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

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Basic information

Entry
Database: PDB / ID: 5grb
TitleCrystal structure of 2C helicase from enterovirus 71 (EV71) bound with ATPgammaS
ComponentsEV71 2C ATPase
KeywordsHYDROLASE/INHIBITOR / Enterovirus 2C ATPase / virus replication / Zinc finger / AAA+ ATPase / HYDROLASE-INHIBITOR complex
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 MDA-5 activity / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid ...RNA-protein covalent cross-linking / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / DNA replication / 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 / structural molecule activity / virion attachment to host cell / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 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 9, 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 / struct_keywords
Item: _struct.title / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.3Nov 8, 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
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: EV71 2C ATPase
B: EV71 2C ATPase
C: EV71 2C ATPase
D: EV71 2C ATPase
E: EV71 2C ATPase
F: EV71 2C ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,78318
Polymers141,2516
Non-polymers3,53212
Water21612
1
A: EV71 2C ATPase
C: EV71 2C ATPase
E: EV71 2C ATPase
F: EV71 2C ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,52212
Polymers94,1674
Non-polymers2,3558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EV71 2C ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1303
Polymers23,5421
Non-polymers5892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: EV71 2C ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1303
Polymers23,5421
Non-polymers5892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.668, 54.912, 163.097
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
EV71 2C ATPase


Mass: 23541.812 Da / Num. of mol.: 6 / Mutation: E207A, K209A
Source method: isolated from a genetically manipulated source
Details: EV71 2C variant lacks N-terminal 1-115aa and contains mutation E207A, K209A.
Source: (gene. exp.) Enterovirus / Production host: Escherichia coli (E. coli) / References: UniProt: B9VUU3*PLUS
#2: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS ACM62759.1 FOR THIS SEQUENCE. THERE ARE ...AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS ACM62759.1 FOR THIS SEQUENCE. THERE ARE ENGINEERED MUTATIONS IN THE PROTEIN SEQUENCE INCLUDING E207A ANS K209A.

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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: 2.29 Å3/Da / Density % sol: 46.29 %
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: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.8→45.548 Å / Num. obs: 59800 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 2.26 % / Biso Wilson estimate: 76.169 Å2 / CC1/2: 0.998 / Rsym value: 0.053 / Net I/σ(I): 10.88
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 1.85 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.06 / CC1/2: 0.583 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GQ1

5gq1


Resolution: 2.803→45.548 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.14 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2958 3039 5.09 %Random
Rwork0.245 ---
obs0.2475 59720 95.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.803→45.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9551 0 192 12 9755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099898
X-RAY DIFFRACTIONf_angle_d1.39513414
X-RAY DIFFRACTIONf_dihedral_angle_d10.3688210
X-RAY DIFFRACTIONf_chiral_restr0.071549
X-RAY DIFFRACTIONf_plane_restr0.011704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8029-2.84660.4041890.42791663X-RAY DIFFRACTION63
2.8466-2.89330.41681470.3662722X-RAY DIFFRACTION98
2.8933-2.94320.39371240.35432670X-RAY DIFFRACTION98
2.9432-2.99670.33691870.33522521X-RAY DIFFRACTION98
2.9967-3.05430.38941890.33772645X-RAY DIFFRACTION95
3.0543-3.11670.38951430.32932614X-RAY DIFFRACTION99
3.1167-3.18440.3591660.30782698X-RAY DIFFRACTION99
3.1844-3.25850.42041460.30482596X-RAY DIFFRACTION98
3.2585-3.33990.39921310.31182677X-RAY DIFFRACTION98
3.3399-3.43020.3251260.32692674X-RAY DIFFRACTION98
3.4302-3.53110.39741290.31182557X-RAY DIFFRACTION94
3.5311-3.6450.54241090.29042648X-RAY DIFFRACTION97
3.645-3.77520.281300.27332462X-RAY DIFFRACTION92
3.7752-3.92630.34081500.26772624X-RAY DIFFRACTION95
3.9263-4.10490.36111270.24692587X-RAY DIFFRACTION96
4.1049-4.32120.23481860.23362517X-RAY DIFFRACTION95
4.3212-4.59170.28951420.19892614X-RAY DIFFRACTION95
4.5917-4.94580.2639960.20082561X-RAY DIFFRACTION95
4.9458-5.44280.28821130.21962660X-RAY DIFFRACTION97
5.4428-6.22870.28681180.22992697X-RAY DIFFRACTION98
6.2287-7.8410.21881300.20142656X-RAY DIFFRACTION97
7.841-45.55420.19621610.17852618X-RAY DIFFRACTION98

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