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- PDB-3sjk: Crystal structure of the C147A mutant 3C from enterovirus 71 -

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Basic information

Entry
Database: PDB / ID: 3sjk
TitleCrystal structure of the C147A mutant 3C from enterovirus 71
Components
  • 3C proteasePicornain 3C
  • KPVLRTATVQGPSLDF peptide
KeywordsHYDROLASE / chymotrypsin-like fold / protease
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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
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 ...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. / 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus 71
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.096 Å
AuthorsLu, G. / Qi, J. / Chen, Z. / Xu, X. / Gao, F. / Lin, D. / Qian, W. / Liu, H. / Jiang, H. / Yan, J. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2011
Title: Enterovirus 71 and Coxsackievirus A16 3C Proteases: Binding to Rupintrivir and Their Substrates and Anti-Hand, Foot, and Mouth Disease Virus Drug Design.
Authors: Lu, G. / Qi, J. / Chen, Z. / Xu, X. / Gao, F. / Lin, D. / Qian, W. / Liu, H. / Jiang, H. / Yan, J. / Gao, G.F.
History
DepositionJun 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C protease
B: KPVLRTATVQGPSLDF peptide


Theoretical massNumber of molelcules
Total (without water)21,9032
Polymers21,9032
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-4 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.261, 74.261, 102.628
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-191-

HOH

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Components

#1: Protein 3C protease / Picornain 3C


Mass: 21117.145 Da / Num. of mol.: 1 / Fragment: UNP residues 1549-1731 / Mutation: C147A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus 71 / Strain: Anhui1-09-China / Gene: 3C / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E0WWC7, UniProt: F6KTB0*PLUS, picornain 3C
#2: Protein/peptide KPVLRTATVQGPSLDF peptide


Mass: 785.974 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT CHAIN B (PEPTIDE KPVLRTATVQGPSLDF) WAS TRUNCATED DURING CRYSTALLIZATION.

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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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 20 mM lithium sulfate, 25% w/v PEG5000 MME, 8 mM 16-mer peptide, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 26, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.096→50 Å / Num. all: 12411 / Num. obs: 12238 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 17.871
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.184 / Num. unique all: 1150 / Rsym value: 0.477 / % possible all: 92.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SJ8

3sj8


Resolution: 2.096→17.573 Å / SU ML: 0.28 / σ(F): 0.14 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 563 4.8 %RANDOM
Rwork0.2073 ---
obs0.2087 11728 94.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.252 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.4804 Å2-0 Å2-0 Å2
2--6.4804 Å20 Å2
3----12.9609 Å2
Refinement stepCycle: LAST / Resolution: 2.096→17.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 0 104 1549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061471
X-RAY DIFFRACTIONf_angle_d0.9031991
X-RAY DIFFRACTIONf_dihedral_angle_d20.564540
X-RAY DIFFRACTIONf_chiral_restr0.059232
X-RAY DIFFRACTIONf_plane_restr0.003257
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.096-2.30650.32461360.27092505250585
2.3065-2.63930.2521490.24382807280795
2.6393-3.32160.24221470.21382880288099
3.3216-17.57410.21221310.182729732973100
Refinement TLS params.Method: refined / Origin x: 14.8545 Å / Origin y: 18.9285 Å / Origin z: 0.6461 Å
111213212223313233
T0.2315 Å2-0.0013 Å20.0025 Å2-0.2942 Å20.0121 Å2--0.2452 Å2
L0.5874 °2-0.1877 °20.7751 °2-1.1 °20.3532 °2--1.4638 °2
S-0.0638 Å °-0.1142 Å °0.05 Å °-0.0804 Å °0.0253 Å °0.0279 Å °-0.0334 Å °-0.2138 Å °0 Å °
Refinement TLS groupSelection details: all

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