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- PDB-2e9t: Foot-and-mouth disease virus RNA-polymerase RNA dependent in comp... -

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Basic information

Entry
Database: PDB / ID: 2e9t
TitleFoot-and-mouth disease virus RNA-polymerase RNA dependent in complex with a template-primer RNA and 5F-UTP
Components
  • 5'-R(*GP*GP*GP*CP*CP*CP*(5FU))-3'
  • 5'-R(P*UP*AP*GP*GP*GP*CP*CP*C)-3'
  • RNA-dependent RNA polymerase
KeywordsTRANSFERASE/RNA / Foot-and-mouth disease virus / RNA-dependent RNA polymerase / 3D polymerase / polymerase / TRANSFERASE-RNA COMPLEX
Function / homology
Function and homology information


symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / regulation of translation / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity ...symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / regulation of translation / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Reverse transcriptase/Diguanylate cyclase domain / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Papain-like cysteine peptidase superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE / RNA / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus C-S8c1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFerrer-Orta, C. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Sequential structures provide insights into the fidelity of RNA replication
Authors: Ferrer-Orta, C. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N.
#1: Journal: Embo J. / Year: 2006
Title: The structure of a protein primer-polymerase complex in the initiation of genome replication
Authors: Ferrer-Orta, C. / Arias, A. / Agudo, R. / Perez-Luque, R. / Escarmis, R. / Domingo, E. / Verdaguer, N.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 2006
Title: A comparison of viral RNA-dependent RNA polymerases
Authors: Ferrer-Orta, C. / Arias, A. / Escarmis, C. / Verdaguer, N.
#3: Journal: J.Biol.Chem. / Year: 2004
Title: Structure of foot-and-mouth disease virus RNA-dependent RNA polymerase and its complex with a template-primer RNA
Authors: Ferrer-Orta, C. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N.
#4: Journal: J.Mol.Biol. / Year: 2005
Title: Mutant viral polymerase in the transition of virus to error catastrophe identifies a critical site for RNA binding
Authors: Arias, A. / Agudo, R. / Ferrer-Orta, C. / Perez-Luque, R. / Airaksinen, A. / Brocchi, E. / Domingo, E. / Verdaguer, N. / Escarmis, C.
History
DepositionJan 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Apr 16, 2014Group: Other
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-R(P*UP*AP*GP*GP*GP*CP*CP*C)-3'
C: 5'-R(*GP*GP*GP*CP*CP*CP*(5FU))-3'
E: 5'-R(P*UP*AP*GP*GP*GP*CP*CP*C)-3'
F: 5'-R(*GP*GP*GP*CP*CP*CP*(5FU))-3'
A: RNA-dependent RNA polymerase
D: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,97012
Polymers116,5176
Non-polymers4536
Water1,17165
1
B: 5'-R(P*UP*AP*GP*GP*GP*CP*CP*C)-3'
C: 5'-R(*GP*GP*GP*CP*CP*CP*(5FU))-3'
A: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4856
Polymers58,2593
Non-polymers2273
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-R(P*UP*AP*GP*GP*GP*CP*CP*C)-3'
F: 5'-R(*GP*GP*GP*CP*CP*CP*(5FU))-3'
D: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4856
Polymers58,2593
Non-polymers2273
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.597, 95.597, 201.155
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 1 - 474 / Label seq-ID: 1 - 474

Dom-IDAuth asym-IDLabel asym-ID
1AE
2DF

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Components

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RNA chain , 2 types, 4 molecules BECF

#1: RNA chain 5'-R(P*UP*AP*GP*GP*GP*CP*CP*C)-3'


Mass: 2541.577 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA template
#2: RNA chain 5'-R(*GP*GP*GP*CP*CP*CP*(5FU))-3'


Mass: 2230.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA primer

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Protein , 1 types, 2 molecules AD

#3: Protein RNA-dependent RNA polymerase


Mass: 53486.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus C-S8c1 / Genus: Aphthovirus / Species: Foot-and-mouth disease virus / Strain: c-s8c1 / Gene: 3D / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q0QEE1, UniProt: Q9QCE4*PLUS, RNA-directed RNA polymerase

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Non-polymers , 3 types, 71 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 33% PEG 4000, 0.2M ammonium acetate, 0.1M sodium citrate, 4% butyrolactone, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2ammonium acetate11
3sodium citrate11
4butyrolactone11
5HOH11
6PEG 400012
7ammonium acetate12
8sodium citrate12
9butyrolactone12
10HOH12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 33329 / Num. obs: 31778 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.9 / Rsym value: 0.74 / Net I/σ(I): 1.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ProDCdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WNE

1wne


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / SU B: 30.249 / SU ML: 0.303 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28931 1691 5.1 %RANDOM
Rwork0.23343 ---
obs0.23616 31778 99.99 %-
all-33329 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.996 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7482 636 22 65 8205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228382
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5542.05211488
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0665946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1923.407364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.918151278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0121556
X-RAY DIFFRACTIONr_chiral_restr0.0910.21272
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026202
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.23794
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.25739
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2347
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0540.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3941.54793
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.66827586
X-RAY DIFFRACTIONr_scbond_it1.1934221
X-RAY DIFFRACTIONr_scangle_it1.8884.53902
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3742 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal0.080.5
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 137 -
Rwork0.264 2271 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: 31.5931 Å / Origin y: 54.2249 Å / Origin z: 150.7128 Å
111213212223313233
T-0.2271 Å20.0494 Å2-0.016 Å2--0.1976 Å2-0.0024 Å2---0.0909 Å2
L0.7763 °2-0.1218 °20.6587 °2-0.5308 °2-0.2485 °2--1.7941 °2
S-0.0565 Å °-0.0048 Å °0.0825 Å °-0.0191 Å °-0.0922 Å °-0.0376 Å °-0.2179 Å °0.1183 Å °0.1487 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 474
2X-RAY DIFFRACTION1B903 - 910
3X-RAY DIFFRACTION1C915 - 921
4X-RAY DIFFRACTION1D1 - 474
5X-RAY DIFFRACTION1E903 - 910
6X-RAY DIFFRACTION1F915 - 921

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