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- PDB-2ijd: Crystal Structure of the Poliovirus Precursor Protein 3CD -

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Entry
Database: PDB / ID: 2ijd
TitleCrystal Structure of the Poliovirus Precursor Protein 3CD
ComponentsPicornain 3C, RNA-directed RNA polymerase
KeywordsHYDROLASE / TRANSFERASE / RNA polymerase / RNA-dependent RNA polymerase / poliovirus / picornavirus / protease
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Thrombin, subunit H - #120 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Thrombin, subunit H - #120 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / 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 / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsMarcotte, L.L. / Gohara, D.W. / Filman, D.J. / Hogle, J.M.
CitationJournal: J.Virol. / Year: 2007
Title: Crystal structure of poliovirus 3CD: virally-encoded protease and precursor to the RNA-dependent RNA polymerase.
Authors: Marcotte, L.L. / Wass, A.B. / Gohara, D.W. / Pathak, H.B. / Arnold, J.J. / Filman, D.J. / Cameron, C.E. / Hogle, J.M.
History
DepositionSep 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Picornain 3C, RNA-directed RNA polymerase
2: Picornain 3C, RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,91812
Polymers144,0182
Non-polymers89910
Water1448
1
1: Picornain 3C, RNA-directed RNA polymerase
hetero molecules

1: Picornain 3C, RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,91812
Polymers144,0182
Non-polymers89910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5310 Å2
ΔGint-180 kcal/mol
Surface area57430 Å2
MethodPISA, PQS
2
2: Picornain 3C, RNA-directed RNA polymerase
hetero molecules

2: Picornain 3C, RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,91812
Polymers144,0182
Non-polymers89910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area5270 Å2
ΔGint-198 kcal/mol
Surface area57030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)208.537, 230.436, 151.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
111 2
211 2
311 2
121 2
221 2
321 2

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALALAALA61A8 - 598 - 59
211VALVALALAALA62B8 - 598 - 59
321ASNASNGLUGLU61A69 - 12169 - 121
121ASNASNGLUGLU62B69 - 12169 - 121
231THRTHRTYRTYR61A132 - 178132 - 178
331THRTHRTYRTYR62B132 - 178132 - 178
112GLNGLNASNASN61A187 - 553187 - 553
212GLNGLNASNASN62B187 - 553187 - 553
322VALVALARGARG21A554 - 559554 - 559
122VALVALARGARG22B554 - 559554 - 559
232PHEPHETRPTRP61A560 - 640560 - 640
332PHEPHETRPTRP62B560 - 640560 - 640

NCS ensembles :
ID
1
2

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Components

#1: Protein Picornain 3C, RNA-directed RNA polymerase / Protease 3C / P3C / RNA-directed RNA polymerase / P3D / 3CD


Mass: 72009.102 Da / Num. of mol.: 2 / Mutation: E55A, D58A, E63A, C147A, L629D, R638D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / Gene: 3CD / Production host: Escherichia coli (E. coli)
References: UniProt: P03300, UniProt: Q1PHW8*PLUS, picornain 3C, RNA-directed RNA polymerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 6.3 Å3/Da / Density % sol: 80.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2 M ammonium sulfate, 0.1 M HEPES, 0.3% Jeffamine M600, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. obs: 49539 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 %
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 4.8 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L1N, PDB ENTRY 1RA6

1l1n

1ra6


Resolution: 3.4→19.9 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.901 / SU B: 33.634 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.912 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23057 2510 5.1 %RANDOM
Rwork0.19915 ---
obs0.20073 46550 98.5 %-
all-249335 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.508 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.4→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10120 0 42 8 10170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210382
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.96614064
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.92951286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.43124.222450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.254151800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7871550
X-RAY DIFFRACTIONr_chiral_restr0.0060.21550
X-RAY DIFFRACTIONr_gen_planes_refined00.027784
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2480.24807
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.27128
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2367
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0730.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.69626571
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.884410332
X-RAY DIFFRACTIONr_scbond_it5.57544352
X-RAY DIFFRACTIONr_scangle_it8.363732
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
21124tight positional0.040.05
22129medium positional0.110.5
1111135loose positional0.315
2313587loose positional0.375
21224tight thermal0.080.5
22229medium thermal0.922
1221135loose thermal2.3210
2323587loose thermal3.310
LS refinement shellResolution: 3.4→3.578 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.281 390 -
Rwork0.239 6600 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.23581.51260.58146.8945-0.7818.8338-0.22691.05550.4836-0.67350.44910.8858-0.1063-1.9608-0.2222-0.32750.3984-0.21940.65010.1557-0.25434.637383.31466.1377
22.48970.21480.04771.39970.67133.7108-0.05370.406-0.3591-0.1424-0.01980.02530.26010.28290.0735-0.4212-0.1102-0.0494-0.2246-0.0316-0.3269-24.902462.898737.8712
36.25081.66831.50596.9055-0.48596.87610.743-0.7673-0.93331.243-0.3955-0.4991.93840.209-0.34760.85880.2876-0.1912-0.30360.1699-0.1823-32.697120.5305107.6592
41.39870.0157-0.59612.78190.17623.11610.0515-0.1990.05430.3186-0.08940.3446-0.5142-0.26730.0379-0.2427-0.09950.0061-0.35860.0348-0.3495-51.947390.384776.3487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION11A4 - 1834 - 183
2X-RAY DIFFRACTION21A184 - 640184 - 640
3X-RAY DIFFRACTION32B4 - 1814 - 181
4X-RAY DIFFRACTION42B185 - 640185 - 640

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