[English] 日本語
Yorodumi
- PDB-5ifd: Crystal structure of polymerase acid protein (PA) from Influenza ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ifd
TitleCrystal structure of polymerase acid protein (PA) from Influenza A virus, WILSON-SMITH/1933 (H1N1) bound to follow on fragment EBSI-4721 1-(4-fluorophenyl)-1H-imidazole
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / NIAID / structural genomics / flu / fragment screening / STD NMR / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds ...RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / 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
1-(4-fluorophenyl)-1H-imidazole / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Fragment screening by STD NMR identifies novel site binders against influenza A virus polymerase PA
Authors: Pierce, P. / Muruthi, M.M. / Abendroth, J. / Moen, S.O. / Begley, D.W. / Davies, D.R. / Marathias, V.M. / Staker, B.L. / Myler, P.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3373
Polymers53,0971
Non-polymers2402
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint3 kcal/mol
Surface area19560 Å2
2
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6746
Polymers106,1932
Non-polymers4814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area3780 Å2
ΔGint-2 kcal/mol
Surface area35890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.030, 69.030, 397.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

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


Mass: 53096.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Wilson-Smith/1933 H1N1)
Strain: A/Wilson-Smith/1933 H1N1 / Gene: PA / Production host: Escherichia coli (E. coli) / References: UniProt: P15659
#2: Chemical ChemComp-6AQ / 1-(4-fluorophenyl)-1H-imidazole


Mass: 162.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7FN2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 mg/mL protein against Morpheus screen condition E10 with 10% PEG 8000, 20% EG, 0.03 M each ethylene glycol, 0.1 M bicine/Trizma pH 8.5, 5 mM soak over 4 days, unique puck ID lum0-5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.99985 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 2.65→47.775 Å / Num. obs: 17423 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 41.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.26
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.65-2.720.5253.31199.8
2.72-2.790.4233.931100
2.79-2.870.3284.94199.9
2.87-2.960.2836.011100
2.96-3.060.2217.191100
3.06-3.170.1748.95199.9
3.17-3.290.15410.18199.9
3.29-3.420.11113.191100
3.42-3.570.0916.39199.5
3.57-3.750.07618.28199.3
3.75-3.950.06621.07199.4
3.95-4.190.05524.13199.9
4.19-4.480.0526.45199.6
4.48-4.840.04727.851100
4.84-5.30.04726.88199.2
5.3-5.930.04924.19199.7
5.93-6.840.04725.28199.3
6.84-8.380.03929.23199.2
8.38-11.850.0334.42198.8
11.85-47.7750.03232.57194.7

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.65→47.775 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 20
RfactorNum. reflection% reflection
Rfree0.2259 861 4.94 %
Rwork0.1752 --
obs0.1776 17421 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.4 Å2 / Biso mean: 48.051 Å2 / Biso min: 18.97 Å2
Refinement stepCycle: final / Resolution: 2.65→47.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 16 106 3292
Biso mean--92.62 41.53 -
Num. residues----408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073257
X-RAY DIFFRACTIONf_angle_d0.8284406
X-RAY DIFFRACTIONf_chiral_restr0.043492
X-RAY DIFFRACTIONf_plane_restr0.004561
X-RAY DIFFRACTIONf_dihedral_angle_d12.2741970
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.8160.30711360.212626432779100
2.816-3.03340.27941360.194426942830100
3.0334-3.33860.24961620.190426842846100
3.3386-3.82150.23171340.15827482882100
3.8215-4.8140.18951500.146927732923100
4.814-47.78310.20671430.18853018316199
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)
11.45670.49150.80832.3557-0.8893.2276-0.0105-0.03550.1239-0.1481-0.1402-0.18240.0461-0.08690.00440.35180.14940.05930.29740.10150.2808-15.5257-30.756750.1203
21.1618-0.01881.16122.7493-0.18763.1552-0.246-0.2252-0.14450.30740.24850.38050.213-0.5533-0.02110.39930.11060.09360.280.09110.3291-23.9304-41.298764.5866
30.7782-0.22940.1161.6581-0.29042.69410.00010.08780.1727-0.11360.0248-0.0423-0.2702-0.1450.00750.30320.12340.05950.25190.06030.2766-18.6897-25.829452.0489
40.9884-0.54161.12361.8539-2.62413.99470.0840.48920.3597-0.2044-0.2074-0.0129-0.32460.32270.2210.68120.15790.08750.380.12940.3949-16.2111-13.488634.3702
53.34142.6674-3.23623.2166-1.93633.5636-0.2899-0.05610.4857-0.6341-0.2505-0.8466-0.33010.97170.50320.5774-0.07890.04390.57820.25010.68444.4468-17.780239.8581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 266 through 302 )A266 - 302
2X-RAY DIFFRACTION2chain 'A' and (resid 303 through 363 )A303 - 363
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 602 )A364 - 602
4X-RAY DIFFRACTION4chain 'A' and (resid 603 through 652 )A603 - 652
5X-RAY DIFFRACTION5chain 'A' and (resid 653 through 713 )A653 - 713

+
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