[English] 日本語
Yorodumi
- PDB-5tg1: 1.40 A resolution structure of Norovirus 3CL protease in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tg1
Title1.40 A resolution structure of Norovirus 3CL protease in complex with the a m-chlorophenyl substituted macrocyclic inhibitor (17-mer)
Components3C-LIKE PROTEASE
KeywordsPROTEASE/PROTEASE INHIBITOR / PROTEASE / NOROVIRUS / NORWALK VIRUS / ANTIVIRAL INHIBITORS / MACROCYCLIC INHIBITOR / PROTEASE-PROTEASE INHIBITOR complex
Function / homology
Function and homology information


calicivirin / host cell membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription ...calicivirin / host cell membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases ...Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
(4S,7S,17S)-17-(3-chlorophenyl)-7-(hydroxymethyl)-4-(2-methylpropyl)-1-oxa-3,6,11-triazacycloheptadecane-2,5,10-trione / Chem-V56 / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsLovell, S. / Battaile, K.P. / Mehzabeen, N. / Damalanka, V.C. / Kim, Y. / Kankanamalage, A.C.G. / Chang, K.-O. / Groutas, W.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109039 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110761 United States
CitationJournal: Eur J Med Chem / Year: 2016
Title: Design, synthesis, and evaluation of a novel series of macrocyclic inhibitors of norovirus 3CL protease.
Authors: Damalanka, V.C. / Kim, Y. / Galasiti Kankanamalage, A.C. / Lushington, G.H. / Mehzabeen, N. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C.
History
DepositionSep 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6794
Polymers20,1261
Non-polymers5533
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.397, 36.495, 61.474
Angle α, β, γ (deg.)90.000, 112.500, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-421-

HOH

-
Components

#1: Protein 3C-LIKE PROTEASE /


Mass: 20126.131 Da / Num. of mol.: 1 / Fragment: UNP residues 1101-1281
Source method: isolated from a genetically manipulated source
Details: N-terminal hexahistidine tag / Source: (gene. exp.) Norwalk virus / Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q83883, calicivirin
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-V56 / (4S,7S,17S)-17-(3-chlorophenyl)-7-(hydroxymethyl)-4-(2-methylpropyl)-1-oxa-3,6,11-triazacycloheptadecane-2,5,10-trione


Type: Cyclic peptide / Class: Inhibitor / Mass: 482.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H36ClN3O5
References: (4S,7S,17S)-17-(3-chlorophenyl)-7-(hydroxymethyl)-4-(2-methylpropyl)-1-oxa-3,6,11-triazacycloheptadecane-2,5,10-trione
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.66 Å3/Da / Density % sol: 25.81 % / Description: prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% (w/v) PEG 2000 MME, 150 potassium bromide

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→31.83 Å / Num. obs: 25218 / % possible obs: 96.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 14.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.4 / Num. measured all: 83610
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.4-1.423.20.6910.704195.3
7.54-31.833.10.0310.998197.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.4 Å29.99 Å
Translation2.4 Å29.99 Å

-
Processing

Software
NameVersionClassification
Aimless0.5.9data scaling
PHASER2.5.7phasing
PHENIXdev_2075refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UR9

3ur9


Resolution: 1.4→31.829 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 20.05
Details: Anisotropic atomic displacement parameters were refined for all atoms except solvent molecules.
RfactorNum. reflection% reflection
Rfree0.1919 1183 4.69 %
Rwork0.1425 --
obs0.1448 25213 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 50.59 Å2 / Biso mean: 19.3069 Å2 / Biso min: 6.61 Å2
Refinement stepCycle: final / Resolution: 1.4→31.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 35 128 1385
Biso mean--21.07 31.43 -
Num. residues----166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091323
X-RAY DIFFRACTIONf_angle_d1.0351807
X-RAY DIFFRACTIONf_chiral_restr0.089209
X-RAY DIFFRACTIONf_plane_restr0.007227
X-RAY DIFFRACTIONf_dihedral_angle_d17.885480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.46370.26411500.19292928307894
1.4637-1.54090.22351550.15732930308595
1.5409-1.63740.23631470.13612925307295
1.6374-1.76380.20211330.12973047318097
1.7638-1.94130.17411350.12313023315897
1.9413-2.22220.17871430.1233030317398
2.2222-2.79940.20571560.15053039319597
2.7994-31.83750.17731640.14793108327297

+
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