[English] 日本語
Yorodumi
- PDB-5omz: Solution structure of domain III (DIII)of Zika virus Envelope protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5omz
TitleSolution structure of domain III (DIII)of Zika virus Envelope protein
ComponentsEnvelope ProteinViral envelope
KeywordsVIRAL PROTEIN / ZIKA virus Envelope protein domain / ZIKV
Function / homology
Function and homology information


suppression by virus of host innate immune response / host cell endoplasmic reticulum / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA (guanine-N7-)-methyltransferase activity / host cell membrane / double-stranded RNA binding / viral capsid / induction by virus of host autophagy / fusion of virus membrane with host endosome membrane / viral RNA genome replication ...suppression by virus of host innate immune response / host cell endoplasmic reticulum / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA (guanine-N7-)-methyltransferase activity / host cell membrane / double-stranded RNA binding / viral capsid / induction by virus of host autophagy / fusion of virus membrane with host endosome membrane / viral RNA genome replication / RNA helicase activity / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / virion attachment to host cell / virion membrane / serine-type endopeptidase activity / structural molecule activity / integral component of membrane / ATP binding / metal ion binding
Flaviviral glycoprotein E, central domain, subdomain 1 / S-adenosyl-L-methionine-dependent methyltransferase / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / DEAD box, Flavivirus / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 2 / Helicase superfamily 1/2, ATP-binding domain / Genome polyprotein, Flavivirus / Immunoglobulin E-set ...Flaviviral glycoprotein E, central domain, subdomain 1 / S-adenosyl-L-methionine-dependent methyltransferase / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / DEAD box, Flavivirus / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 2 / Helicase superfamily 1/2, ATP-binding domain / Genome polyprotein, Flavivirus / Immunoglobulin E-set / Flavivirus envelope glycoprotein E, Stem/Anchor domain / mRNA cap 0/1 methyltransferase / Flavivirus glycoprotein E, immunoglobulin-like domain / P-loop containing nucleoside triphosphate hydrolase / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flavivirus polyprotein propeptide / Flavivirus capsid protein C superfamily / Flaviviral glycoprotein E, dimerisation domain / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus polyprotein propeptide superfamily / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus non-structural Protein NS1 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus RNA-directed RNA polymerase / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus envelope glycoprotein M / Flavivirus non-structural protein NS2A / Ribosomal RNA methyltransferase FtsJ domain / Flavivirus NS3, petidase S7 / Flavivirus non-structural protein NS4A / FtsJ-like methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus NS2B domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Flavivirus DEAD domain / Helicase, C-terminal / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus non-structural protein NS4B / Flavivirus polyprotein propeptide / RNA-directed RNA polymerase, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS1 / Flavivirus non-structural protein NS4A / Envelope glycoprotein M, flavivirus / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS2A / Flavivirus capsid protein C
Genome polyprotein / Genome polyprotein
Biological speciesZika virus
MethodSOLUTION NMR / simulated annealing
AuthorsZerbe, O. / Bardelli, M.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope Protein


Theoretical massNumber of molelcules
Total (without water)12,4791
Polymers12,4791
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9230 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Envelope Protein / Viral envelope


Mass: 12479.393 Da / Num. of mol.: 1 / Fragment: DOMAIN DIII, UNP residues 585-699
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus (strain Mr 766) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V0E2E5, UniProt: A0A0X8GJ44*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment

Conditions-ID: 1 / Sample state: isotropic

Experiment-IDSolution-IDSpectrometer-IDType
1112D 1H-15N HSQC
15122D 1H-13C HSQC aliphatic
16122D 1H-13C HSQC aromatic
5123D HNCO
10123D HN(CA)CO
3123D CBCA(CO)NH
4123D HN(CA)CB
12123D (H)CCH-TOCSY
14123D H(C)CH
11123D HBHA(CO)NH
9123D 1H-15N NOESY
8123D 1H-13C NOESY aliphatic
7123D 1H-13C NOESY aromatic
2222D 1H-15N HSQC
6223D 1H-15N NOESY
13223D HNCO

-
Sample preparation

Details

Solvent system: 90% H2O/10% D2O / Type: solution

Solution-IDContentsDetailsLabel
1800 uM 15N,13C ZIKA Envelope DIII, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2Osample for resonance assignment and structure determinationsample_H2O
2400 uM 2H,13C,15N ZIKA Envelope DIII, 20 mM sodium phosphate, 50 mM sodium chloride, 440 uM ZKA190 Fab, 90% H2O/10% D2Operdeuterated 13C,15N samplesample for mapping
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
800 uMZIKA Envelope DIII15N,13C1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
400 uMZIKA Envelope DIII2H,13C,15N2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
440 uMZKA190 Fabnatural abundance2
Sample conditionsIonic strength: 0.27 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 300 K

-
NMR measurement

NMR spectrometer

Manufacturer: Bruker

TypeModelField strength (MHz)Spectrometer-ID
Bruker AV 4AV 46001
Bruker AvanceAvance7002

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospinprocessing
CARA1.93Keller and Wuthrichchemical shift assignment
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: further refinement in AMBER
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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