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- PDB-3sjo: structure of EV71 3C in complex with Rupintrivir (AG7088) -

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Basic information

Entry
Database: PDB / ID: 3sjo
Titlestructure of EV71 3C in complex with Rupintrivir (AG7088)
Components3C protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / in complex with Rupintrivir / Chymotrypsin-like fold / protease / C147 covalently binds to Rupintrivir / HYDROLASE-HYDROLASE INHIBITOR complex
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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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
Chem-AG7 / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C protease
B: 3C protease
C: 3C protease
D: 3C protease
E: 3C protease
F: 3C protease
G: 3C protease
H: 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,99916
Polymers169,1948
Non-polymers4,8058
Water16,556919
1
A: 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7502
Polymers21,1491
Non-polymers6011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7502
Polymers21,1491
Non-polymers6011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7502
Polymers21,1491
Non-polymers6011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7502
Polymers21,1491
Non-polymers6011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7502
Polymers21,1491
Non-polymers6011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7502
Polymers21,1491
Non-polymers6011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7502
Polymers21,1491
Non-polymers6011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7502
Polymers21,1491
Non-polymers6011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.258, 82.171, 97.952
Angle α, β, γ (deg.)89.96, 89.99, 90.13
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
3C protease


Mass: 21149.209 Da / Num. of mol.: 8 / Fragment: UNP residues 1549-1731
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, picornain 3C
#2: Chemical
ChemComp-AG7 / 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER / RUPINTRIVIR, bound form


Mass: 600.678 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C31H41FN4O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 919 / 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: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, 25% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2011
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 140985 / Num. obs: 136411 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 20.642
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 3.182 / Num. unique all: 13450 / Rsym value: 0.312 / % possible all: 95.6

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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: 1.702→34.536 Å / σ(F): 0.1 / Phase error: 23.26 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 6953 5.28 %RANDOM
Rwork0.2052 ---
obs0.2079 131629 93.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.774 Å2 / ksol: 0.401 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1787 Å2-2.1023 Å20.1564 Å2
2---0.9909 Å20.3548 Å2
3----0.1878 Å2
Refinement stepCycle: LAST / Resolution: 1.702→34.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11128 0 344 919 12391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811704
X-RAY DIFFRACTIONf_angle_d1.0615840
X-RAY DIFFRACTIONf_dihedral_angle_d21.2044488
X-RAY DIFFRACTIONf_chiral_restr0.0771816
X-RAY DIFFRACTIONf_plane_restr0.0072032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7017-1.7310.34152820.3215534X-RAY DIFFRACTION78
1.731-1.76250.28032720.30715721X-RAY DIFFRACTION82
1.7625-1.79640.32643070.28465975X-RAY DIFFRACTION83
1.7964-1.8330.32643040.26635914X-RAY DIFFRACTION85
1.833-1.87290.25323180.25686061X-RAY DIFFRACTION85
1.8729-1.91640.29193130.24486087X-RAY DIFFRACTION86
1.9164-1.96430.24373340.2326232X-RAY DIFFRACTION88
1.9643-2.01740.23823630.2276125X-RAY DIFFRACTION88
2.0174-2.07670.2493220.21996394X-RAY DIFFRACTION90
2.0767-2.14370.24523070.20786383X-RAY DIFFRACTION91
2.1437-2.22030.23873390.21056371X-RAY DIFFRACTION91
2.2203-2.30910.2223460.20466477X-RAY DIFFRACTION91
2.3091-2.41410.21333370.20946483X-RAY DIFFRACTION92
2.4141-2.54120.24433580.21986437X-RAY DIFFRACTION92
2.5412-2.70030.22563570.22316478X-RAY DIFFRACTION92
2.7003-2.90840.2333590.21056538X-RAY DIFFRACTION92
2.9084-3.20050.20063560.19036587X-RAY DIFFRACTION93
3.2005-3.66220.20523610.17826536X-RAY DIFFRACTION93
3.6622-4.60860.17123560.16226490X-RAY DIFFRACTION92
4.6086-23.91460.22233190.20516180X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: -8.7098 Å / Origin y: -9.1947 Å / Origin z: -32.5069 Å
111213212223313233
T0.0102 Å2-0.0183 Å2-0.0173 Å2-0.0274 Å20.0032 Å2--0.0069 Å2
L0.0795 °2-0.0248 °2-0.0163 °2-0.0935 °20.0906 °2--0.0674 °2
S-0.0194 Å °-0.0129 Å °-0.0025 Å °-0.0515 Å °-0.0067 Å °-0.0061 Å °0.0546 Å °0.0421 Å °-0.0172 Å °
Refinement TLS groupSelection details: all

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