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- PDB-2f8e: Foot and Mouth Disease Virus RNA-dependent RNA polymerase in comp... -

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Basic information

Entry
Database: PDB / ID: 2f8e
TitleFoot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with uridylylated VPg protein
Components
  • RNA-dependent RNA polymerase
  • VPg protein
KeywordsTRANSFERASE / Foot and Mouth Disease Virus / RNA-dependent RNA polymerase / VPg protein / protein primer
Function / homology
Function and homology information


T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / viral protein processing / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription ...T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / viral protein processing / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding / membrane
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / 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 / Reverse transcriptase/Diguanylate cyclase domain ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / 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 / Reverse transcriptase/Diguanylate cyclase domain / Papain-like cysteine peptidase superfamily / 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 / 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
: / URIDINE-5'-MONOPHOSPHATE / : / Genome polyprotein / Polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus - type C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFerrer-Orta, C. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N.
Citation
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, C. / Domingo, E. / Verdaguer, N.
#1: 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.
History
DepositionDec 2, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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_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.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 / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: RNA-dependent RNA polymerase
A: VPg protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1665
Polymers55,7622
Non-polymers4033
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-22 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.381, 94.381, 99.726
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RNA-dependent RNA polymerase


Mass: 53210.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type C / Genus: Aphthovirus / Species: Foot-and-mouth disease virus / Strain: c-s8c1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: GenBank: 6318192, UniProt: Q0QEE0*PLUS, RNA-directed RNA polymerase
#2: Protein/peptide VPg protein


Mass: 2552.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: VPg was prepared by solid phase peptide synthesis / References: UniProt: Q9DS05*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 33% PEG4K, 0.2M ammonium acetate, 0.1M sodium citrate pH 5.6, 4% butyrolactone, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→81.65 Å / Num. all: 11795 / Num. obs: 11795 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.5
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Foot and Mouth disease Virus

Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 51.876 / SU ML: 0.432 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28426 555 4.8 %RANDOM
Rwork0.23414 ---
all0.285 11795 --
obs0.2369 11125 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3859 0 22 0 3881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223830
X-RAY DIFFRACTIONr_angle_refined_deg0.9981.9495186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9765473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27123.407182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.54715639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8741528
X-RAY DIFFRACTIONr_chiral_restr0.0710.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022941
X-RAY DIFFRACTIONr_nbd_refined0.2010.21793
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.24
X-RAY DIFFRACTIONr_mcbond_it0.2751.52399
X-RAY DIFFRACTIONr_mcangle_it0.49623791
X-RAY DIFFRACTIONr_scbond_it0.531591
X-RAY DIFFRACTIONr_scangle_it0.8584.51395
LS refinement shellResolution: 2.898→2.973 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 46 -
Rwork0.323 800 -
obs--98.95 %

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