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- PDB-6qpg: Influenza A virus Polymerase Heterotrimer A/nt/60/1968(H3N2) in c... -

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Basic information

Entry
Database: PDB / ID: 6qpg
TitleInfluenza A virus Polymerase Heterotrimer A/nt/60/1968(H3N2) in complex with Nanobody NB8205
Components
  • Nanobody NB8205
  • 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 / Nanobody / antiviral inhibitor
Function / homology
Function and homology information


cap snatching / suppression by virus of host RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / viral transcription / suppression by virus of host MAVS activity / virion / RNA-directed RNA polymerase / viral RNA genome replication / endonuclease activity ...cap snatching / suppression by virus of host RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / viral transcription / suppression by virus of host MAVS activity / virion / RNA-directed RNA polymerase / viral RNA genome replication / endonuclease activity / RNA-directed 5'-3' RNA polymerase activity / host cell cytoplasm / Hydrolases, Acting on ester bonds / transcription, DNA-templated / host cell nucleus / nucleotide binding / RNA binding / metal ion binding
Influenza RNA-dependent RNA polymerase subunit PB2 / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PB1 / PA/PA-X superfamily / Polymerase acidic protein / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA-dependent RNA polymerase subunit PA / RNA-directed RNA polymerase, negative-strand RNA virus
Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Biological speciesInfluenza A virus
Camelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 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/R009945/1 United Kingdom
Medical Research Council (United Kingdom)MR/K000241/1 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 / Refinement description / Category: refine_ls_shell / Item: _refine_ls_shell.R_factor_R_free
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
M: Nanobody NB8205
N: Nanobody NB8205
O: Nanobody NB8205
P: Nanobody NB8205


Theoretical massNumber of molelcules
Total (without water)1,085,67416
Polymers1,085,67416
Non-polymers00
Water0
1
A: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2
M: Nanobody NB8205


Theoretical massNumber of molelcules
Total (without water)271,4194
Polymers271,4194
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Polymerase acidic protein
E: RNA-directed RNA polymerase catalytic subunit
F: Polymerase basic protein 2
N: Nanobody NB8205


Theoretical massNumber of molelcules
Total (without water)271,4194
Polymers271,4194
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Polymerase acidic protein
H: RNA-directed RNA polymerase catalytic subunit
I: Polymerase basic protein 2
O: Nanobody NB8205


Theoretical massNumber of molelcules
Total (without water)271,4194
Polymers271,4194
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Polymerase acidic protein
K: RNA-directed RNA polymerase catalytic subunit
L: Polymerase basic protein 2
P: Nanobody NB8205


Theoretical massNumber of molelcules
Total (without water)271,4194
Polymers271,4194
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)335.181, 192.900, 235.096
Angle α, β, γ (deg.)90.000, 91.781, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43
14
24
34
44

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 1 through 327 or resid 331 through 716))A1 - 326
121(chain 'A' and (resid 1 through 327 or resid 331 through 716))A331 - 371
131(chain 'A' and (resid 1 through 327 or resid 331 through 716))A398 - 716
241(chain 'D' and (resid 1 through 327 or resid 331 through 372 or resid 398 through 716))D1 - 326
251(chain 'D' and (resid 1 through 327 or resid 331 through 372 or resid 398 through 716))D331 - 371
261(chain 'D' and (resid 1 through 327 or resid 331 through 372 or resid 398 through 716))D398 - 716
371(chain 'G' and (resid 1 through 327 or resid 331 through 372 or resid 398 through 716))G1 - 326
381(chain 'G' and (resid 1 through 327 or resid 331 through 372 or resid 398 through 716))G331 - 371
391(chain 'G' and (resid 1 through 327 or resid 331 through 372 or resid 398 through 716))G398 - 716
4101(chain 'J' and (resid 1 through 372 or resid 398 through 716))J1 - 326
4111(chain 'J' and (resid 1 through 372 or resid 398 through 716))J331 - 371
4121(chain 'J' and (resid 1 through 372 or resid 398 through 716))J398 - 716
1132(chain 'C' and (resid 1 through 79 or resid 89 through 524 or resid 537 through 756))C1 - 181
1142(chain 'C' and (resid 1 through 79 or resid 89 through 524 or resid 537 through 756))C208 - 225
1152(chain 'C' and (resid 1 through 79 or resid 89 through 524 or resid 537 through 756))C243 - 350
1162(chain 'C' and (resid 1 through 79 or resid 89 through 524 or resid 537 through 756))C368 - 627
1172(chain 'C' and (resid 1 through 79 or resid 89 through 524 or resid 537 through 756))C687 - 755
2182(chain 'F' and (resid 1 through 177 or resid 183 through 524 or resid 537 through 756))F1 - 181
2192(chain 'F' and (resid 1 through 177 or resid 183 through 524 or resid 537 through 756))F208 - 225
2202(chain 'F' and (resid 1 through 177 or resid 183 through 524 or resid 537 through 756))F243 - 350
2212(chain 'F' and (resid 1 through 177 or resid 183 through 524 or resid 537 through 756))F368 - 627
2222(chain 'F' and (resid 1 through 177 or resid 183 through 524 or resid 537 through 756))F687 - 755
3232(chain 'I' and (resid 1 through 79 or resid 89 through 177 or resid 183 through 524 or resid 537 through 756))I1 - 181
3242(chain 'I' and (resid 1 through 79 or resid 89 through 177 or resid 183 through 524 or resid 537 through 756))I208 - 225
3252(chain 'I' and (resid 1 through 79 or resid 89 through 177 or resid 183 through 524 or resid 537 through 756))I243 - 350
3262(chain 'I' and (resid 1 through 79 or resid 89 through 177 or resid 183 through 524 or resid 537 through 756))I368 - 627
3272(chain 'I' and (resid 1 through 79 or resid 89 through 177 or resid 183 through 524 or resid 537 through 756))I687 - 755
4282(chain 'L' and (resid 1 through 79 or resid 89 through 177 or resid 183 through 528 or resid 537 through 756))L1 - 181
4292(chain 'L' and (resid 1 through 79 or resid 89 through 177 or resid 183 through 528 or resid 537 through 756))L208 - 225
4302(chain 'L' and (resid 1 through 79 or resid 89 through 177 or resid 183 through 528 or resid 537 through 756))L243 - 350
4312(chain 'L' and (resid 1 through 79 or resid 89 through 177 or resid 183 through 528 or resid 537 through 756))L368 - 627
4322(chain 'L' and (resid 1 through 79 or resid 89 through 177 or resid 183 through 528 or resid 537 through 756))L687 - 755
1333(chain 'B' and (resid 1 through 628 or resid 687 through 756))B1 - 78
1343(chain 'B' and (resid 1 through 628 or resid 687 through 756))B89 - 176
1353(chain 'B' and (resid 1 through 628 or resid 687 through 756))B183 - 522
1363(chain 'B' and (resid 1 through 628 or resid 687 through 756))B537 - 674
1373(chain 'B' and (resid 1 through 628 or resid 687 through 756))B693 - 755
2383(chain 'E' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))E1 - 78
2393(chain 'E' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))E89 - 176
2403(chain 'E' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))E183 - 522
2413(chain 'E' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))E537 - 674
2423(chain 'E' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))E693 - 755
3433(chain 'H' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))H1 - 78
3443(chain 'H' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))H89 - 176
3453(chain 'H' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))H183 - 522
3463(chain 'H' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))H537 - 674
3473(chain 'H' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))H693 - 755
4483(chain 'K' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))K1 - 78
4493(chain 'K' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))K89 - 176
4503(chain 'K' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))K183 - 522
4513(chain 'K' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))K537 - 674
4523(chain 'K' and (resid 1 through 351 or resid 368 through 628 or resid 687 through 756))K693 - 755
1534chain 'M'M1 - 120
2544chain 'N'N1 - 120
3554chain 'O'O1 - 120
4564chain 'P'P1 - 120

