[English] 日本語
Yorodumi
- PDB-1lvb: CATALYTICALLY INACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lvb
TitleCATALYTICALLY INACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH SUBSTRATE
Components
  • CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
  • OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
KeywordsVIRAL PROTEIN / Beta Barrel / Protein-Peptide Complex / Chymotrypsin-like Cystein Protease
Function / homology
Function and homology information


nuclear-inclusion-a endopeptidase / helper-component proteinase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / Hydrolases; Acting on peptide bonds (peptidases) / helical viral capsid / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RNA-directed RNA polymerase ...nuclear-inclusion-a endopeptidase / helper-component proteinase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / Hydrolases; Acting on peptide bonds (peptidases) / helical viral capsid / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Potyvirus P1 protease / Potyviridae polyprotein / Protein P3 of Potyviral polyprotein ...Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Potyvirus P1 protease / Potyviridae polyprotein / Protein P3 of Potyviral polyprotein / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain profile. / Potyviridae P1 protease domain profile. / Potyvirus NIa protease (NIa-pro) domain / Peptidase family C4 / Potyvirus NIa protease (NIa-pro) domain profile. / Potyvirus coat protein / Potyvirus coat protein / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Trypsin-like serine proteases / 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 / 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
Biological speciesTobacco etch virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsPhan, J. / Zdanov, A. / Evdokimov, A.G. / Tropea, J.E. / Peters III, H.K. / Kapust, R.B. / Li, M. / Wlodawer, A. / Waugh, D.S.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structural basis for the substrate specificity of tobacco etch virus protease.
Authors: Phan, J. / Zdanov, A. / Evdokimov, A.G. / Tropea, J.E. / Peters III, H.K. / Kapust, R.B. / Li, M. / Wlodawer, A. / Waugh, D.S.
History
DepositionMay 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5126
Polymers58,3284
Non-polymers1842
Water3,261181
1
A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2563
Polymers29,1642
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-8 kcal/mol
Surface area10570 Å2
MethodPISA
2
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2563
Polymers29,1642
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-9 kcal/mol
Surface area10550 Å2
MethodPISA
3
A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules

A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules

A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules

A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,04824
Polymers233,31116
Non-polymers7378
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area26620 Å2
ΔGint-135 kcal/mol
Surface area73700 Å2
MethodPISA
4
A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules

A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,02412
Polymers116,6568
Non-polymers3684
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area12790 Å2
ΔGint-60 kcal/mol
Surface area37370 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-28 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.317, 125.317, 127.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)


Mass: 28004.715 Da / Num. of mol.: 2 / Mutation: C151A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tobacco etch virus / Genus: Potyvirus / Plasmid: pRK529 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04517
#2: Protein/peptide OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE


Mass: 1159.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
References: UniProt: P04517
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 4.3 Å3/Da / Density % sol: 71.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 6000, Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113.5 mg/mlprotein1drop
28 %(w/v)PEG60001reservoir
3100 mMTris-HCl1reservoirpH8.0

-
Data collection

DiffractionMean temperature: 112 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9755,0.9794,0.9796
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 19, 2001 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97551
20.97941
30.97961
ReflectionResolution: 2.2→50 Å / Num. all: 51139 / Num. obs: 38759 / % possible obs: 93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.2→2.28 Å / % possible all: 90.3
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. obs: 51139 / % possible obs: 97.8 % / Rmerge(I) obs: 0.08

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.2→33.69 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 272840.06 / Data cutoff high rms absF: 272840.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2411 5 %RANDOM
Rwork0.236 ---
all-38759 --
obs-38759 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.6121 Å2 / ksol: 0.360486 e/Å3
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.47 Å20 Å20 Å2
2---7.47 Å20 Å2
3---14.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.2→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3590 0 12 181 3783
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it2.051.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.152.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.435 400 5.6 %
Rwork0.394 6703 -
obs--83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3TOPP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. reflection obs: 45949
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

+
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