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- PDB-2vb0: Crystal structure of coxsackievirus B3 proteinase 3C -

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Basic information

Entry
Database: PDB / ID: 2vb0
TitleCrystal structure of coxsackievirus B3 proteinase 3C
ComponentsPOLYPROTEIN 3BCD
KeywordsHYDROLASE / CHYMOTRYPSIN-LIKE FOLD / AG7088 / RNA-BINDING PROTEIN / PICORNAVIRIDAE / CYSTEINE PROTEASE / HUMAN ENTEROVIRUS B
Function / homology
Function and homology information


: / symbiont-mediated perturbation of host gene expression / 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 / 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 perturbation of host gene expression / 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 / 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 / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / host cell cytoplasm / RNA helicase activity / DNA replication / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Picornavirus coat protein VP4 superfamily / 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) ...Picornavirus coat protein VP4 superfamily / 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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Trypsin-like serine proteases / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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 speciesCOXSACKIEVIRUS B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAnand, K. / Mesters, J.R. / Goerlach, R. / Zell, R. / Hilgenfeld, R.
Citation
Journal: To be Published
Title: Crystal Structure of Coxsackie Virus B3 Proteinase 3C
Authors: Anand, K. / Mesters, J.R. / Goerlach, R. / Zell, R. / Hilgenfeld, R.
#1: Journal: RNA / Year: 2002
Title: Determinants of the Recognition of Enteroviral Cloverleaf RNA by Coxsackievirus B3 Proteinase 3C.
Authors: Zell, R. / Sidigi, K. / Bucci, E. / Stelzner, A. / Gorlach, M.
History
DepositionSep 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 24, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYPROTEIN 3BCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4102
Polymers20,3741
Non-polymers351
Water84747
1
A: POLYPROTEIN 3BCD
hetero molecules

A: POLYPROTEIN 3BCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8204
Polymers40,7492
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1510 Å2
ΔGint-16 kcal/mol
Surface area20120 Å2
MethodPQS
Unit cell
Length a, b, c (Å)78.706, 64.550, 39.196
Angle α, β, γ (deg.)90.00, 115.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein POLYPROTEIN 3BCD / COXSACKIEVIRUS B3 PROTEINASE 3C


Mass: 20374.410 Da / Num. of mol.: 1 / Fragment: 3C PROTEINASE, RESIDUES 14-196
Source method: isolated from a genetically manipulated source
Details: BETA-MERCAPTOETHANOL LINKED TO ACTIVE-SITE CYSTEINE
Source: (gene. exp.) COXSACKIEVIRUS B3 / Strain: NANCY / Plasmid: PET23A-3CSTOP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q90092, UniProt: P03313*PLUS, picornain 3C
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.17 Å3/Da / Density % sol: 42.85 % / Description: NONE
Crystal growpH: 5.5 / Details: pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.804
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 23, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.804 Å / Relative weight: 1
ReflectionResolution: 2.4→35.36 Å / Num. obs: 6931 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.95
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HAV 3CPRO

Resolution: 2.4→35.36 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.896 / SU B: 9.986 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.715 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 330 4.8 %RANDOM
Rwork0.207 ---
obs0.21 6582 99.1 %-
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: 47.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å2-0.25 Å2
2---0.3 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 1 47 1477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221447
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.9691954
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3375182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93124.39466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53115243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.069158
X-RAY DIFFRACTIONr_chiral_restr0.1240.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021104
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.2633
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.2935
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9371.5931
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56821444
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2163584
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0444.5510
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.323 26
Rwork0.242 427

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