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- PDB-5epi: CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EX... -

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Basic information

Entry
Database: PDB / ID: 5epi
TitleCRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT
Components
  • CRNA 5' END
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA-directed RNA polymerase catalytic subunit
KeywordsTRANSFERASE / INFLUENZA B VIRUS / RNA-DEPENDENT RNA POLYMERASE / HETEROTRIMER / SUBUNITS PA / PB1 / PB2 / VIRAL RNA / CRNA 5' END / INFLUENZA
Function / homology
Function and homology information


cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / virion component / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / virion component / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA / RNA (> 10) / Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsGuilligay, D. / Cusack, S.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council322586 France
Citation
Journal: Mol.Cell / Year: 2016
Title: Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains.
Authors: Thierry, E. / Guilligay, D. / Kosinski, J. / Bock, T. / Gaudon, S. / Round, A. / Pflug, A. / Hengrung, N. / El Omari, K. / Baudin, F. / Hart, D.J. / Beck, M. / Cusack, S.
#1: Journal: To Be Published
Title: Crystal Structure Of Influenza A Polymerase Bound To The Viral RNA Promoter
Authors: Reich, S. / Guilligay, D. / Pflug, A. / Cusack, S.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Apr 3, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / ndb_struct_na_base_pair ...entity_src_gen / ndb_struct_na_base_pair / pdbx_audit_support / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _ndb_struct_na_base_pair.hbond_type_12 ..._entity_src_gen.pdbx_host_org_cell_line / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
E: Polymerase acidic protein
I: Polymerase acidic protein
M: Polymerase acidic protein
Q: Polymerase acidic protein
U: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
F: RNA-directed RNA polymerase catalytic subunit
J: RNA-directed RNA polymerase catalytic subunit
N: RNA-directed RNA polymerase catalytic subunit
R: RNA-directed RNA polymerase catalytic subunit
V: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2
G: Polymerase basic protein 2
K: Polymerase basic protein 2
O: Polymerase basic protein 2
S: Polymerase basic protein 2
W: Polymerase basic protein 2
D: CRNA 5' END
H: CRNA 5' END
L: CRNA 5' END
P: CRNA 5' END
T: CRNA 5' END
X: CRNA 5' END


Theoretical massNumber of molelcules
Total (without water)1,600,85624
Polymers1,600,85624
Non-polymers00
Water00
1
A: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2
D: CRNA 5' END


Theoretical massNumber of molelcules
Total (without water)266,8094
Polymers266,8094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40800 Å2
ΔGint-249 kcal/mol
Surface area93610 Å2
MethodPISA
2
E: Polymerase acidic protein
F: RNA-directed RNA polymerase catalytic subunit
G: Polymerase basic protein 2
H: CRNA 5' END


Theoretical massNumber of molelcules
Total (without water)266,8094
Polymers266,8094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41290 Å2
ΔGint-249 kcal/mol
Surface area93090 Å2
MethodPISA
3
I: Polymerase acidic protein
J: RNA-directed RNA polymerase catalytic subunit
K: Polymerase basic protein 2
L: CRNA 5' END


Theoretical massNumber of molelcules
Total (without water)266,8094
Polymers266,8094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41250 Å2
ΔGint-250 kcal/mol
Surface area93490 Å2
MethodPISA
4
M: Polymerase acidic protein
N: RNA-directed RNA polymerase catalytic subunit
O: Polymerase basic protein 2
P: CRNA 5' END


Theoretical massNumber of molelcules
Total (without water)266,8094
Polymers266,8094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41270 Å2
ΔGint-249 kcal/mol
Surface area93110 Å2
MethodPISA
5
Q: Polymerase acidic protein
R: RNA-directed RNA polymerase catalytic subunit
S: Polymerase basic protein 2
T: CRNA 5' END


Theoretical massNumber of molelcules
Total (without water)266,8094
Polymers266,8094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41370 Å2
ΔGint-250 kcal/mol
Surface area92250 Å2
MethodPISA
6
U: Polymerase acidic protein
V: RNA-directed RNA polymerase catalytic subunit
W: Polymerase basic protein 2
X: CRNA 5' END


Theoretical massNumber of molelcules
Total (without water)266,8094
Polymers266,8094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41190 Å2
ΔGint-249 kcal/mol
Surface area85240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.730, 209.980, 210.600
Angle α, β, γ (deg.)117.71, 92.81, 113.68
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Polymerase acidic protein / PA subunit