NCS ensembles:
ID
1
2
3
4

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Components

#1: Protein/peptide
Polymerase acidic protein


Mass: 83100.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Northern Territory/60/1968 H3N2)
Strain: A/Northern Territory/60/1968 H3N2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03434
#2: Protein/peptide
RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 1 / PB1 / RNA-directed RNA polymerase subunit P1


Mass: 86524.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Northern Territory/60/1968 H3N2)
Strain: A/Northern Territory/60/1968 H3N2 / Gene: PB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03432, RNA-directed RNA polymerase
#3: Protein/peptide
Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 86958.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Northern Territory/60/1968 H3N2)
Strain: A/Northern Territory/60/1968 H3N2 / Gene: PB2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03429
#4: Protein/peptide
Nanobody NB8205


Mass: 14835.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)

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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: 3.5 Å3/Da / Density % sol: 64.84 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.9-1.2M Phosphate Potassium Sodium, pH6.7

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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: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.34→235 Å / Num. obs: 89646 / % possible obs: 41.5 % / Redundancy: 7 % / Biso Wilson estimate: 78.39 Å2 / CC1/2: 0.99 / Net I/σ(I): 4.8
Reflection shellResolution: 3.34→3.87 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4718 / CC1/2: 0.7 / % possible all: 6.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5d98
Resolution: 3.34→234.98 Å / SU ML: 0.517 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.658
RfactorNum. reflection% reflection
Rfree0.3049 4533 5.06 %
Rwork0.2512 --
Obs0.254 89539 41.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 78.84 Å2
Refinement stepCycle: LAST / Resolution: 3.34→234.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms70549 0 0 0 70549
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.002671910
f_angle_d0.660296973
f_chiral_restr0.04310664
f_plane_restr0.003712491
f_dihedral_angle_d8.597343929
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.34-3.3800.2126170.24
3.38-3.420.391830.3507580.86
3.42-3.460.41270.35921221.83
3.46-3.50.3694100.34121892.8
3.5-3.550.4035160.30822974.4
3.55-3.60.3208210.32284035.95
3.6-3.650.3665260.3455187.57
3.65-3.710.3324290.3536068.88
3.71-3.760.4314450.301372710.8
3.76-3.830.348360.289487312.78
3.83-3.890.3297490.2938102915
3.89-3.960.3698780.2937118417.57
3.96-4.040.3314690.2742132119.37
4.04-4.120.3285820.2469147421.54
4.12-4.210.3381940.2485170925.23
4.21-4.310.3532940.2413200529.34
4.31-4.420.31261290.2365237534.79
4.42-4.540.30411490.2386277940.69
4.54-4.670.30971790.2386309145.64
4.67-4.820.31641760.233362052.47
4.82-4.990.32782240.2412414160.95
4.99-5.190.32782770.2544474869.8
5.19-5.430.31862720.2657534177.99
5.43-5.710.33943080.2798575883.99
5.71-6.070.33083330.2912625191.22
6.07-6.540.35263610.2831677198.86
6.54-7.20.32553680.28566871100
7.2-8.240.28853600.2372686699.97
8.24-10.380.23233710.1901691399.93
10.38-235.570.26913670.2544694998.84

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