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- PDB-6qpf: Influenza A virus Polymerase Heterotrimer A/duck/Fujian/01/2002(H5N1) -

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Basic information

Entry
Database: PDB / ID: 6qpf
TitleInfluenza A virus Polymerase Heterotrimer A/duck/Fujian/01/2002(H5N1)
Components
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA-directed RNA polymerase catalytic subunit
KeywordsRNA BINDING PROTEIN / Influenza A / RNA polymerase / Influenza polymerase / Influenza dimer / RDRP
Function / homology
Function and homology information


cap snatching / suppression by virus of host RNA polymerase II activity / 7-methylguanosine mRNA capping / viral transcription / virion / viral RNA genome replication / endonuclease activity / RNA-directed RNA polymerase / host cell cytoplasm / RNA-directed 5'-3' RNA polymerase activity ...cap snatching / suppression by virus of host RNA polymerase II activity / 7-methylguanosine mRNA capping / viral transcription / virion / viral RNA genome replication / endonuclease activity / RNA-directed RNA polymerase / host cell cytoplasm / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / Hydrolases; Acting on ester bonds / nucleotide binding / host cell nucleus / RNA binding / metal ion binding
Influenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB2 / RNA-directed RNA polymerase, negative-strand RNA virus / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PA / Polymerase acidic protein / PA/PA-X superfamily / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PB1
Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.634 Å
AuthorsFan, H.T. / Keown, J.R. / Fodor, E. / Grimes, J.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust200835/Z/16/Z United Kingdom
Medical Research Council (United Kingdom)MR/K000241/1 United Kingdom
Medical Research Council (United Kingdom)MR/R009945/1 United Kingdom
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 25, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2
D: Polymerase acidic protein
E: RNA-directed RNA polymerase catalytic subunit
F: Polymerase basic protein 2
G: Polymerase acidic protein
H: RNA-directed RNA polymerase catalytic subunit
I: Polymerase basic protein 2
J: Polymerase acidic protein
K: RNA-directed RNA polymerase catalytic subunit
L: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)1,024,31412
Polymers1,024,31412
Non-polymers00
Water0
1
A: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)256,0793
Polymers256,0793
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33260 Å2
ΔGint-188 kcal/mol
Surface area95620 Å2
MethodPISA
2
D: Polymerase acidic protein
E: RNA-directed RNA polymerase catalytic subunit
F: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)256,0793
Polymers256,0793
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32480 Å2
ΔGint-192 kcal/mol
Surface area97440 Å2
MethodPISA
3
G: Polymerase acidic protein
H: RNA-directed RNA polymerase catalytic subunit
I: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)256,0793
Polymers256,0793
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34120 Å2
ΔGint-187 kcal/mol
Surface area95810 Å2
MethodPISA
4
J: Polymerase acidic protein
K: RNA-directed RNA polymerase catalytic subunit
L: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)256,0793
Polymers256,0793
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32960 Å2
ΔGint-182 kcal/mol
Surface area94100 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)337.122, 192.859, 235.688
Angle α, β, γ (deg.)90.000, 91.460, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and (resid 1 through 79 or resid 89 through 537 or resid 544 through 756))
21(chain F and (resid 1 through 79 or resid 89 through 537 or resid 544 through 756))
31(chain I and (resid 1 through 79 or resid 89 through 756))
41(chain L and (resid 1 through 79 or resid 89 through 537 or resid 544 through 756))
12(chain B and (resid 1 through 179 or resid 209...
22(chain E and (resid 1 through 348 or resid 374 through 632 or resid 657 through 756))
32(chain H and (resid 1 through 179 or resid 209...
42(chain K and (resid 1 through 179 or resid 209...
13(chain A and (resid 1 through 374 or resid 381 through 716))
23(chain D and (resid 1 through 374 or resid 381 through 716))
33(chain G and (resid 1 through 374 or resid 381 through 716))
43chain J

