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- PDB-3cm8: A RNA polymerase subunit structure from virus -

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Basic information

Entry
Database: PDB / ID: 3cm8
TitleA RNA polymerase subunit structure from virus
Components
  • Polymerase acidic protein
  • peptide from RNA-directed RNA polymerase catalytic subunit
KeywordsRNA BINDING PROTEIN/Transferase / Protein-peptide Complex / Nucleotide-binding / Nucleotidyltransferase / RNA replication / RNA-directed RNA polymerase / Transferase / RNA BINDING PROTEIN-Transferase COMPLEX
Function / homology
Function and homology information


cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / RNA-dependent RNA polymerase activity ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / 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 / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
Polymerase acidic protein / RNA-directed RNA polymerase catalytic subunit
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.899 Å
AuthorsHe, X. / Zhou, J. / Zeng, Z. / Ma, J. / Zhang, R. / Rao, Z. / Liu, Y.
CitationJournal: Nature / Year: 2008
Title: Crystal structure of the polymerase PAC-PB1N complex from an avian influenza H5N1 virus
Authors: He, X. / Zhou, J. / Bartlam, M. / Zhang, R. / Ma, J. / Lou, Z. / Li, X. / Li, J. / Joachimiak, A. / Zeng, Z. / Ge, R. / Rao, Z. / Liu, Y.
History
DepositionMar 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
B: peptide from RNA-directed RNA polymerase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)57,0652
Polymers57,0652
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-15.9 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.942, 121.942, 134.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-35-

HOH

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Components

#1: Protein Polymerase acidic protein


Mass: 53870.789 Da / Num. of mol.: 1 / Fragment: residues in database 256-716
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Environment/Hong Kong/437-6/99 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EA60
#2: Protein/peptide peptide from RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 1 / PB1 / RNA-directed RNA polymerase subunit P1


Mass: 3194.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/156/1997 H5N1 genotype Gs/Gd / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WLS3, RNA-directed RNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.38 Å3/Da / Density % sol: 71.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1M sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
2771
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9795, 0.9897
ROTATING ANODERIGAKU FR-E+ DW21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDDec 10, 2007
RIGAKU RAXIS IV++2IMAGE PLATENov 20, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITEMADMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.98971
31.54181
ReflectionResolution: 2.899→50 Å / Num. all: 23042 / Num. obs: 22964 / % possible obs: 99.7 % / Observed criterion σ(F): 4.6 / Observed criterion σ(I): 4.6 / Biso Wilson estimate: 75.44 Å2
Reflection shellHighest resolution: 2.899 Å / % possible all: 99

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.899→45.184 Å / FOM work R set: 0.787 / σ(F): 1.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1176 5.12 %RANDOM
Rwork0.224 ---
obs0.226 22964 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.261 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 42.23 Å2 / Biso mean: 84.28 Å2 / Biso min: 166.55 Å2
Baniso -1Baniso -2Baniso -3
1--16.402 Å2-0 Å20 Å2
2---16.402 Å2-0 Å2
3---32.804 Å2
Refinement stepCycle: LAST / Resolution: 2.899→45.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 0 49 3674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063701
X-RAY DIFFRACTIONf_angle_d14990
X-RAY DIFFRACTIONf_chiral_restr0.074550
X-RAY DIFFRACTIONf_plane_restr0.004634
X-RAY DIFFRACTIONf_dihedral_angle_d19.5111412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.899-3.0310.2991540.2682613276798
3.031-3.1910.2621470.22826872834100
3.191-3.3910.2421300.21627052835100
3.391-3.6530.2641510.226942845100
3.653-4.020.2221530.19227062859100
4.02-4.6010.211440.17927342878100
4.601-5.7950.2551530.20927802933100
5.795-45.190.3071440.272869301398

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