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)
Cellular locationVirion  Q5V8X3
Total number of polymer chains6
Total molecular weight274970.18
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

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


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
the highest resolution shell value0.434
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
the highest resolution shell value2.220
the highest resolution shell value8.63

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit

Crystallization Reagents

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

> Functional details


Functional Information from GO Data

X0005665cellular_componentDNA-directed RNA polymerase II, core complex
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
C0003723molecular_functionRNA binding
C0003968molecular_functionRNA-directed 5'-3' RNA polymerase activity
C0006370biological_process7-methylguanosine mRNA capping
C0075526biological_processcap snatching
C0006351biological_processtranscription, DNA-templated

Functional Information from PDB Data

site_idNumber of ResiduesDetails

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

site_idNumber of ResiduesDetails

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails

Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2017 Protein Data Bank Japan