[English] 日本語
Yorodumi
- PDB-5d9a: Influenza C Virus RNA-dependent RNA Polymerase - Space group P212121 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d9a
TitleInfluenza C Virus RNA-dependent RNA Polymerase - Space group P212121
Components
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA-directed RNA polymerase catalytic subunit
KeywordsVIRAL PROTEIN / RNA-dependent RNA polymerase / Influenza / Influenza C virus / Negative-strand virus
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 / virion component / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / 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 / RNA-directed RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / 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 / 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
Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsHengrung, N. / El Omari, K. / Serna Martin, I. / Vreede, F.T. / Cusack, S. / Rambo, R.P. / Vonrhein, C. / Bricogne, G. / Stuart, D.I. / Grimes, J.M. / Fodor, E.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Wellcome Trust092931/Z/10/Z United Kingdom
Wellcome Trust075491/Z/04 United Kingdom
Medical Research Council (United Kingdom)MR/K000241/1 United Kingdom
Medical Research Council (United Kingdom)G1000099 United Kingdom
Medical Research Council (United Kingdom)G1100138 United Kingdom
CitationJournal: Nature / Year: 2015
Title: Crystal structure of the RNA-dependent RNA polymerase from influenza C virus.
Authors: Hengrung, N. / El Omari, K. / Serna Martin, I. / Vreede, F.T. / Cusack, S. / Rambo, R.P. / Vonrhein, C. / Bricogne, G. / Stuart, D.I. / Grimes, J.M. / Fodor, E.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)1,028,57612
Polymers1,028,57612
Non-polymers00
Water00
1
A: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)257,1443
Polymers257,1443
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35400 Å2
ΔGint-193 kcal/mol
Surface area91520 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)257,1443
Polymers257,1443
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35710 Å2
ΔGint-193 kcal/mol
Surface area91650 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)257,1443
Polymers257,1443
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35450 Å2
ΔGint-193 kcal/mol
Surface area91900 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)257,1443
Polymers257,1443
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35420 Å2
ΔGint-194 kcal/mol
Surface area92040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.280, 217.500, 597.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22G
13A
23J
14B
24E
15B
25H
16B
26K
17C
27F
18C
28I
19C
29L
110D
210G
111D
211J
112E
212H
113E
213K
114F
214I
115F
215L
116G
216J
117H
217K
118I
218L

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHRAA4 - 7084 - 708
21THRTHRTHRTHRDD4 - 7084 - 708
12THRTHRTHRTHRAA4 - 7084 - 708
22THRTHRTHRTHRGG4 - 7084 - 708
13THRTHRTHRTHRAA4 - 7084 - 708
23THRTHRTHRTHRJJ4 - 7084 - 708
14METMETSERSERBB1 - 7531 - 753
24METMETSERSEREE1 - 7531 - 753
15METMETSERSERBB1 - 7531 - 753
25METMETSERSERHH1 - 7531 - 753
16METMETSERSERBB1 - 7531 - 753
26METMETSERSERKK1 - 7531 - 753
17METMETLYSLYSCC1 - 7711 - 771
27METMETLYSLYSFF1 - 7711 - 771
18METMETLYSLYSCC1 - 7711 - 771
28METMETLYSLYSII1 - 7711 - 771
19METMETLYSLYSCC1 - 7711 - 771
29METMETLYSLYSLL1 - 7711 - 771
110THRTHRTHRTHRDD4 - 7084 - 708
210THRTHRTHRTHRGG4 - 7084 - 708
111THRTHRTHRTHRDD4 - 7084 - 708
211THRTHRTHRTHRJJ4 - 7084 - 708
112METMETSERSEREE1 - 7531 - 753
212METMETSERSERHH1 - 7531 - 753
113METMETSERSEREE1 - 7531 - 753
213METMETSERSERKK1 - 7531 - 753
114METMETLYSLYSFF1 - 7711 - 771
214METMETLYSLYSII1 - 7711 - 771
115METMETLYSLYSFF1 - 7711 - 771
215METMETLYSLYSLL1 - 7711 - 771
116THRTHRTHRTHRGG4 - 7084 - 708
216THRTHRTHRTHRJJ4 - 7084 - 708
117METMETSERSERHH1 - 7531 - 753
217METMETSERSERKK1 - 7531 - 753
118METMETLYSLYSII1 - 7711 - 771
218METMETLYSLYSLL1 - 7711 - 771

