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- PDB-4x2z: Structural view and substrate specificity of papain-like protease... -

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Basic information

Entry
Database: PDB / ID: 4x2z
TitleStructural view and substrate specificity of papain-like protease from Avian Infectious Bronchitis Virus
ComponentsNonstructural protein 3
KeywordsHYDROLASE / PLpro / de-ubiquitination / IBV / Coronavirus
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / mRNA guanylyltransferase / omega peptidase activity / methyltransferase cap1 / endonuclease activity ...Transferases; Transferring one-carbon groups; Methyltransferases / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / mRNA guanylyltransferase / omega peptidase activity / methyltransferase cap1 / endonuclease activity / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / host cell endoplasmic reticulum membrane / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Nonstructural protein 14, gammacoronavirus / Nonstructural protein 15, middle domain, gammacoronavirus / Nonstructural protein 15, N-terminal, gammacoronavirus / RNA-dependent RNA polymerase, gammacoronavirus / 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 / Viral (Superfamily 1) RNA helicase ...Nonstructural protein 14, gammacoronavirus / Nonstructural protein 15, middle domain, gammacoronavirus / Nonstructural protein 15, N-terminal, gammacoronavirus / RNA-dependent RNA polymerase, gammacoronavirus / 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 / Viral (Superfamily 1) RNA helicase / NSP15, NendoU domain, coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Papain-like viral protease, palm and finger domains, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Coronavirus 3Ecto 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. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, 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 / Papain-like protease, thumb domain 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
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesAvian infectious bronchitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsKong, L. / Shaw, N. / Yan, L. / Lou, Z. / Rao, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Major Project (973 Program)2014CB542800 and 2013CB911100 China
National Natural Science Foundation of China81330036 and 81322023 China
Tsinghua University Initiative Scientific Research Program20141080146 China
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural View and Substrate Specificity of Papain-like Protease from Avian Infectious Bronchitis Virus.
Authors: Kong, L. / Shaw, N. / Yan, L. / Lou, Z. / Rao, Z.
History
DepositionNov 27, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references / Derived calculations
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nonstructural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1192
Polymers36,0541
Non-polymers651
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.312, 95.123, 118.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Nonstructural protein 3 / papain-like proteinase


Mass: 36053.652 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1174-1483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avian infectious bronchitis virus / Strain: Beaudette / Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli)
References: UniProt: P0C6Y1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M BIS-TRIS (pH 6.0), 18% Polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 27773 / % possible obs: 100 % / Redundancy: 12.4 % / Net I/σ(I): 26
Reflection shellResolution: 2→2.07 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 2.75 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.15→37.072 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 1124 5.05 %
Rwork0.175 --
obs0.1771 22247 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→37.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 1 128 2504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082430
X-RAY DIFFRACTIONf_angle_d1.0273300
X-RAY DIFFRACTIONf_dihedral_angle_d13.801860
X-RAY DIFFRACTIONf_chiral_restr0.041365
X-RAY DIFFRACTIONf_plane_restr0.005421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.24790.2651260.19922576X-RAY DIFFRACTION100
2.2479-2.36630.24591170.1942635X-RAY DIFFRACTION100
2.3663-2.51460.26671320.20542614X-RAY DIFFRACTION100
2.5146-2.70870.28371500.20342621X-RAY DIFFRACTION100
2.7087-2.98110.25581660.21022620X-RAY DIFFRACTION100
2.9811-3.41230.22641360.20062616X-RAY DIFFRACTION100
3.4123-4.29810.18981520.15262659X-RAY DIFFRACTION100
4.2981-37.0780.17191450.14332782X-RAY DIFFRACTION100

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