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- PDB-3ld1: Crystal Structure of IBV Nsp2a -

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Basic information

Entry
Database: PDB / ID: 3ld1
TitleCrystal Structure of IBV Nsp2a
ComponentsReplicase polyprotein 1a
KeywordsHYDROLASE / Globular like / Host cytoplasm / Host membrane / Membrane / Metal-binding / Protease / RNA-binding / Thiol protease / Transmembrane / Zinc-finger
Function / homology
Function and homology information


viral genome replication / transferase activity / omega peptidase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / induction by virus of host autophagy ...viral genome replication / transferase activity / omega peptidase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / proteolysis / RNA binding / zinc ion binding / membrane
Similarity search - Function
Non-structural protein 2, gammacoronavirus / Non-structural protein 6, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 5, gammacoronavirus / Non-structural protein 2, IBV-like / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus 3Ecto domain profile. / : / Coronavirus (CoV) Nsp3 Y domain profile. ...Non-structural protein 2, gammacoronavirus / Non-structural protein 6, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 5, gammacoronavirus / Non-structural protein 2, IBV-like / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus 3Ecto domain profile. / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Replicase polyprotein 1a
Similarity search - Component
Biological speciesAvian infectious bronchitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.498 Å
AuthorsXu, Y. / Cong, L. / Wei, L. / Fu, J. / Chen, C. / Yang, A. / Tang, H. / Bartlam, M. / Rao, Z.
CitationJournal: To be Published
Title: IBV nsp2 is an endosome-associated protein and viral pathogenicity factor
Authors: Xu, Y. / Ye, Z. / Wei, L. / Cong, L. / Fu, J. / Chen, C. / Yang, A. / Wu, W. / Tang, H. / Bartlam, M. / Rao, Z.
History
DepositionJan 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replicase polyprotein 1a


Theoretical massNumber of molelcules
Total (without water)39,7571
Polymers39,7571
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.179, 114.179, 60.979
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Replicase polyprotein 1a / pp1a / ORF1a polyprotein / Non-structural protein 2 / nsp2 / p87 / Non-structural protein 3 / nsp3 ...pp1a / ORF1a polyprotein / Non-structural protein 2 / nsp2 / p87 / Non-structural protein 3 / nsp3 / Papain-like proteinase / PL-PRO / p195 / Non-structural protein 4 / nsp4 / Peptide HD2 / p41 / 3C-like proteinase / 3CL-PRO / 3CLp / M-PRO / p33 / nsp5 / Non-structural protein 6 / nsp6 / p34 / Non-structural protein 7 / nsp7 / p9 / Non-structural protein 8 / nsp8 / p24 / Non-structural protein 9 / nsp9 / p10 / Non-structural protein 10 / nsp10 / Growth factor-like peptide / GFL / p16 / Non-structural protein 11 / nsp11


Mass: 39757.324 Da / Num. of mol.: 1 / Fragment: IBV Nsp2a / Mutation: Q132L, K195A, L270F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avian infectious bronchitis virus (strain M41)
Strain: M41 / Gene: 1a, 1ab / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0C6V5, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.89 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 12% (w/v) PEG8000, 10% (v/v) Ethylene Glycol, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2008 / Details: monochromater
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 17086 / % possible obs: 95 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 30.1
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4 / Num. unique all: 1489 / % possible all: 83.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.498→29.14 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.177 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.488 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 792 5 %RANDOM
Rwork0.216 ---
obs0.219 15851 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.54 Å2 / Biso mean: 51.975 Å2 / Biso min: 32.18 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å2-1.08 Å20 Å2
2---2.17 Å20 Å2
3---3.25 Å2
Refinement stepCycle: LAST / Resolution: 2.498→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 0 90 2882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222845
X-RAY DIFFRACTIONr_angle_refined_deg2.2171.9613845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9825358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29123.75120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.8115501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9791518
X-RAY DIFFRACTIONr_chiral_restr0.1390.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022105
X-RAY DIFFRACTIONr_nbd_refined0.2810.21387
X-RAY DIFFRACTIONr_nbtor_refined0.3310.21983
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.22
X-RAY DIFFRACTIONr_mcbond_it1.2581.51836
X-RAY DIFFRACTIONr_mcangle_it2.10622873
X-RAY DIFFRACTIONr_scbond_it3.02531148
X-RAY DIFFRACTIONr_scangle_it4.5174.5972
LS refinement shellResolution: 2.498→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 59 -
Rwork0.27 1097 -
all-1156 -
obs--98.05 %

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