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- PDB-6i7p: Crystal structure of the full-length Zika virus NS5 protein (Huma... -

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Basic information

Entry
Database: PDB / ID: 6i7p
TitleCrystal structure of the full-length Zika virus NS5 protein (Human isolate Z1106033)
ComponentsNS5
KeywordsVIRAL PROTEIN / Zika / Polymerase
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 / negative regulation of innate immune response / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding ...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 / negative regulation of innate immune response / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / 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 / RNA helicase activity / molecular adaptor activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / centrosome / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor 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 NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus envelope glycoprotein E, stem/anchor 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 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 / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.975 Å
AuthorsFerrero, D.S. / Ruiz-Arroyo, V.M. / Soler, N. / Uson, I. / Verdaguer, N.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministry of Economy and CompetitivenessBIO2014-54588 Spain
Spanish Ministry of Economy and CompetitivenessMDM-2014-0435 Spain
CitationJournal: Plos Pathog. / Year: 2019
Title: Supramolecular arrangement of the full-length Zika virus NS5.
Authors: Ferrero, D.S. / Ruiz-Arroyo, V.M. / Soler, N. / Uson, I. / Guarne, A. / Verdaguer, N.
History
DepositionNov 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS5
B: NS5
C: NS5
D: NS5
E: NS5
F: NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)630,43038
Polymers625,9806
Non-polymers4,45132
Water0
1
A: NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0356
Polymers104,3301
Non-polymers7055
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9705
Polymers104,3301
Non-polymers6404
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9405
Polymers104,3301
Non-polymers6104
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2258
Polymers104,3301
Non-polymers8957
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0356
Polymers104,3301
Non-polymers7055
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2258
Polymers104,3301
Non-polymers8957
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.060, 192.060, 407.230
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
NS5


Mass: 104329.922 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B2ZC85, UniProt: A0A024B7W1*PLUS
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / 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: 5.97 Å3/Da / Density % sol: 79.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 100 mM Sodium Acetate, 0.950 M di-potassium hydrogen phosphate, 1.1 M sodium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 3.97→49.52 Å / Num. obs: 128656 / % possible obs: 99.6 % / Redundancy: 30.2 % / Rmerge(I) obs: 0.963 / Rpim(I) all: 0.175 / Net I/σ(I): 5.2
Reflection shellResolution: 3.975→4.05 Å / Redundancy: 22.2 % / Rmerge(I) obs: 1.941 / Mean I/σ(I) obs: 2 / Num. unique obs: 6433 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5m2x

5m2x


Resolution: 3.975→49.517 Å / SU ML: 0.72 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.63
RfactorNum. reflection% reflection
Rfree0.2804 128652 100 %
Rwork0.2804 --
obs0.2804 128652 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.975→49.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42575 0 242 0 42817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743793
X-RAY DIFFRACTIONf_angle_d0.96359198
X-RAY DIFFRACTIONf_dihedral_angle_d21.69816372
X-RAY DIFFRACTIONf_chiral_restr0.056226
X-RAY DIFFRACTIONf_plane_restr0.0077565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9751-4.02030.365736890.36573689X-RAY DIFFRACTION87
4.0203-4.06760.367842710.36784271X-RAY DIFFRACTION100
4.0676-4.11720.35842370.3584237X-RAY DIFFRACTION100
4.1172-4.16920.359343100.35934310X-RAY DIFFRACTION100
4.1692-4.22410.361242270.36124227X-RAY DIFFRACTION100
4.2241-4.28190.362642750.36264275X-RAY DIFFRACTION100
4.2819-4.34310.359242740.35924274X-RAY DIFFRACTION100
4.3431-4.40780.359942560.35994256X-RAY DIFFRACTION100
4.4078-4.47670.355242790.35524279X-RAY DIFFRACTION100
4.4767-4.550.351442850.35144285X-RAY DIFFRACTION100
4.55-4.62840.346442180.34644218X-RAY DIFFRACTION100
4.6284-4.71250.341542700.34154270X-RAY DIFFRACTION100
4.7125-4.80310.347743030.34774303X-RAY DIFFRACTION100
4.8031-4.9010.338342780.33834278X-RAY DIFFRACTION100
4.901-5.00750.332142910.33214291X-RAY DIFFRACTION100
5.0075-5.12390.31242650.3124265X-RAY DIFFRACTION100
5.1239-5.25190.309642770.30964277X-RAY DIFFRACTION100
5.2519-5.39370.310442900.31044290X-RAY DIFFRACTION100
5.3937-5.55220.311943040.31194304X-RAY DIFFRACTION100
5.5522-5.73120.294443060.29444306X-RAY DIFFRACTION100
5.7312-5.93570.292543110.29254311X-RAY DIFFRACTION100
5.9357-6.17290.276743320.27674332X-RAY DIFFRACTION100
6.1729-6.45330.268142960.26814296X-RAY DIFFRACTION100
6.4533-6.79270.243643290.24364329X-RAY DIFFRACTION100
6.7927-7.21710.226843180.22684318X-RAY DIFFRACTION100
7.2171-7.77240.199643700.19964370X-RAY DIFFRACTION100
7.7724-8.55090.158443420.15844342X-RAY DIFFRACTION100
8.5509-9.780.127844010.12784401X-RAY DIFFRACTION100
9.78-12.29060.120744400.12074440X-RAY DIFFRACTION100
12.2906-49.52120.232546080.23254608X-RAY DIFFRACTION100

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