[English] 日本語
Yorodumi
- PDB-9doj: Influenza A virus polymerase PA subunit endonuclease domain bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9doj
TitleInfluenza A virus polymerase PA subunit endonuclease domain bound to inhibitor Compound 19a
ComponentsPolymerase acidic protein
KeywordsHYDROLASE/INHIBITOR / viral polymerase endonuclease / HYDROLASE-INHIBITOR / HYDROLASE-INHIBITOR complex
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 / 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
: / MALONATE ION / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsHollenstein, K. / Price, I.R. / Eddins, M.J. / Su, H.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Org.Chem. / Year: 2025
Title: Highly Diastereoselective Access to Densely Functionalized Piperidine Cores of Influenza Endonuclease Inhibitors via a Metal-Free S N 1 Approach.
Authors: Zhang, Y. / Sun, C. / Guo, L. / Zhao, K. / Bennett, F. / Lam, Y.H. / Gao, Q. / Ruhl, K.E. / Pirnot, M.T. / Emmert, M.H. / Hollenstein, K. / Eddins, M.J. / Su, H.P. / Shao, G. / Song, C. / ...Authors: Zhang, Y. / Sun, C. / Guo, L. / Zhao, K. / Bennett, F. / Lam, Y.H. / Gao, Q. / Ruhl, K.E. / Pirnot, M.T. / Emmert, M.H. / Hollenstein, K. / Eddins, M.J. / Su, H.P. / Shao, G. / Song, C. / Lo, M.M. / Peng, F. / Qi, J. / Crowley, B.M. / McCauley, J.A. / Price, I.R.
History
DepositionSep 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,2469
Polymers49,0942
Non-polymers1,1537
Water7,494416
1
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0724
Polymers24,5471
Non-polymers5253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1745
Polymers24,5471
Non-polymers6274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.796, 65.736, 66.164
Angle α, β, γ (deg.)90.00, 115.03, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 24546.879 Da / Num. of mol.: 2 / Fragment: endonuclease domain (UNP residues 1-204)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A075EM28, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-A1A8U / (2aS,4aR,10bS,11S,12R)-4a-(2,2-difluoroethyl)-16-hydroxy-2-methyl-2,2a,3,4,4a,5,6,10b-octahydrobenzo[h]pyrido[1',2':1,6][1,2,4]triazino[2,3-a]quinoline-1,15-dione


Mass: 415.433 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23F2N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 1.2 M ammonium sulfate, 5% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.476→59.95 Å / Num. obs: 81810 / % possible obs: 96.7 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.02 / Rrim(I) all: 0.037 / Net I/σ(I): 12.7
Reflection shellResolution: 1.476→1.501 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4024 / CC1/2: 0.858 / Rpim(I) all: 0.259 / Rrim(I) all: 0.494 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→59.95 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.349 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16214 3810 4.7 %RANDOM
Rwork0.12304 ---
obs0.12485 78000 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.928 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0 Å2-0.47 Å2
2--0.57 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.48→59.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3258 0 71 416 3745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133582
X-RAY DIFFRACTIONr_bond_other_d0.0020.0153354
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.6534868
X-RAY DIFFRACTIONr_angle_other_deg1.4881.67781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.47921.797217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8815673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8571530
X-RAY DIFFRACTIONr_chiral_restr0.1160.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02860
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0152.7031638
X-RAY DIFFRACTIONr_mcbond_other5.0112.7021636
X-RAY DIFFRACTIONr_mcangle_it5.6774.0622056
X-RAY DIFFRACTIONr_mcangle_other5.6764.0612057
X-RAY DIFFRACTIONr_scbond_it6.6423.2231944
X-RAY DIFFRACTIONr_scbond_other6.6213.221941
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.574.6092791
X-RAY DIFFRACTIONr_long_range_B_refined7.39733.3214344
X-RAY DIFFRACTIONr_long_range_B_other7.26632.5694227
X-RAY DIFFRACTIONr_rigid_bond_restr6.97936936
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.514 Å
RfactorNum. reflection% reflection
Rfree0.27 278 -
Rwork0.218 5676 -
obs--95.71 %

+
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