Mass: 85822.781 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: N-terminal extension, his-tag. C-terminal extension, linker and TEV site
Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Gene: PA / Plasmid: PKL-PBAC / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8Z9
#2: Protein
RNA-directed RNA polymerase catalytic subunit / PB1 subunit


Mass: 86207.016 Da / Num. of mol.: 6 / Fragment: PB1 SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Gene: PB1 / Plasmid: PKL-PBAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8Y6, RNA-directed RNA polymerase
#3: Protein
Polymerase basic protein 2 / PB2 subunit


Mass: 90858.133 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Gene: PB2 / Plasmid: PKL-PBAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8X3
#4: RNA chain
CRNA 5' END


Mass: 3921.464 Da / Num. of mol.: 6 / Fragment: FIRST 12 NUCLEOTIDES / Source method: obtained synthetically / Source: (synth.) Influenza B virus (B/Memphis/13/2003)
Sequence detailsN-TERMINAL EXTENSION, HIS-TAG AND LINKER. C-TERMINAL EXTENSION, LINKER AND TEV SITE. N-TERMINAL ...N-TERMINAL EXTENSION, HIS-TAG AND LINKER. C-TERMINAL EXTENSION, LINKER AND TEV SITE. N-TERMINAL EXTENSION, LINKER. C-TERMINAL EXTENSION, LINKER AND TEV SITE. N-TERMINAL EXTENSION, LINKER. C-TERMINAL EXTENSION, LINKER, STREP-TAG AND TEV SITE.

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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: 4.2 Å3/Da / Density % sol: 70.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07228 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07228 Å / Relative weight: 1
ReflectionResolution: 4.1→50 Å / Num. obs: 195792 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 1.75 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.49
Reflection shellResolution: 4.1→4.3 Å / Redundancy: 1.77 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.23 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WSA

4wsa


Resolution: 4.1→49.945 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 7760 4.13 %
Rwork0.2571 --
obs0.2584 188032 93.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.1→49.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms104724 1590 0 0 106314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003108491
X-RAY DIFFRACTIONf_angle_d0.539146493
X-RAY DIFFRACTIONf_dihedral_angle_d13.65366096
X-RAY DIFFRACTIONf_chiral_restr0.03816139
X-RAY DIFFRACTIONf_plane_restr0.00418519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0999-4.14650.41982540.36916107X-RAY DIFFRACTION95
4.1465-4.19530.39582620.36186177X-RAY DIFFRACTION95
4.1953-4.24640.34642140.35556140X-RAY DIFFRACTION95
4.2464-4.30010.36282520.34326178X-RAY DIFFRACTION95
4.3001-4.35670.38222210.32846043X-RAY DIFFRACTION94
4.3567-4.41630.33982460.326103X-RAY DIFFRACTION94
4.4163-4.47940.3612790.31796140X-RAY DIFFRACTION95
4.4794-4.54620.3582580.30396019X-RAY DIFFRACTION94
4.5462-4.61720.32592620.30035999X-RAY DIFFRACTION93
4.6172-4.69280.31832480.29246033X-RAY DIFFRACTION93
4.6928-4.77370.31672510.28215965X-RAY DIFFRACTION92
4.7737-4.86040.30492730.28895862X-RAY DIFFRACTION91
4.8604-4.95380.30792080.28285647X-RAY DIFFRACTION87
4.9538-5.05480.30992320.2826102X-RAY DIFFRACTION94
5.0548-5.16460.32412670.27556136X-RAY DIFFRACTION95
5.1646-5.28470.31812810.27396129X-RAY DIFFRACTION95
5.2847-5.41670.3042840.276090X-RAY DIFFRACTION95
5.4167-5.56290.31342460.26716095X-RAY DIFFRACTION94
5.5629-5.72640.30252490.2536103X-RAY DIFFRACTION94
5.7264-5.9110.32072640.26056034X-RAY DIFFRACTION94
5.911-6.12190.32882060.26316012X-RAY DIFFRACTION93
6.1219-6.36650.28392260.2515940X-RAY DIFFRACTION91
6.3665-6.65560.27052640.23765782X-RAY DIFFRACTION90
6.6556-7.00560.2632860.24086053X-RAY DIFFRACTION94
7.0056-7.44320.27093070.23066025X-RAY DIFFRACTION94
7.4432-8.01580.24833210.21375960X-RAY DIFFRACTION94
8.0158-8.81840.22862600.19095928X-RAY DIFFRACTION92
8.8184-10.08540.21862090.18595824X-RAY DIFFRACTION90
10.0854-12.67210.22053250.19055881X-RAY DIFFRACTION93
12.6721-49.94890.3033050.30225765X-RAY DIFFRACTION90

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