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- PDB-5x45: Crystal structure of 2A protease from Human rhinovirus C15 -

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Basic information

Entry
Database: PDB / ID: 5x45
TitleCrystal structure of 2A protease from Human rhinovirus C15
Componentsprotease 2A
KeywordsVIRAL PROTEIN / protease / human rhinovirus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / 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 ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / 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 / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
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. / 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
Biological speciesRhinovirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å
AuthorsLing, H. / Yang, P. / Shaw, N. / Sun, Y. / Wang, X.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2018
Title: Structural view of the 2A protease from human rhinovirus C15.
Authors: Ling, H. / Yang, P. / Hou, H. / Sun, Y.
History
DepositionFeb 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protease 2A
B: protease 2A
C: protease 2A
D: protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2108
Polymers60,9484
Non-polymers2624
Water2,126118
1
A: protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3022
Polymers15,2371
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3022
Polymers15,2371
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3022
Polymers15,2371
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3022
Polymers15,2371
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.992, 85.370, 208.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1chain AAA1 - 1363 - 138
2chain BBB1 - 1373 - 139
3chain CCC1 - 1373 - 139
4chain DDD1 - 1363 - 138

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Components

#1: Protein
protease 2A


Mass: 15237.057 Da / Num. of mol.: 4 / Fragment: UNP residues 847-983
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhinovirus C / Production host: Escherichia coli (E. coli) / References: UniProt: E5D8F2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium chloride, 0.1 M magnesium acetate tetrahydrate, 0.05 M sodium cacodylate and 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 22666 / % possible obs: 99.9 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.153 / Χ2: 1.031 / Net I/σ(I): 9.6 / Num. measured all: 200681
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.698.10.63622481.049199.8
2.69-2.88.20.5222211.056199.9
2.8-2.938.30.35522331.055199.8
2.93-3.088.40.25622241.063199.9
3.08-3.288.60.20122571.0491100
3.28-3.538.80.1622240.9841100
3.53-3.889.10.14522851.0441100
3.88-4.459.70.1322571.041100
4.45-5.69.70.10822980.973199.9
5.6-509.60.10924191.0141100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata reduction
PDB_EXTRACT3.22data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.602→42.685 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 1155 5.11 %
Rwork0.1649 21460 -
obs0.1674 22615 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.51 Å2 / Biso mean: 42.9412 Å2 / Biso min: 15.45 Å2
Refinement stepCycle: final / Resolution: 2.602→42.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4197 0 4 118 4319
Biso mean--83.57 37.27 -
Num. residues----546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064317
X-RAY DIFFRACTIONf_angle_d1.1125884
X-RAY DIFFRACTIONf_chiral_restr0.048638
X-RAY DIFFRACTIONf_plane_restr0.006773
X-RAY DIFFRACTIONf_dihedral_angle_d12.5021540
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2533X-RAY DIFFRACTION8.722TORSIONAL
12B2533X-RAY DIFFRACTION8.722TORSIONAL
13C2533X-RAY DIFFRACTION8.722TORSIONAL
14D2533X-RAY DIFFRACTION8.722TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6023-2.72070.32131430.22912618276199
2.7207-2.86410.30691500.227526502800100
2.8641-3.04350.26061710.197326152786100
3.0435-3.27840.23351360.188226822818100
3.2784-3.60820.2181150.168826792794100
3.6082-4.12990.17621580.140826722830100
4.1299-5.20180.18361430.124827112854100
5.2018-42.69070.18421390.15928332972100
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)
14.1711-1.9904-0.69195.1262-0.08262.25260.08680.34020.0702-0.4956-0.0830.11160.08090.0726-0.00710.39290.1517-0.02790.2910.00290.235-31.71315.430830.2212
23.3527-0.88030.8584.43051.72731.2806-0.00960.0168-0.0561-0.1214-0.1533-0.07670.047-0.15550.08930.3670.0880.02420.26840.01410.2113-24.95826.09639.4863
31.8846-1.8054-0.77337.0631.85474.9560.0208-0.20570.1768-0.02830.1396-0.4888-0.43230.271-0.1250.30320.07140.01120.28780.00130.2789-25.323915.947743.4738
45.2582-1.26950.29333.27410.71172.4021-0.1911-0.4809-0.09580.48050.2634-0.0420.03080.0466-0.04210.30350.15150.06550.29430.04610.2401-68.77014.173121.4624
53.649-0.5608-0.32064.3105-0.76851.5339-0.2743-0.01730.039-0.23190.0984-0.0615-0.1673-0.10060.1850.2560.09520.01840.29990.0170.2131-73.70515.227913.1085
62.6938-0.58250.16441.0677-0.40512.95810.2245-0.33170.58960.3309-0.1858-0.44910.00440.4896-0.0230.35760.01840.05240.44570.01190.3514-55.779514.216513.5918
75.8251-1.34410.5844.66110.07585.5283-0.21690.00130.22780.2384-0.0267-0.07180.03360.25430.19610.22880.10030.01750.26440.03030.1848-68.330115.02413.4101
82.7421-1.48670.31254.69370.70181.35710.25270.14190.0978-0.6161-0.1582-0.3818-0.05180.1469-0.06030.37060.16970.11970.30190.06410.2748-44.41932.199831.044
92.81070.44-0.97064.0792-0.50710.35480.0422-0.0974-0.06570.1584-0.1160.1178-0.24940.0480.05660.31710.09070.00650.27470.00970.1506-55.108937.408339.3898
103.2986-0.99410.79696.08721.50565.61270.11610.6821-0.2454-0.67550.1330.62840.5645-0.3093-0.23840.4464-0.0006-0.02570.41220.03650.332-56.199819.578139.2035
114.0656-1.594-0.35644.999-0.69744.86750.11640.2634-0.19650.0186-0.16780.24870.3296-0.21440.13510.31720.07530.04150.29140.02790.164-55.395531.984538.9344
123.9474-2.25090.61942.7625-0.55880.8593-0.5558-0.84480.14490.6720.32330.2909-0.0294-0.21430.05970.44710.29070.00680.4683-0.00910.3746-52.8005-9.16722.3794
134.191-1.40130.98414.32691.55291.5196-0.2088-0.02720.25130.0940.1703-0.241-0.24860.0145-0.0120.29810.1245-0.00650.31570.03940.234-43.732-16.404813.1077
145.9512-1.88832.13192.8031-1.5144.79570.0557-0.042-0.2114-0.018-0.03680.24210.0973-0.4829-0.07310.29070.1159-0.01090.332-0.00280.2933-53.4611-15.43429.0123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 40 )A1 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 75 )A41 - 75
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 136 )A76 - 136
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 40 )B1 - 40
5X-RAY DIFFRACTION5chain 'B' and (resid 41 through 75 )B41 - 75
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 98 )B76 - 98
7X-RAY DIFFRACTION7chain 'B' and (resid 99 through 137 )B99 - 137
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 41 )C1 - 41
9X-RAY DIFFRACTION9chain 'C' and (resid 42 through 76 )C42 - 76
10X-RAY DIFFRACTION10chain 'C' and (resid 77 through 99 )C77 - 99
11X-RAY DIFFRACTION11chain 'C' and (resid 100 through 137 )C100 - 137
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 40 )D1 - 40
13X-RAY DIFFRACTION13chain 'D' and (resid 41 through 75 )D41 - 75
14X-RAY DIFFRACTION14chain 'D' and (resid 76 through 136 )D76 - 136

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