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- PDB-5m2z: Crystal structure of the full-length Zika virus NS5 protein (Huma... -

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Basic information

Entry
Database: PDB / ID: 5m2z
TitleCrystal structure of the full-length Zika virus NS5 protein (Human isolate Z1106033)
ComponentsNS5
KeywordsHYDROLASE / Zika / Polymerase
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / 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 / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / 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 / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / 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 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / 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 central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus glycoprotein, immunoglobulin-like 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 / 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
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: 4.8 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
Maria de Maeztu Unit of ExcellenceMDM-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
DepositionOct 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
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
Revision 1.2Jan 17, 2024Group: 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)629,46737
Polymers625,9806
Non-polymers3,48731
Water00
1
A: NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7466
Polymers104,3301
Non-polymers4165
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 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
B: NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7466
Polymers104,3301
Non-polymers4165
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6515
Polymers104,3301
Non-polymers3214
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2258
Polymers104,3301
Non-polymers8957
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1307
Polymers104,3301
Non-polymers8006
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)234.578, 234.578, 406.123
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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 (strain Mr 766) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A172HA24, UniProt: A0A0X8GJ44*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S

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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: 5.15 Å3/Da / Density % sol: 76.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 100 mM Sodium Acetate, 1 M di-potassium hydrogen phosphate, 0.95 M sodium di-hydrogen phosphate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97928 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 4.8→44.07 Å / Num. obs: 61390 / % possible obs: 99.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 5.9
Reflection shellResolution: 4.8→5.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.495 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5m2x

5m2x


Resolution: 4.8→44.323 Å / SU ML: 0.71 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2657 3118 5.1 %
Rwork0.2407 --
obs0.2419 61148 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.8→44.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42582 0 174 0 42756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243725
X-RAY DIFFRACTIONf_angle_d0.5359100
X-RAY DIFFRACTIONf_dihedral_angle_d19.21926034
X-RAY DIFFRACTIONf_chiral_restr0.0396213
X-RAY DIFFRACTIONf_plane_restr0.0047560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.8-4.8750.33671730.34012516X-RAY DIFFRACTION98
4.875-4.95480.33661460.34132642X-RAY DIFFRACTION99
4.9548-5.04010.34251100.33212646X-RAY DIFFRACTION99
5.0401-5.13160.39161400.33332655X-RAY DIFFRACTION99
5.1316-5.23020.33461380.33182572X-RAY DIFFRACTION99
5.2302-5.33680.34251510.31762689X-RAY DIFFRACTION99
5.3368-5.45260.35011190.31932651X-RAY DIFFRACTION99
5.4526-5.57920.34811480.29872629X-RAY DIFFRACTION100
5.5792-5.71840.30681350.28562652X-RAY DIFFRACTION100
5.7184-5.87270.32131400.30852644X-RAY DIFFRACTION100
5.8727-6.04510.3171240.29912651X-RAY DIFFRACTION100
6.0451-6.23970.33341210.28582632X-RAY DIFFRACTION99
6.2397-6.46210.29981590.27522638X-RAY DIFFRACTION100
6.4621-6.720.26921510.25852616X-RAY DIFFRACTION99
6.72-7.02470.2671430.23772639X-RAY DIFFRACTION100
7.0247-7.39340.24041940.22492625X-RAY DIFFRACTION100
7.3934-7.85430.25041600.20652643X-RAY DIFFRACTION100
7.8543-8.45680.24711650.19252630X-RAY DIFFRACTION100
8.4568-9.30080.19451150.17032676X-RAY DIFFRACTION100
9.3008-10.63040.1981410.16272647X-RAY DIFFRACTION100
10.6304-13.33240.19361240.17432667X-RAY DIFFRACTION99
13.3324-44.32460.29811210.29972670X-RAY DIFFRACTION98

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