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- PDB-5gq1: Crystal structure of 2C helicase from enterovirus 71 (EV71) -

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Basic information

Entry
Database: PDB / ID: 5gq1
TitleCrystal structure of 2C helicase from enterovirus 71 (EV71)
ComponentsGenome polyprotein
KeywordsHYDROLASE / Enterovirus 2C / virus replication / Zinc finger / AAA+ ATPase
Function / homology
Function and homology information


RNA-protein covalent cross-linking / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / 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 ...RNA-protein covalent cross-linking / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / 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 / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / clathrin-dependent endocytosis of virus by host cell / 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 / 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
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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.493 Å
AuthorsGuan, H.X. / Tian, J. / Qin, B. / Wojdyla, J. / Wang, M.T. / Cui, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81572005 China
CitationJournal: SCI ADV / Year: 2017
Title: Crystal structure of 2C helicase from enterovirus 71
Authors: Guan, H.X. / Tian, J. / Qin, B. / Wojdyla, J. / Wang, B. / Zhao, Z.D. / Wang, M.T. / Cui, S.
History
DepositionAug 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Jul 18, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,83314
Polymers141,2516
Non-polymers5828
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-179 kcal/mol
Surface area57240 Å2
Unit cell
Length a, b, c (Å)52.109, 159.654, 75.606
Angle α, β, γ (deg.)90.00, 90.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Genome polyprotein


Mass: 23541.812 Da / Num. of mol.: 6 / Mutation: E207A, K209A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Production host: Escherichia coli (E. coli) / References: UniProt: B9VUU3*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 10% PEG6000, 5% MPD and 0.5% w/v polyvinylpyrrolidone K15

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 2.5→43.6 Å / Num. obs: 84048 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.38 % / Biso Wilson estimate: 70.008 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.32
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.07 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 1.67 / CC1/2: 0.71 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.493→43.635 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.54 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 4219 5.03 %Random
Rwork0.2287 ---
obs0.2317 83915 98.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.493→43.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8923 0 16 35 8974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129051
X-RAY DIFFRACTIONf_angle_d1.15612200
X-RAY DIFFRACTIONf_dihedral_angle_d12.8585573
X-RAY DIFFRACTIONf_chiral_restr0.0581415
X-RAY DIFFRACTIONf_plane_restr0.0081561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4934-2.52170.39211080.38172065X-RAY DIFFRACTION76
2.5217-2.55140.37451670.35272622X-RAY DIFFRACTION100
2.5514-2.58250.40841310.33532702X-RAY DIFFRACTION100
2.5825-2.61520.37041460.30932738X-RAY DIFFRACTION100
2.6152-2.64960.3931450.31432575X-RAY DIFFRACTION100
2.6496-2.68590.33971570.30342734X-RAY DIFFRACTION100
2.6859-2.72420.36041280.29942682X-RAY DIFFRACTION100
2.7242-2.76490.34551360.2882705X-RAY DIFFRACTION100
2.7649-2.80810.40131460.27642668X-RAY DIFFRACTION100
2.8081-2.85410.38321160.26612723X-RAY DIFFRACTION100
2.8541-2.90330.27411440.25992721X-RAY DIFFRACTION100
2.9033-2.95610.34631250.26282614X-RAY DIFFRACTION100
2.9561-3.0130.34461490.26592713X-RAY DIFFRACTION100
3.013-3.07440.3411350.26832743X-RAY DIFFRACTION100
3.0744-3.14130.3281460.26522635X-RAY DIFFRACTION99
3.1413-3.21430.35821520.25872686X-RAY DIFFRACTION100
3.2143-3.29470.30941420.25262709X-RAY DIFFRACTION100
3.2947-3.38370.3151040.26492665X-RAY DIFFRACTION100
3.3837-3.48330.36441350.27072742X-RAY DIFFRACTION100
3.4833-3.59560.3131590.25462608X-RAY DIFFRACTION99
3.5956-3.72410.33081810.24262653X-RAY DIFFRACTION99
3.7241-3.87310.27661370.21812645X-RAY DIFFRACTION100
3.8731-4.04930.25781360.21272688X-RAY DIFFRACTION99
4.0493-4.26260.22011380.19822680X-RAY DIFFRACTION99
4.2626-4.52940.21411420.17962655X-RAY DIFFRACTION99
4.5294-4.87870.22721350.18332684X-RAY DIFFRACTION99
4.8787-5.36880.25721470.1982660X-RAY DIFFRACTION99
5.3688-6.14390.27721470.22132673X-RAY DIFFRACTION99
6.1439-7.73360.25791340.21652647X-RAY DIFFRACTION99
7.7336-43.64160.26451510.19852661X-RAY DIFFRACTION99

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