[English] 日本語
Yorodumi
- PDB-5ccv: Crystal structure of full-length NS5 from dengue virus type 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ccv
TitleCrystal structure of full-length NS5 from dengue virus type 3
ComponentsRNA-directed RNA polymerase NS5
KeywordsTRANSFERASE / methyltransferase / nonstructural protein
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / 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 / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 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 / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus type 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å
AuthorsKlema, V.J. / Choi, K.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 A1 087856 United States
CitationJournal: Plos Pathog. / Year: 2016
Title: Dengue Virus Nonstructural Protein 5 (NS5) Assembles into a Dimer with a Unique Methyltransferase and Polymerase Interface.
Authors: Klema, V.J. / Ye, M. / Hindupur, A. / Teramoto, T. / Gottipati, K. / Padmanabhan, R. / Choi, K.H.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Data collection
Revision 1.2May 12, 2021Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-directed RNA polymerase NS5
B: RNA-directed RNA polymerase NS5
C: RNA-directed RNA polymerase NS5
D: RNA-directed RNA polymerase NS5
E: RNA-directed RNA polymerase NS5
F: RNA-directed RNA polymerase NS5
G: RNA-directed RNA polymerase NS5
H: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)837,24232
Polymers833,1208
Non-polymers4,12224
Water0
1
A: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6554
Polymers104,1401
Non-polymers5153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6554
Polymers104,1401
Non-polymers5153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6554
Polymers104,1401
Non-polymers5153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6554
Polymers104,1401
Non-polymers5153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6554
Polymers104,1401
Non-polymers5153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6554
Polymers104,1401
Non-polymers5153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6554
Polymers104,1401
Non-polymers5153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6554
Polymers104,1401
Non-polymers5153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: RNA-directed RNA polymerase NS5
F: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,3108
Polymers208,2802
Non-polymers1,0306
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-17 kcal/mol
Surface area73510 Å2
MethodPISA
10
A: RNA-directed RNA polymerase NS5
B: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,3108
Polymers208,2802
Non-polymers1,0306
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-12 kcal/mol
Surface area74500 Å2
MethodPISA
11
C: RNA-directed RNA polymerase NS5
D: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,3108
Polymers208,2802
Non-polymers1,0306
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-12 kcal/mol
Surface area74230 Å2
MethodPISA
12
D: RNA-directed RNA polymerase NS5
G: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,3108
Polymers208,2802
Non-polymers1,0306
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-15 kcal/mol
Surface area73640 Å2
MethodPISA
13
E: RNA-directed RNA polymerase NS5
F: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,3108
Polymers208,2802
Non-polymers1,0306
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-10 kcal/mol
Surface area74260 Å2
MethodPISA
14
G: RNA-directed RNA polymerase NS5
H: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,3108
Polymers208,2802
Non-polymers1,0306
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-87 kcal/mol
Surface area79220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.314, 215.314, 480.683
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein
RNA-directed RNA polymerase NS5 / Non-structural protein 5


Mass: 104139.984 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus type 3 / Strain: Philippines/H87/1956 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: P27915, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H20N6O5S

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M succinic acid (pH 7.0), 0.1 M HEPES (pH 7.0), 1% PEG monomethylether 2000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 2, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 149778 / % possible obs: 100 % / Redundancy: 16.4 % / Biso Wilson estimate: 100.57 Å2 / Rmerge(I) obs: 0.33 / Rpim(I) all: 0.097 / Rrim(I) all: 0.339 / Χ2: 1.155 / Net I/av σ(I): 6.803 / Net I/σ(I): 4.6 / Num. measured all: 2458145
Reflection shell

Diffraction-ID: 1 / Rejects: 0 / % possible all: 100

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2Rmerge(I) obsRrim(I) all
3.6-3.666.273920.1570.8661.198
3.66-3.737.473990.2660.7251.173
3.73-3.88.573970.3770.5691.151
3.8-3.889.874370.5240.4711.192
3.88-3.9611.374230.6280.3821.233
3.96-4.0513.274250.7470.2971.214
4.05-4.1614.673930.8230.2441.2310.9030.936
4.16-4.2715.774090.8860.21.2370.7690.795
4.27-4.3917.374880.9080.1561.2370.630.649
4.39-4.5419.973780.9350.1311.2360.5710.586
4.54-4.720.574920.9420.1221.2040.5410.555
4.7-4.8920.674580.9540.1061.2110.4720.484
4.89-5.1120.674920.9580.1021.2140.4520.463
5.11-5.3820.674640.960.0971.2010.430.441
5.38-5.7120.674790.9650.0921.1090.4090.419
5.71-6.1520.675410.9710.0831.0910.3680.378
6.15-6.7720.675470.9760.0711.0760.3150.323
6.77-7.7520.575640.9820.0591.0310.2630.269
7.75-9.7520.276500.9890.0470.9820.210.215
9.75-501979500.9640.0391.0690.1640.169

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
Coot0.7model building
HKL-20002.3.7data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3P97 and 4HHJ

3p97

4hhj


Resolution: 3.6→49.217 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2737 2004 1.34 %Random selection
Rwork0.2381 ---
obs0.2386 149621 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→49.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52457 0 224 0 52681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253947
X-RAY DIFFRACTIONf_angle_d0.47873136
X-RAY DIFFRACTIONf_dihedral_angle_d9.72719771
X-RAY DIFFRACTIONf_chiral_restr0.0217854
X-RAY DIFFRACTIONf_plane_restr0.0029440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.690.39931440.365210366X-RAY DIFFRACTION100
3.69-3.78970.43661400.352310419X-RAY DIFFRACTION100
3.7897-3.90120.37961380.329310475X-RAY DIFFRACTION100
3.9012-4.02710.30561440.309710416X-RAY DIFFRACTION100
4.0271-4.17090.37211400.286910463X-RAY DIFFRACTION100
4.1709-4.33780.29361430.264910490X-RAY DIFFRACTION100
4.3378-4.53510.27341400.24910453X-RAY DIFFRACTION100
4.5351-4.77410.29471440.239710553X-RAY DIFFRACTION100
4.7741-5.07290.26081440.231710504X-RAY DIFFRACTION100
5.0729-5.46410.24121430.231510524X-RAY DIFFRACTION100
5.4641-6.01310.35251420.239910601X-RAY DIFFRACTION100
6.0131-6.88120.25991470.221710603X-RAY DIFFRACTION100
6.8812-8.66190.21271410.192710718X-RAY DIFFRACTION100
8.6619-49.22110.1751540.155511032X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -115.4143 Å / Origin y: 62.2044 Å / Origin z: 39.5627 Å
111213212223313233
T0.9142 Å20.0592 Å2-0.0504 Å2-1.0036 Å2-0.0643 Å2--0.8998 Å2
L0.34 °2-0.0476 °2-0.0977 °2-0.138 °20.0636 °2--0.197 °2
S0.0488 Å °0.07 Å °-0.0423 Å °-0.0699 Å °-0.0656 Å °0.0799 Å °0.0097 Å °-0.0846 Å °0.0177 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more