[English] 日本語
Yorodumi
- PDB-5f17: Structure of EAV NSP11 K170A mutant at 3.19A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f17
TitleStructure of EAV NSP11 K170A mutant at 3.19A
ComponentsNon-structural protein 11
KeywordsHYDROLASE / nsp11 / Equine arteritis virus / Endoribonuclease / Nonstructural Protein 11 / Nidovirus / NF-kappaB
Function / homology
Function and homology information


serine-type exopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / RNA nuclease activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / ubiquitinyl hydrolase 1 ...serine-type exopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / RNA nuclease activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Protein of unknown function DUF3756 / Equine arteritis virus, non-structural protein 1 / Nsp2, transmembrane domain / Replicase polyprotein 1ab / Nidovirus helicase, RING/Ubox like zinc-binding domain / Protein of unknown function (DUF3756) / Papain-like auto-proteinase / Nsp2, transmembrane domain / Replicase polyprotein 1ab / RING/Ubox like zinc-binding domain ...Protein of unknown function DUF3756 / Equine arteritis virus, non-structural protein 1 / Nsp2, transmembrane domain / Replicase polyprotein 1ab / Nidovirus helicase, RING/Ubox like zinc-binding domain / Protein of unknown function (DUF3756) / Papain-like auto-proteinase / Nsp2, transmembrane domain / Replicase polyprotein 1ab / RING/Ubox like zinc-binding domain / Nonstructural protein 10, zinc-binding domain, arterivirus / NSP11, NendoU domain, arterivirus / NSP11, N-terminal, arterivirus / Arteriviridae zinc-binding (AV ZBD) domain profile. / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain / Arterivirus Nsp2, peptidase C33 / Equine arteritis virus peptidase S32 / Serine protease, chymotrypsin-like serine protease, C-terminal / Arterivirus NSP4 peptidase domain / Arterivirus papain-like cysteine protease beta (PCPbeta) domain / Arterivirus nonstructural protein 7 alpha / Arterivirus nsp7 alpha superfamily / Equine arterivirus Nsp2-type cysteine proteinase / Equine arteritis virus serine endopeptidase S32 / Arterivirus nonstructural protein 7 alpha / Arterivirus nsp4 proteinase domain profile. / Arterivirus nsp2 cysteine protease (AV CP) domain profile. / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain profile. / Arterivirus papain-like cysteine protease beta (PCPbeta) domain profile. / Viral (Superfamily 1) RNA helicase / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesEquine arteritis virus Bucyrus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsZhang, M.F. / Chen, Z.Z.
CitationJournal: To Be Published
Title: Structure of EAV NSP11 K170A mutant at 3.19A
Authors: Zhang, M.F. / Chen, Z.Z.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-structural protein 11
B: Non-structural protein 11
C: Non-structural protein 11
D: Non-structural protein 11
E: Non-structural protein 11
F: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)144,8736
Polymers144,8736
Non-polymers00
Water00
1
A: Non-structural protein 11
D: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)48,2912
Polymers48,2912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural protein 11
F: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)48,2912
Polymers48,2912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-structural protein 11
E: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)48,2912
Polymers48,2912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)249.184, 249.184, 226.899
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein
Non-structural protein 11


Mass: 24145.541 Da / Num. of mol.: 6 / Mutation: K170A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine arteritis virus Bucyrus / Strain: Bucyrus / Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) / References: UniProt: P19811

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.68 Å3/Da / Density % sol: 73.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 44911 / Num. obs: 44774 / % possible obs: 99.7 % / Redundancy: 7.6 % / Net I/σ(I): 23
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EYI

5eyi


Resolution: 3.2→50 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 2101 4.7 %Random selection
Rwork0.2148 ---
obs0.2162 44699 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9879 0 0 0 9879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410186
X-RAY DIFFRACTIONf_angle_d0.86413935
X-RAY DIFFRACTIONf_dihedral_angle_d15.0263581
X-RAY DIFFRACTIONf_chiral_restr0.0611522
X-RAY DIFFRACTIONf_plane_restr0.0041814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1911-3.26530.37591190.35442783X-RAY DIFFRACTION98
3.2653-3.34690.35111490.32932808X-RAY DIFFRACTION100
3.3469-3.43730.34681360.29772837X-RAY DIFFRACTION100
3.4373-3.53840.33921630.27852830X-RAY DIFFRACTION100
3.5384-3.65260.28521310.26022819X-RAY DIFFRACTION100
3.6526-3.7830.27841230.24082873X-RAY DIFFRACTION100
3.783-3.93440.26971470.22922809X-RAY DIFFRACTION100
3.9344-4.11330.28861410.21472830X-RAY DIFFRACTION100
4.1133-4.32990.24781430.18692844X-RAY DIFFRACTION100
4.3299-4.60080.211470.1852855X-RAY DIFFRACTION100
4.6008-4.95540.20441550.17492841X-RAY DIFFRACTION100
4.9554-5.4530.23821350.19452858X-RAY DIFFRACTION100
5.453-6.23950.23961470.20282880X-RAY DIFFRACTION100
6.2395-7.85150.21241280.20462883X-RAY DIFFRACTION99
7.8515-40.14230.19461370.19662848X-RAY DIFFRACTION96

+
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://pdbjlvh1.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