8.88990.24051710.16862591X-RAY DIFFRACTION98
8.8899-11.18630.16521230.15872666X-RAY DIFFRACTION98
11.1863-56.78380.26591460.25922595X-RAY DIFFRACTION97

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