5M3J

Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD

> Summary

Summary for 5M3J

DescriptorPolymerase acidic protein, RNA-directed RNA polymerase catalytic subunit, Polymerase basic protein 2, DNA-directed RNA polymerase subunit/RNA Complex
Functional Keywordsinfluenza b virus rna-dependent rna polymerase, vrna promoter, pol ii serine 5 phosphorylated ctd peptide, viral protein
Biological sourceInfluenza B virus (B/Memphis/13/2003)
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Cellular locationVirion  Q5V8X3
Total number of polymer chains6
Total molecular weight274970.18
Authors
Lukarska, M.,Pflug, A.,Cusack, S. (deposition date: 2016-10-14, release date: 2016-12-21, Last modification date: 2017-01-18)
Primary citation
Lukarska, M.,Fournier, G.,Pflug, A.,Resa-Infante, P.,Reich, S.,Naffakh, N.,Cusack, S.
Structural basis of an essential interaction between influenza polymerase and Pol II CTD.
Nature, 541:117-121, 2017
PubMed: 28002402
DOI: 10.1038/nature20594
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3.5 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliersRNA backbone0.26710.4%1.9%2.3%0.40MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5m3j
no rotation
Molmil generated image of 5m3j
rotated about x axis by 90°
Molmil generated image of 5m3j
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
APolymerase acidic proteinpolymer75185822.81
UniProt (Q5V8Z9)
Pfam (PF00603)
Influenza B virus (B/Memphis/13/2003)
BRNA-directed RNA polymerase catalytic subunitpolymer77286207.01
UniProt (Q5V8Y6)
Pfam (PF00602)
Influenza B virus (B/Memphis/13/2003)
CPolymerase basic protein 2polymer79890844.11
UniProt (Q5V8X3)
Pfam (PF00604)
Influenza B virus
RRNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*C)-3')polymer144321.61
Influenza B virus
VRNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3')polymer144557.81
Influenza B virus
XDNA-directed RNA polymerase subunitpolymer283216.91
Pfam (PF05001)
UniProt (by SIFTS) (P24928)
Homo Sapiens

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains6
Total molecular weight274970.2
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight274970.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (3.5 Å)

Cell axes200.160200.160250.380
Cell angles90.0090.00120.00
SpacegroupP 32 2 1
Resolution limits49.07 - 3.50
the highest resolution shell value3.548 - 3.500
R-factor0.2401
R-work0.23870
the highest resolution shell value0.434
R-free0.26820
the highest resolution shell value0.428
RMSD bond length0.002
RMSD bond angle0.472

Data Collection Statistics

Resolution limits50.00 - 3.50
the highest resolution shell value -
Number of reflections73405
Rmerge_l_obs0.191
the highest resolution shell value2.220
Completeness99.9
Redundancy8.54
the highest resolution shell value8.63

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP9277

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
X0005665cellular_componentDNA-directed RNA polymerase II, core complex
X0005654cellular_componentnucleoplasm
X0005634cellular_componentnucleus
X0003677molecular_functionDNA binding
X0003899molecular_functionDNA-directed 5'-3' RNA polymerase activity
X0046872molecular_functionmetal ion binding
X0003723molecular_functionRNA binding
X0003968molecular_functionRNA-directed 5'-3' RNA polymerase activity
X0031625molecular_functionubiquitin protein ligase binding
X0006370biological_process7-methylguanosine mRNA capping
X0006353biological_processDNA-templated transcription, termination
X0008543biological_processfibroblast growth factor receptor signaling pathway
X0010467biological_processgene expression
X0031047biological_processgene silencing by RNA
X0000398biological_processmRNA splicing, via spliceosome
X0033120biological_processpositive regulation of RNA splicing
X0050434biological_processpositive regulation of viral transcription
X0006355biological_processregulation of transcription, DNA-templated
X0042795biological_processsnRNA transcription from RNA polymerase II promoter
X0035019biological_processsomatic stem cell population maintenance
X0006368biological_processtranscription elongation from RNA polymerase II promoter
X0006366biological_processtranscription from RNA polymerase II promoter
X0006367biological_processtranscription initiation from RNA polymerase II promoter
X0006283biological_processtranscription-coupled nucleotide-excision repair
A0003723molecular_functionRNA binding
A0003968molecular_functionRNA-directed 5'-3' RNA polymerase activity
A0006351biological_processtranscription, DNA-templated
B0000166molecular_functionnucleotide binding
B0003968molecular_functionRNA-directed 5'-3' RNA polymerase activity
B0006351biological_processtranscription, DNA-templated
B0039694biological_processviral RNA genome replication
C0033650cellular_componenthost cell mitochondrion
C0042025cellular_componenthost cell nucleus
C0019012cellular_componentvirion
C0003723molecular_functionRNA binding
C0003968molecular_functionRNA-directed 5'-3' RNA polymerase activity
C0006370biological_process7-methylguanosine mRNA capping
C0075526biological_processcap snatching
C0006351biological_processtranscription, DNA-templated
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Functional Information from PDB Data

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

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Functional Information from PROSITE/UniProt

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Functional Information from SwissProt/UniProt

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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