[English] 日本語
Yorodumi
- PDB-6w5h: 1.85 A resolution structure of Norovirus 3CL protease in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w5h
Title1.85 A resolution structure of Norovirus 3CL protease in complex with inhibitor 5d
Components3C-LIKE PROTEASE
KeywordsHYDROLASE/HYDROLASE Inhibitor / PROTEASE / Norovirus 3CL protease / Inhhibitors / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication ...calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / extracellular region / ATP binding / metal ion 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 / RNA-directed RNA polymerase, C-terminal domain ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2-(3-chlorophenyl)-2-methylpropyl [(2S)-3-cyclohexyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate / Chem-TKP / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Rathnayake, A.D. / Kim, Y. / 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)R01 AI109039 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structure-Guided Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease.
Authors: Rathnayake, A.D. / Kim, Y. / Dampalla, C.S. / Nguyen, H.N. / Jesri, A.M. / Kashipathy, M.M. / Lushington, G.H. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C.
History
DepositionMar 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Structure summary / Category: pdbx_molecule_features
Revision 1.2Nov 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3C-LIKE PROTEASE
B: 3C-LIKE PROTEASE
C: 3C-LIKE PROTEASE
D: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0688
Polymers79,9804
Non-polymers2,0884
Water2,648147
1
A: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5172
Polymers19,9951
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5172
Polymers19,9951
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5172
Polymers19,9951
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5172
Polymers19,9951
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.943, 38.028, 115.241
Angle α, β, γ (deg.)92.310, 98.310, 96.640
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
3C-LIKE PROTEASE


Mass: 19994.934 Da / Num. of mol.: 4
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)
Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q83883, calicivirin
#2: Chemical
ChemComp-TKP / 2-(3-chlorophenyl)-2-methylpropyl [(2S)-3-cyclohexyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate


Type: Peptide-like / Class: Inhibitor / Mass: 522.077 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H40ClN3O5 / Feature type: SUBJECT OF INVESTIGATION
References: 2-(3-chlorophenyl)-2-methylpropyl [(2S)-3-cyclohexyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 20% w/v PEG 2000 MME, 0.1 M Tris, 200 mM NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→37.95 Å / Num. obs: 50861 / % possible obs: 96.8 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.8 / Num. measured all: 178212 / Scaling rejects: 3
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.759 / Num. measured all: 10940 / Num. unique obs: 3063 / CC1/2: 0.784 / Net I/σ(I) obs: 1.8 / % possible all: 95.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.25 Å113.84 Å
Translation3.25 Å113.84 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
PHENIXdev_3342refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UR9

3ur9


Resolution: 1.85→36.433 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.05 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 2449 4.82 %
Rwork0.1827 48363 -
obs0.1846 50812 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.9 Å2 / Biso mean: 40.2077 Å2 / Biso min: 20.58 Å2
Refinement stepCycle: final / Resolution: 1.85→36.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4833 0 144 147 5124
Biso mean--40.55 43.4 -
Num. residues----663
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.88780.2851350.2352278295
1.8878-1.92880.28861590.2279283096
1.9288-1.97370.28851590.2161275496
1.9737-2.0230.24641430.2016287597
2.023-2.07770.26151480.195284396
2.0777-2.13890.22691460.1816282597
2.1389-2.20790.24721360.1816283897
2.2079-2.28680.22121380.1841287197
2.2868-2.37830.23491380.1887290997
2.3783-2.48650.27321600.1958281997
2.4865-2.61760.26191540.1998285697
2.6176-2.78150.25931160.2052288797
2.7815-2.99620.2451400.1989287197
2.9962-3.29760.23541500.1965284696
3.2976-3.77430.2021590.1752284997
3.7743-4.75360.17251260.1494284596
4.7536-36.4330.2121420.1785286398

+
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