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain C and (resid 1 through 79 or resid 89 through 537 or resid 544 through 756))C1 - 79
121(chain C and (resid 1 through 79 or resid 89 through 537 or resid 544 through 756))C89 - 537
131(chain C and (resid 1 through 79 or resid 89 through 537 or resid 544 through 756))C544 - 756
211(chain F and (resid 1 through 79 or resid 89 through 537 or resid 544 through 756))F1 - 79
221(chain F and (resid 1 through 79 or resid 89 through 537 or resid 544 through 756))F89 - 537
231(chain F and (resid 1 through 79 or resid 89 through 537 or resid 544 through 756))F544 - 756
311(chain I and (resid 1 through 79 or resid 89 through 756))I1 - 79
321(chain I and (resid 1 through 79 or resid 89 through 756))I89 - 756
411(chain L and (resid 1 through 79 or resid 89 through 537 or resid 544 through 756))L1 - 79
421(chain L and (resid 1 through 79 or resid 89 through 537 or resid 544 through 756))L89 - 537
431(chain L and (resid 1 through 79 or resid 89 through 537 or resid 544 through 756))L544 - 756
112(chain B and (resid 1 through 179 or resid 209...B1 - 179
122(chain B and (resid 1 through 179 or resid 209...B209 - 348
132(chain B and (resid 1 through 179 or resid 209...B1 - 756
142(chain B and (resid 1 through 179 or resid 209...B657 - 668
152(chain B and (resid 1 through 179 or resid 209...B685 - 756
212(chain E and (resid 1 through 348 or resid 374 through 632 or resid 657 through 756))E1 - 348
222(chain E and (resid 1 through 348 or resid 374 through 632 or resid 657 through 756))E374 - 632
232(chain E and (resid 1 through 348 or resid 374 through 632 or resid 657 through 756))E657 - 756
312(chain H and (resid 1 through 179 or resid 209...H1 - 179
322(chain H and (resid 1 through 179 or resid 209...H209 - 348
332(chain H and (resid 1 through 179 or resid 209...H374 - 632
342(chain H and (resid 1 through 179 or resid 209...H657 - 668
352(chain H and (resid 1 through 179 or resid 209...H685 - 756
412(chain K and (resid 1 through 179 or resid 209...K1 - 179
422(chain K and (resid 1 through 179 or resid 209...K209 - 348
432(chain K and (resid 1 through 179 or resid 209...K374 - 668
442(chain K and (resid 1 through 179 or resid 209...K685 - 756
113(chain A and (resid 1 through 374 or resid 381 through 716))A1 - 374
123(chain A and (resid 1 through 374 or resid 381 through 716))A381 - 716
213(chain D and (resid 1 through 374 or resid 381 through 716))D1 - 374
223(chain D and (resid 1 through 374 or resid 381 through 716))D381 - 716
313(chain G and (resid 1 through 374 or resid 381 through 716))G1 - 374
323(chain G and (resid 1 through 374 or resid 381 through 716))G381 - 716
413chain JJ1 - 716

NCS ensembles:
ID
1
2
3

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Components

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


Mass: 82710.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: PA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: D3YNB8, Hydrolases; Acting on ester bonds
#2: Protein
RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 1 / PB1 / RNA-directed RNA polymerase subunit P1


Mass: 86546.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: PB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D3YNB6, RNA-directed RNA polymerase
#3: Protein
Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 86821.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: PB2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D3YNB5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.64 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 1M Phosphate Potassium Sodium pH6.9, 0.07% Dichloromethane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.634→235.611 Å / Num. obs: 143100 / % possible obs: 100 % / Redundancy: 3.4 % / Biso Wilson estimate: 76.82 Å2 / CC1/2: 0.88 / Rmerge(I) obs: 0.484 / Rpim(I) all: 0.31 / Rrim(I) all: 0.576 / Net I/σ(I): 1.5
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
3.85-4.053.52.539208780.3751.6083.013
12.16-235.613.20.25446590.8820.1630.302

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.7.3data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5d98
Resolution: 3.634→235.611 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.15
RfactorNum. reflection% reflection
Rfree0.3229 4059 4.99 %
Rwork0.277 --
Obs0.2794 81274 47.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 252.81 Å2 / Biso mean: 101.2285 Å2 / Biso min: 15.26 Å2
Refinement stepCycle: final / Resolution: 3.634→235.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms67760 0 0 0 67760
Num. residues----8449
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefinement-IDRmsType
11C8668X-RAY DIFFRACTION2.831TORSIONAL
12F8668X-RAY DIFFRACTION2.831TORSIONAL
13I8668X-RAY DIFFRACTION2.831TORSIONAL
14L8668X-RAY DIFFRACTION2.831TORSIONAL
21B7744X-RAY DIFFRACTION2.831TORSIONAL
22E7744X-RAY DIFFRACTION2.831TORSIONAL
23H7744X-RAY DIFFRACTION2.831TORSIONAL
24K7744X-RAY DIFFRACTION2.831TORSIONAL
31A8816X-RAY DIFFRACTION2.831TORSIONAL
32D8816X-RAY DIFFRACTION2.831TORSIONAL
33G8816X-RAY DIFFRACTION2.831TORSIONAL
34J8816X-RAY DIFFRACTION2.831TORSIONAL
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6344-3.67720.457220.50622123
3.6772-3.7220.569230.427686892
3.722-3.76910.224570.3291351422
3.7691-3.81870.4272120.33832212334
3.8187-3.87110.3486150.33552993145
3.8711-3.92640.3297220.32323854077
3.9264-3.9850.4342240.33194314558
3.985-4.04730.3315240.352357359710
4.0473-4.11360.3477410.309174578613
4.1136-4.18460.3307540.3058946100017
4.1846-4.26070.3776630.28541144120721
4.2607-4.34260.3638670.29681387145425
4.3426-4.43130.3241860.2951643172930
4.4313-4.52760.3617930.291920201334
4.5276-4.63290.36151360.27872280241641
4.6329-4.74880.30711390.26072671281048
4.7488-4.87720.31391590.26393037319655
4.8772-5.02080.34451880.27733334352260
5.0208-5.18280.34442010.28613601380265
5.1828-5.36810.322090.29893967417671
5.3681-5.5830.3792300.31394428465880
5.583-5.83710.37772760.30995065534191
5.8371-6.14490.32422860.31575452573898
6.1449-6.52990.36412920.330155665858100
6.5299-7.03410.37622940.317455655859100
7.0341-7.7420.32032930.287555925885100
7.742-8.86240.31142820.236255975879100
8.8624-11.16570.22062810.195456035884100
11.1657-236.10790.31082800.2725521580196

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