[English] 日本語
Yorodumi
- PDB-7nuh: Influenza A/California/07/2009(H1N1) endonuclease with I38T mutat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nuh
TitleInfluenza A/California/07/2009(H1N1) endonuclease with I38T mutation in complex with orientin
ComponentsPolymerase acidic protein,Polymerase acidic protein
KeywordsVIRAL PROTEIN / endonuclease / protein-ligand complex / RNA polymerase / Flavonoids
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Orientin / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRadilova, K. / Brynda, J.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Ministry of Education (MoE, Czech Republic)LM2015064 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000729 Czech Republic
CitationJournal: Int J Mol Sci / Year: 2021
Title: Synthesis and In Vitro Evaluation of C-7 and C-8 Luteolin Derivatives as Influenza Endonuclease Inhibitors.
Authors: Reiberger, R. / Radilova, K. / Kral, M. / Zima, V. / Majer, P. / Brynda, J. / Dracinsky, M. / Konvalinka, J. / Kozisek, M. / Machara, A.
History
DepositionMar 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polymerase acidic protein,Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,23911
Polymers21,1961
Non-polymers1,04310
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-1 kcal/mol
Surface area9020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.967, 73.967, 127.575
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

21A-471-

HOH

31A-477-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Polymerase acidic protein,Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 21196.129 Da / Num. of mol.: 1 / Mutation: I38T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/07/2009(H1N1))
Strain: A/California/07/2009(H1N1) / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3W5X6, Hydrolases; Acting on ester bonds

-
Non-polymers , 6 types, 202 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-USE / Orientin / 2-[3,4-bis(oxidanyl)phenyl]-8-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5,7-bis(oxidanyl)chromen-4-one / 5281675 / 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-8-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one


Mass: 448.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20O11 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MDP, PEG 1000, PEG 3350, Sodium HEPES, MOPS (acid), Magnesium chloride, Calcium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.2→45.24 Å / Num. obs: 10985 / % possible obs: 99.2 % / Redundancy: 6.793 % / Biso Wilson estimate: 41.708 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.095 / Χ2: 0.891 / Net I/σ(I): 15.96 / Num. measured all: 74623 / Scaling rejects: 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.264.1871.1661.2132247857700.3861.32598.1
2.26-2.324.1680.9611.5232437867780.4931.09199
2.32-2.394.1850.9341.6231607587550.5461.06299.6
2.39-2.464.3290.7441.9931607317300.6830.84599.9
2.46-2.544.4640.6452.3931477077050.7580.72899.7
2.54-2.634.5460.483.1830876806790.8620.54199.9
2.63-2.735.6010.4324.1337476786690.8790.47898.7
2.73-2.846.8370.3315.8944586526520.9410.36100
2.84-2.977.430.267.8645996196190.9650.281100
2.97-3.117.8290.17611.7346665965960.9840.189100
3.11-3.288.5760.1411547515655540.9860.1598.1
3.28-3.488.7750.09322.3147125455370.9950.09998.5
3.48-3.7210.0450.06730.4551335125110.9990.07199.8
3.72-4.0210.2620.05339.3249264814800.9990.05699.8
4.02-4.410.3290.04245.9646484514500.9990.04599.8
4.4-4.9210.0120.03948.8641254144120.9990.04299.5
4.92-5.6810.0190.04939.9536573693650.9990.05298.9
5.68-6.969.5850.05240.4729813163110.9990.05598.4
6.96-9.848.8670.02563.69226126325510.02797
9.84-45.245.9750.02359.0693816715710.02594

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YA5

6ya5


Resolution: 2.2→45.24 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.2268 / WRfactor Rwork: 0.1533 / FOM work R set: 0.7638 / SU B: 9.178 / SU ML: 0.216 / SU R Cruickshank DPI: 0.2974 / SU Rfree: 0.2397 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 549 5 %RANDOM
Rwork0.1927 ---
obs0.1963 10437 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 115.09 Å2 / Biso mean: 42.106 Å2 / Biso min: 18.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å2-0 Å2
2---0.28 Å20 Å2
3---0.9 Å2
Refinement stepCycle: final / Resolution: 2.2→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 66 192 1687
Biso mean--55.92 54.8 -
Num. residues----180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131541
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181386
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.6932078
X-RAY DIFFRACTIONr_angle_other_deg1.2761.5923183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7565187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91121.62886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02915254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1291512
X-RAY DIFFRACTIONr_chiral_restr0.060.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021729
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02367
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 36 -
Rwork0.314 731 -
all-767 -
obs--97.96 %

+
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