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

-
Components

#1: Protein
Polymerase acidic protein / Polymerase 3 / RNA-directed RNA polymerase subunit P2


Mass: 82025.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza C virus (strain C/Johannesburg/1/1966)
Strain: C/Johannesburg/1/1966 / Gene: PA, P3 / Plasmid: MultiBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IMP5
#2: Protein
RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 1 / PB1 / RNA-directed RNA polymerase subunit P1


Mass: 86145.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza C virus (strain C/Johannesburg/1/1966)
Strain: C/Johannesburg/1/1966 / Gene: PB1 / Plasmid: MultiBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IMP4, RNA-directed RNA polymerase
#3: Protein
Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 88972.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza C virus (strain C/Johannesburg/1/1966)
Strain: C/Johannesburg/1/1966 / Gene: PB2 / Plasmid: MultiBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IMP3
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Drops were set up by mixing polymerase (5 mg/ml in 25 mM Hepes:NaOH, pH 7.5, 10% (v/v) glycerol, 0.5 M NaCl, 0.5 mM TCEP, 10 mM CaCl2) with 0.2 M NaCl, 0.1 M Na:HEPES, pH 7.5, 25% (w/v) ...Details: Drops were set up by mixing polymerase (5 mg/ml in 25 mM Hepes:NaOH, pH 7.5, 10% (v/v) glycerol, 0.5 M NaCl, 0.5 mM TCEP, 10 mM CaCl2) with 0.2 M NaCl, 0.1 M Na:HEPES, pH 7.5, 25% (w/v) PEG4000 and microseeds in a 2:1:1 protein:precipitant:seed ratio.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4.3→80.9 Å / Num. obs: 95264 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.204 / Net I/σ(I): 5.5
Reflection shellResolution: 4.3→4.41 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 1.1 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D98

5d98


Resolution: 4.3→50.01 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.818 / SU B: 168.293 / SU ML: 1.971 / Cross valid method: THROUGHOUT / ESU R Free: 1.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.36847 4744 5 %RANDOM
Rwork0.31575 ---
obs0.31839 90390 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 191.76 Å2
Baniso -1Baniso -2Baniso -3
1-4.39 Å20 Å20 Å2
2--3.98 Å2-0 Å2
3----8.38 Å2
Refinement stepCycle: LAST / Resolution: 4.3→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms69371 0 0 0 69371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01970656
X-RAY DIFFRACTIONr_bond_other_d0.0030.0268906
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9794958
X-RAY DIFFRACTIONr_angle_other_deg0.9863159126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30358607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.38824.1833189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.331513672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.57415484
X-RAY DIFFRACTIONr_chiral_restr0.0660.210434
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02178271
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0215733
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.20518.87434575
X-RAY DIFFRACTIONr_mcbond_other10.20518.87434574
X-RAY DIFFRACTIONr_mcangle_it17.78728.27743133
X-RAY DIFFRACTIONr_mcangle_other17.78728.27743134
X-RAY DIFFRACTIONr_scbond_it8.11519.64236081
X-RAY DIFFRACTIONr_scbond_other8.11519.64236082
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.13829.16251826
X-RAY DIFFRACTIONr_long_range_B_refined27.7682723
X-RAY DIFFRACTIONr_long_range_B_other27.75982723
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A825520.06
12D825520.06
21A829740.03
22G829740.03
31A829800.03
32J829800.03
41B859880
42E859880
51B859780
52H859780
61B859920
62K859920
71C894680.02
72F894680.02
81C892800.03
82I892800.03
91C895660.01
92L895660.01
101D825700.06
102G825700.06
111D825900.05
112J825900.05
121E859780
122H859780
131E859960
132K859960
141F900880.04
142I900880.04
151F904540.01
152L904540.01
161G831980
162J831980
171H859980
172K859980
181I901700.03
182L901700.03
LS refinement shellResolution: 4.301→4.412 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 352 -
Rwork0.423 6096 -
obs--92.88 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more