5M3H

Bat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD

> Summary

Summary for 5M3H

DescriptorPolymerase acidic protein, RNA-directed RNA polymerase catalytic subunit, Polymerase basic protein 2, TYR-SER-PRO-THR-SEP-PRO/RNA Complex
Functional Keywordsinfluenza rna-dependent rna polymerase, vrna promoter, pol ii serine 5 phosphorylated ctd peptide, transferase
Biological sourceInfluenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))
More
Cellular locationVirion  H6QM90
Total number of polymer chains7
Total molecular weight281102.49
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 (2.5 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliersRNA backbone0.24420.8%3.1%11.5%0.57MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5m3h
no rotation
Molmil generated image of 5m3h
rotated about x axis by 90°
Molmil generated image of 5m3h
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
APolymerase acidic proteinpolymer72884241.61
UniProt (H6QM92)
Pfam (PF00603)
Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))
BRNA-directed RNA polymerase catalytic subunitpolymer77687936.31
UniProt (H6QM91)
Pfam (PF00602)
Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))
CPolymerase basic protein 2polymer79790168.31
UniProt (H6QM90)
Pfam (PF00604)
Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))
RRNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3')polymer185584.31
Influenza A virus
VRNA 5'-pAGUAGUAACAAGAGGGpolymer165248.21
Influenza A virus
X, YTYR-SER-PRO-THR-SEP-PROpolymer283216.92
Pfam (PF05001)
UniProt (by SIFTS) (P24928)
Homo sapiens
ZINC IONnon-polymer65.41
PHOSPHATE IONnon-polymer95.015
waterwater18.0250

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains7
Total molecular weight279612.5
Non-Polymers*Number of molecules16
Total molecular weight1490.0
All*Total molecular weight281102.5
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.5 Å)

Cell axes269.490147.52088.480
Cell angles90.0097.2290.00
SpacegroupC 1 2 1
Resolution limits49.53 - 2.50
the highest resolution shell value2.528 - 2.500
R-factor0.2118
R-work0.21000
the highest resolution shell value0.326
R-free0.24490
the highest resolution shell value0.357
RMSD bond length0.002
RMSD bond angle0.529

Data Collection Statistics

Resolution limits50.00 - 2.50
the highest resolution shell value -
Number of reflections117997
Rmerge_l_obs0.118
the highest resolution shell value1.250
Completeness99.6
Redundancy5.84
the highest resolution shell value5.9

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP5278

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
Y0005665cellular_componentDNA-directed RNA polymerase II, core complex
Y0005654cellular_componentnucleoplasm
Y0005634cellular_componentnucleus
Y0003677molecular_functionDNA binding
Y0003899molecular_functionDNA-directed 5'-3' RNA polymerase activity
Y0046872molecular_functionmetal ion binding
Y0003723molecular_functionRNA binding
Y0003968molecular_functionRNA-directed 5'-3' RNA polymerase activity
Y0031625molecular_functionubiquitin protein ligase binding
Y0006370biological_process7-methylguanosine mRNA capping
Y0006353biological_processDNA-templated transcription, termination
Y0008543biological_processfibroblast growth factor receptor signaling pathway
Y0010467biological_processgene expression
Y0031047biological_processgene silencing by RNA
Y0000398biological_processmRNA splicing, via spliceosome
Y0033120biological_processpositive regulation of RNA splicing
Y0050434biological_processpositive regulation of viral transcription
Y0006355biological_processregulation of transcription, DNA-templated
Y0042795biological_processsnRNA transcription from RNA polymerase II promoter
Y0035019biological_processsomatic stem cell population maintenance
Y0006368biological_processtranscription elongation from RNA polymerase II promoter
Y0006366biological_processtranscription from RNA polymerase II promoter
Y0006367biological_processtranscription initiation from RNA polymerase II promoter
Y0006283biological_processtranscription-coupled nucleotide-excision repair
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
C0039545biological_processsuppression by virus of host MAVS activity
C0039523biological_processsuppression by virus of host RNA polymerase II activity
C0006351biological_processtranscription, DNA-templated
A0046872molecular_functionmetal ion binding
A0003723molecular_functionRNA binding
A0003968molecular_functionRNA-directed 5'-3' RNA polymerase activity
A0006351biological_processtranscription, DNA-templated
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC11binding site for residue ZN A 801
ChainResidue
AASP421

AC22binding site for residue PO4 A 802
ChainResidue
AASP524
AASN527

AC35binding site for residue PO4 A 803
ChainResidue
ACYS276
ATHR277
AARG279
AASN691
APRO693

AC41binding site for residue PO4 A 804
ChainResidue
AASN331

AC56binding site for residue PO4 B 801
ChainResidue
BASP305
BTHR307
BLYS308
BLYS481
BHOH906
BHOH973

AC63binding site for residue PO4 B 802
ChainResidue
BARG560
BTHR570
BARG571

AC75binding site for residue PO4 B 803
ChainResidue
BGLY275
BASN276
BGLU277
CPHE217
CPO4801

AC84binding site for residue PO4 B 804
ChainResidue
AARG578
BPHE512
BLEU550
BASP554

AC98binding site for residue PO4 B 805
ChainResidue
BTRP309
BASN310
BGLN313
BPHE412
BASN413
BSER416
BSER444
BHOH932

AD14binding site for residue PO4 B 806
ChainResidue
AGLU656
ALYS659
BLYS235
BLYS481

AD24binding site for residue PO4 B 807
ChainResidue
BLYS531
BILE535
CLEU218
CVAL229

AD36binding site for residue PO4 C 801
ChainResidue
BGLY274
BGLU277
BPO4803
CARG144
CARG216
CPHE217

AD44binding site for residue PO4 C 802
ChainResidue
CARG264
CGLU305
CGLN306
CSER519

AD53binding site for residue PO4 C 803
ChainResidue
CMET53
CLYS54
CTYR55

AD64binding site for residue PO4 C 804
ChainResidue
BASN16
BARG498
CGLU662
CILE666

AD76binding site for residue PO4 C 805
ChainResidue
BPRO701
BARG721
CPHE168
CPRO169
CASN170
CGLU171

AD84binding site for Ligand residues SEP X 5 through PRO X 6 bound to THR X 4
ChainResidue
ALYS630
AARG633
XTHR4
XHOH101

AD99binding site for Ligand residues SEP Y 19 through PRO Y 20 bound to THR Y 18
ChainResidue
AMET288
ALYS289
ATRP417
AARG449
YSER16
YPRO17
YTHR18
YSER21
YTYR22

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

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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