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- PDB-3p06: Crystal structure of Tellina virus 1 VP4 protease in the form of ... -

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Basic information

Entry
Database: PDB / ID: 3p06
TitleCrystal structure of Tellina virus 1 VP4 protease in the form of an intra-molecular(cis)acyl-enzyme complex.
ComponentsVP4 protein
KeywordsHYDROLASE / cis-cleavage / intramolecular acyl-enzyme / ester-linkage / alpha/beta protein / protease / polyprotein processing / acyl-enzyme
Function / homology
Function and homology information


serine-type peptidase activity / viral capsid / host cell cytoplasm / structural molecule activity / proteolysis / metal ion binding
Similarity search - Function
Ribosomal Protein S5; domain 2 - #110 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Ribosomal Protein S5; domain 2 ...Ribosomal Protein S5; domain 2 - #110 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Ribosomal Protein S5; domain 2 / Viral coat protein subunit / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / UREA / Structural polyprotein
Similarity search - Component
Biological speciesTellina virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsChung, I.Y.W. / Paetzel, M.
Citation
Journal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of a Viral Protease Intramolecular Acyl-enzyme Complex: INSIGHTS INTO cis-CLEAVAGE AT THE VP4/VP3 JUNCTION OF TELLINA BIRNAVIRUS.
Authors: Chung, I.Y. / Paetzel, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Expression, purification and crystallization of VP4 protease from Tellina virus 1.
Authors: Chung, I.Y. / Paetzel, M.
History
DepositionSep 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
A: VP4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1108
Polymers20,5641
Non-polymers5467
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: VP4 protein
hetero molecules

A: VP4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,22016
Polymers41,1282
Non-polymers1,09214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
Buried area4390 Å2
ΔGint-51 kcal/mol
Surface area15450 Å2
MethodPISA
3
A: VP4 protein
hetero molecules

A: VP4 protein
hetero molecules

A: VP4 protein
hetero molecules

A: VP4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,43932
Polymers82,2564
Non-polymers2,18428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_554x,x-y,-z-1/31
Buried area11480 Å2
ΔGint-155 kcal/mol
Surface area28700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.140, 59.140, 208.142
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein VP4 protein


Mass: 20563.883 Da / Num. of mol.: 1 / Fragment: UNP residues 637-830
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tellina virus 1 / Gene: viral protein 4 (VP4) / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: Q2PBR5, EC: 3.4.21.115

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Non-polymers , 6 types, 54 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.55 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 296 K / pH: 5
Details: reservoir: 21% PEG8000, 0.55M ammonium sulfate. drop: On a coverslip, 1 microliter of VP4 was mixed with 1 microliter of reservoir reagent(21% PEG8000, 0.55M ammonium sulfate) and 1 ...Details: reservoir: 21% PEG8000, 0.55M ammonium sulfate. drop: On a coverslip, 1 microliter of VP4 was mixed with 1 microliter of reservoir reagent(21% PEG8000, 0.55M ammonium sulfate) and 1 microliter of 0.2M urea as additive. To aid in crystal nucleation, this drop was seeded with 1 microliter of selenomethionine- labelled crystal from an older drop, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97893
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 28, 2010
Details: DCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR.
RadiationMonochromator: A DOUBLE CRYSTAL MONOCHROMATOR (DCM) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.1→52 Å / Num. obs: 13466 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 11.4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 14.5
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MxData Collectordata collection
PHENIXAutosolmodel building
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.221 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 662 4.9 %RANDOM
Rwork0.182 ---
obs0.185 12743 99.7 %-
all-13466 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 32 47 1503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221471
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.9961993
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4225193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94426.07851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68315248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.371156
X-RAY DIFFRACTIONr_chiral_restr0.1380.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211064
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1861.5968
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12621555
X-RAY DIFFRACTIONr_scbond_it3.9653502
X-RAY DIFFRACTIONr_scangle_it6.4464.5437
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 45 -
Rwork0.209 867 -
obs--96.41 %
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)
12.4647-1.6644-0.57373.52190.23621.84710.06480.1334-0.2991-0.0673-0.06760.40710.0658-0.34280.00270.09830.0225-0.04840.084-0.01210.0944-8.473414.2418-18.0287
21.1936-0.27060.24261.18320.17192.31230.0773-0.0973-0.0910.17450.0277-0.05320.09040.1115-0.1050.11420.0108-0.040.0242-0.00580.10140.144414.2549-10.6512
32.8957-0.6013-0.05882.56180.20212.20860.0007-0.01210.0862-0.08920.0794-0.4584-0.01710.2152-0.080.08230.0126-0.00060.0532-0.01770.09815.389215.3881-25.9335
42.6124-1.49491.498415.7599-7.48926.26770.01960.1674-0.1219-0.11920.44340.81480.227-0.3866-0.4630.08690.0172-0.02160.0949-0.00880.0814-8.906415.6744-21.8862
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A637 - 657
2X-RAY DIFFRACTION2A658 - 748
3X-RAY DIFFRACTION3A749 - 814
4X-RAY DIFFRACTION4A815 - 830

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