[English] 日本語
Yorodumi
- PDB-3ur9: 1.65A resolution structure of Norwalk Virus Protease Containing a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ur9
Title1.65A resolution structure of Norwalk Virus Protease Containing a covalently bound dipeptidyl inhibitor
Components3C-like protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / NOROVIRUS / NORWALK VIRUS / ANTIVIRAL INHIBITORS / DIPEPTIDYL INHIBITOR / HYDROLASE-HYDROLASE 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
Chem-K36 / Genome polyprotein
Similarity search - Component
Biological speciesNorovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsLovell, S. / Battaile, K.P. / Kim, Y. / Tiew, K.C. / Mandadapu, S.R. / Alliston, K.R. / Groutas, W.C. / Chang, K.O.
CitationJournal: J.Virol. / Year: 2012
Title: Broad-Spectrum Antivirals against 3C or 3C-Like Proteases of Picornaviruses, Noroviruses, and Coronaviruses.
Authors: Kim, Y. / Lovell, S. / Tiew, K.C. / Mandadapu, S.R. / Alliston, K.R. / Battaile, K.P. / Groutas, W.C. / Chang, K.O.
History
DepositionNov 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3May 20, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / struct_conn / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Sep 13, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3C-like protease
B: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3658
Polymers40,2522
Non-polymers1,1136
Water2,846158
1
A: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6834
Polymers20,1261
Non-polymers5563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6834
Polymers20,1261
Non-polymers5563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-49 kcal/mol
Surface area14800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.649, 66.865, 125.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 3C-like protease / / 3CLpro


Mass: 20126.131 Da / Num. of mol.: 2 / Fragment: unp residues 1101-1281
Source method: isolated from a genetically manipulated source
Details: N-terminal hexahistidine tag / Source: (gene. exp.) Norovirus / 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.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K36 / (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid / GC376 / GC376


Type: peptide-like / Mass: 485.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31N3O8S / Comment: medication, antivirus*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsWHEN THE K36 LIGAND IS MIXED WITH THE NORWALK VIRUS PROTEASE, IT FORMS A COVALENT COMPLEX WITH A ...WHEN THE K36 LIGAND IS MIXED WITH THE NORWALK VIRUS PROTEASE, IT FORMS A COVALENT COMPLEX WITH A LINKAGE BETWEEN C21 OF THE LIGAND AND THE SULFUR ATOM (SG) OF CYS139. THE BISULFITE FUNCTIONAL GROUP IS REMOVED DURING THIS REACTION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 30% PEG 2000 MME, 150 mM sodium bromide, vapor diffusion, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→125.11 Å / Num. all: 38969 / Num. obs: 38969 / % possible obs: 99.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.56 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.1525
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.65-1.746.770.662.8837704557099.98
1.74-1.846.620.434.21350525292100
1.84-1.976.420.246.98323735039100
1.97-2.136.810.1511.1731594463999.99
2.13-2.336.610.1114.57285634323100
2.33-2.616.510.0818.4225299388999.97
2.61-3.016.740.0626.8235143488100
3.01-3.696.220.0436.2618555298499.95
3.69-5.226.370.0346.0714999235399.98
5.22-125.115.710.0342.727953139299.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.88 Å62.56 Å
Translation1.88 Å62.56 Å

-
Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20data scaling
MOLREPphasing
PHENIXdev_842refinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UR6

