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- PDB-4mg3: Crystal Structural Analysis of 2A Protease from Coxsackievirus A16 -

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Basic information

Entry
Database: PDB / ID: 4mg3
TitleCrystal Structural Analysis of 2A Protease from Coxsackievirus A16
ComponentsProtease 2A
KeywordsHYDROLASE / beta barrel
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / channel activity / symbiont-mediated suppression of host NF-kappaB cascade / monoatomic ion transmembrane transport / 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 / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein / 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 / 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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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
Biological speciesCoxsackievirus A16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.798 Å
AuthorsSun, Y. / Wang, X. / Dang, M. / Yuan, S.
CitationJournal: Protein Cell / Year: 2013
Title: An open conformation determined by a structural switch for 2A protease from coxsackievirus A16.
Authors: Sun, Y. / Wang, X. / Yuan, S. / Dang, M. / Li, X. / Zhang, X.C. / Rao, Z.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 30, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: Protease 2A
B: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3636
Polymers31,8722
Non-polymers4914
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-6 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.271, 101.271, 193.914
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-312-

HOH

21B-349-

HOH

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Components

#1: Protein Protease 2A


Mass: 15935.845 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 863-1007
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A16 / Strain: Tainan/5079/98 / Gene: 2A / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9QF31, picornain 2A
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M MgCl2, 0.1M HEPES-Na (pH 7.5), 18% (w/v) PEG 400, hanging drop, temperature 289K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.798→50 Å / Num. obs: 35773 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 19.38 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.8-1.861100
1.86-1.941100
1.94-2.031100
2.03-2.131100
2.13-2.271100
2.27-2.44198.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.47 Å
Translation2.5 Å35.47 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 35772
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.46-10029.20.618504
5.92-7.4629.10.784524
5.06-5.9225.70.804629
4.49-5.0617.50.867718
4.08-4.4919.60.843790
3.76-4.0818.70.837856
3.51-3.7618.50.803912
3.3-3.5120.50.802987
3.13-3.318.70.7941031
2.98-3.1320.20.7841075
2.85-2.9821.10.7811136
2.73-2.85210.7781173
2.63-2.7322.50.7721245
2.54-2.6323.80.7711264
2.46-2.5422.50.781315
2.38-2.4624.20.751374
2.32-2.3822.80.7841387
2.25-2.3224.30.7481416
2.2-2.2521.10.7721485
2.14-2.222.80.7521502
2.09-2.1423.90.7611544
2.05-2.0923.80.7511576
2-2.0524.80.7421616
1.96-227.10.7071652
1.92-1.9627.60.7091668
1.89-1.9226.90.7011707
1.85-1.8929.90.6851743
1.8-1.8537.70.6242943

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
DM6.2phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.798→35.47 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8613 / SU ML: 0.18 / σ(F): 1.35 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 1789 5 %RANDOM
Rwork0.1735 ---
obs0.1749 35767 99.77 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.051 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 105.27 Å2 / Biso mean: 27.4112 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1--4.2804 Å2-0 Å20 Å2
2---4.2804 Å20 Å2
3---8.5609 Å2
Refinement stepCycle: LAST / Resolution: 1.798→35.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 26 296 2536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062294
X-RAY DIFFRACTIONf_angle_d1.2683112
X-RAY DIFFRACTIONf_chiral_restr0.122334
X-RAY DIFFRACTIONf_plane_restr0.009401
X-RAY DIFFRACTIONf_dihedral_angle_d13.013813
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7985-1.84710.28031430.2032576271999
1.8471-1.90150.21131230.180525992722100
1.9015-1.96280.26051220.176725892711100
1.9628-2.0330.2371540.172225852739100
2.033-2.11440.20361250.173726022727100
2.1144-2.21060.20791630.172525742737100
2.2106-2.32710.23991320.176426132745100
2.3271-2.47290.20841420.175626002742100
2.4729-2.66370.22321310.181526282759100
2.6637-2.93170.2221480.192425942742100
2.9317-3.35560.2051390.185526492788100
3.3556-4.22660.16971400.154826472787100
4.2266-35.47650.16931270.16412722284998
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)
11.0873-0.92910.24930.789-0.11760.9171-0.01590.06430.2219-0.08220.0095-0.0654-0.00530.10880.01690.1118-0.0077-0.01910.13610.02910.172268.0159-9.710213.4472
21.581-0.2611-0.72821.0073-0.34680.53920.0812-0.19070.2771-0.04120.0597-0.3757-0.1080.0338-0.06260.1678-0.02620.00980.1604-0.02280.218161.58794.427114.6648
31.2595-0.0751-0.19310.4898-0.22420.5941-0.1490.1303-0.4063-0.0010.17390.13590.0694-0.1031-0.00990.143-0.02970.02540.2294-0.0010.219851.1233-11.13115.6354
41.0797-0.9043-0.57750.89090.3030.4870.04430.03630.1234-0.04430.0715-0.0668-0.0853-0.018-0.070.1092-0.0087-0.01160.1410.00780.137855.5564-0.245613.8579
50.31850.17150.09510.12850.03950.03240.0372-0.7586-0.11620.45730.2106-0.27870.343-0.186-0.05850.25360.0595-0.11370.3632-0.04580.220367.4015-5.111325.5751
60.5883-0.2844-0.11290.5104-0.03910.32070.0437-0.14240.2903-0.0165-0.14440.4245-0.1351-0.24520.04170.09970.0552-0.02770.1424-0.08320.300719.20181.432218.1056
71.13050.5941-0.23521.39230.39920.58540.0591-0.00210.08810.0255-0.07950.0821-0.15260.07240.01420.14640.0267-0.00990.12030.00830.081433.52892.751417.7765
80.84870.2264-0.13070.75690.14010.42650.0497-0.01920.0261-0.0471-0.1323-0.0811-0.13530.04580.03810.18130.0189-0.01080.13160.02030.110733.32554.8618.3084
91.4668-0.39460.66570.1066-0.18080.57390.07280.28970.2923-0.4327-0.08110.2542-0.0450.0520.02370.27350.0697-0.12660.23980.0170.227322.34785.98996.8415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 4:44)A4 - 44
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 45:75)A45 - 75
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 76:97)A76 - 97
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 98:136)A98 - 136
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 137:145)A137 - 145
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 1:44)B1 - 44
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 45:106)B45 - 106
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 107:136)B107 - 136
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 137:145)B137 - 145

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