3ur6


Resolution: 1.65→45.681 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.13 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 1950 5.05 %RANDOM
Rwork0.1777 ---
obs0.1794 38898 99.72 %-
all-38898 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.142 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 80.21 Å2 / Biso mean: 26.4147 Å2 / Biso min: 10.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.0416 Å20 Å2-0 Å2
2--6.4748 Å2-0 Å2
3----5.4332 Å2
Refinement stepCycle: LAST / Resolution: 1.65→45.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 50 158 2660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142578
X-RAY DIFFRACTIONf_angle_d1.5293502
X-RAY DIFFRACTIONf_chiral_restr0.086403
X-RAY DIFFRACTIONf_plane_restr0.008441
X-RAY DIFFRACTIONf_dihedral_angle_d17.884924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.67170.32761310.283526572788100
1.6717-1.69460.28011600.267426602820100
1.6946-1.71880.28261460.250926712817100
1.7188-1.74450.23591720.221626502822100
1.7445-1.77170.26761300.21726932823100
1.7717-1.80080.23451520.207826762828100
1.8008-1.83180.21051740.204426412815100
1.8318-1.86520.26421460.188626582804100
1.8652-1.9010.27161260.18726912817100
1.901-1.93980.1951450.174326352780100
1.9398-1.9820.22651530.167727412894100
1.982-2.02810.1891500.155526332783100
2.0281-2.07880.23771540.155426952849100
2.0788-2.13510.20231200.153826802800100
2.1351-2.19790.21471400.16326942834100
2.1979-2.26880.20841180.162526652783100
2.2688-2.34990.21461290.166327082837100
2.3499-2.4440.27231140.165326812795100
2.444-2.55520.21211560.178326592815100
2.5552-2.68990.22281580.177826812839100
2.6899-2.85840.21611440.168126722816100
2.8584-3.07910.21841390.172126812820100
3.0791-3.38880.19811370.1872651278899
3.3888-3.8790.20891430.16992659280299
3.879-4.88620.14891470.147926732820100
4.8862-45.69810.21861100.20592703281399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.68180.08660.5051.1276-0.61291.80470.0930.207-0.0931-0.0325-0.07440.04010.08180.1005-0.0080.13870.0108-0.00540.096-0.02610.1353-7.5545-10.516524.3855
21.62260.2878-0.79250.0895-0.26980.8512-0.04970.5472-0.60210.0376-0.14270.22580.68530.05490.08010.40840.1218-0.03250.2651-0.12550.3305-2.7796-25.045618.3625
32.1473-0.0051-0.32550.41320.25112.79160.1130.1827-0.3547-0.04430.0948-0.15590.41760.63520.13450.33460.1771-0.10260.1441-0.07080.28420.0599-21.493327.8462
43.327-1.2680.54322.0443-1.35162.31580.1890.3641-0.0469-0.1048-0.1669-0.28470.01370.5202-0.02990.12250.02250.01530.36560.02110.1953.595-9.288719.1866
51.0389-0.3735-0.06240.7996-0.2852.0590.0271-0.1351-0.0060.11410.0390.0203-0.0931-0.0313-0.07710.1722-0.01890.00150.1399-0.01430.1523-11.6165-7.117432.0793
60.61710.2712-0.0360.7787-0.36881.1060.0933-0.1562-0.28830.0527-0.02040.03710.1963-0.5405-0.05640.2458-0.06210.0120.24190.01050.1748-16.2705-12.545837.9342
71.7226-0.93740.48164.4441-0.20661.99780.2806-0.1342-0.53550.1096-0.18490.180.4293-0.3347-0.03160.2495-0.03760.00010.1590.04430.2123-14.5468-16.398439.8356
81.6216-0.1980.04781.8866-0.19541.56190.0103-0.1009-0.07190.0910.0622-0.0898-0.1447-0.126-0.06380.1602-0.0273-0.01480.0986-0.00930.1201-11.569-7.79732.2997
96.66080.031-0.29664.66550.43993.8613-0.0276-0.1399-0.38890.4150.04260.25640.2538-0.4014-0.03710.1881-0.0380.0140.19230.05560.1458-16.2995-14.575437.8602
101.6512-0.5271-0.53362.04640.69533.67520.0250.0534-0.00140.19130.0931-0.1017-0.0014-0.197-0.09750.11020.02850.01860.13240.02640.1386-15.049-2.015610.9581
112.0611-0.1458-0.69561.3217-1.34821.7456-0.26430.2031-0.4876-0.18450.25960.51120.5428-0.85970.47190.0952-0.10170.07460.27990.02620.1401-21.2821-8.13571.1964
121.6971.3986-1.54951.8151-1.52031.50310.05070.23840.0446-0.16950.15660.55350.3194-0.8165-0.10650.189-0.0899-0.00450.46850.02460.2358-25.8636-6.3824-0.702
130.4552-0.3532-0.03020.36670.03150.3375-0.00980.2146-0.09630.02940.18880.2961-0.0197-0.38970.79610.02930.07250.07890.66260.16060.2172-28.1052-3.918912.4465
141.4617-0.09280.07430.8852-0.37651.87070.11920.08150.2171-0.0024-0.0765-0.015-0.47350.0972-0.03190.22940.03340.04790.13760.02930.2006-10.34045.18436.3462
152.3245-0.3472-0.16352.51561.21142.23050.1710.4304-0.0573-0.3441-0.1854-0.0853-0.0798-0.19980.0730.25540.00760.02520.19790.05920.17-10.45534.6547-9.1821
161.6370.6327-0.03176.0435-1.02030.492-0.04320.05360.1309-0.0775-0.1028-0.5455-0.19870.47570.08410.1627-0.02590.01750.21810.03370.2409-1.64690.91312.813
171.7868-0.11190.14312.24541.18132.10730.06820.28610.36090.006-0.0212-0.0707-0.5848-0.0645-0.03970.20550.03770.03850.1340.04260.1751-11.68236.27862.1714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq -1:31)A-1 - 31
2X-RAY DIFFRACTION2chain 'A' and (resseq 32:43)A32 - 43
3X-RAY DIFFRACTION3chain 'A' and (resseq 44:60)A44 - 60
4X-RAY DIFFRACTION4chain 'A' and (resseq 61:70)A61 - 70
5X-RAY DIFFRACTION5chain 'A' and (resseq 71:93)A71 - 93
6X-RAY DIFFRACTION6chain 'A' and (resseq 94:111)A94 - 111
7X-RAY DIFFRACTION7chain 'A' and (resseq 112:121)A112 - 121
8X-RAY DIFFRACTION8chain 'A' and (resseq 122:160)A122 - 160
9X-RAY DIFFRACTION9chain 'A' and (resseq 161:173)A161 - 173
10X-RAY DIFFRACTION10chain 'B' and (resseq 0:19)B0 - 19
11X-RAY DIFFRACTION11chain 'B' and (resseq 20:39)B20 - 39
12X-RAY DIFFRACTION12chain 'B' and (resseq 40:59)B40 - 59
13X-RAY DIFFRACTION13chain 'B' and (resseq 60:69)B60 - 69
14X-RAY DIFFRACTION14chain 'B' and (resseq 70:99)B70 - 99
15X-RAY DIFFRACTION15chain 'B' and (resseq 100:119)B100 - 119
16X-RAY DIFFRACTION16chain 'B' and (resseq 120:138)B120 - 138
17X-RAY DIFFRACTION17chain 'B' and (resseq 139:173)B139 - 173

+
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