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- PDB-6kwr: Crystal structure of enterovirus 71 polymerase elongation complex... -

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Basic information

Entry
Database: PDB / ID: 6kwr
TitleCrystal structure of enterovirus 71 polymerase elongation complex (ddCTP form)
Components
  • RNA (31-MER)
  • RNA (5'-R(*UP*GP*UP*UP*CP*CP*GP*AP*GP*AP*GP*A)-D(P*(DOC))-3')
  • RNA-dependent RNA polymerase
KeywordsTRANSFERASE/RNA / polymerase-RNA complex / elongation / enterovirus / VIRAL PROTEIN / TRANSFERASE-RNA 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 / picornain 2A / 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 ...RNA-protein covalent cross-linking / : / 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 / 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / 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 / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Reverse transcriptase/Diguanylate cyclase 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 ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Reverse transcriptase/Diguanylate cyclase 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 / Alpha-Beta Plaits / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / RNA / RNA (> 10) / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShi, W. / Gong, P.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2018YFA0507200 China
Ministry of Science and Technology (China)2016YFC1200400 China
National Natural Science Foundation of China31670154 China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: A nucleobase-binding pocket in a viral RNA-dependent RNA polymerase contributes to elongation complex stability.
Authors: Shi, W. / Ye, H.Q. / Deng, C.L. / Li, R. / Zhang, B. / Gong, P.
History
DepositionSep 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-dependent RNA polymerase
B: RNA (31-MER)
C: RNA (5'-R(*UP*GP*UP*UP*CP*CP*GP*AP*GP*AP*GP*A)-D(P*(DOC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0656
Polymers67,5243
Non-polymers5413
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-60 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.008, 76.454, 68.075
Angle α, β, γ (deg.)90.000, 94.920, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RNA-dependent RNA polymerase


Mass: 53360.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Gene: CN12_49082gpPOL / Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pCG1
References: UniProt: A0A023RBB6, UniProt: M4QLY4*PLUS, RNA-directed RNA polymerase

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RNA chain , 2 types, 2 molecules BC

#2: RNA chain RNA (31-MER)


Mass: 10038.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(*UP*GP*UP*UP*CP*CP*GP*AP*GP*AP*GP*A)-D(P*(DOC))-3')


Mass: 4125.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 108 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O12P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5 / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→38.23 Å / Num. obs: 22884 / % possible obs: 98.9 % / Redundancy: 2.88 % / Biso Wilson estimate: 56.91 Å2 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.092 / Χ2: 1.14 / Net I/σ(I): 7.6 / Num. measured all: 66443 / Scaling rejects: 499
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Rejects% possible all
2.5-2.592.90.4631.6663522680.5691.466199.6
2.59-2.692.910.4121.8681023230.5071.415099.7
2.69-2.822.880.3152.5657322590.3881.396299.5
2.82-2.962.880.2363.3665522930.2911.285099.3
2.96-3.152.880.1724.6663722820.2121.185999.2
3.15-3.392.880.1186.4665222860.1451.046299.2
3.39-3.732.880.0948.1663122790.1151.016699.1
3.73-4.272.880.07110663822960.0870.913398.7
4.27-5.382.810.04815645522840.0580.822897.7
5.38-38.232.910.03323675723140.0410.862897.6

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Processing

Software
NameVersionClassification
d*TREK9.9.9.4Ddata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.25data extraction
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F8G

5f8g


Resolution: 2.5→38.227 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.69
RfactorNum. reflection% reflection
Rfree0.2571 1187 5.19 %
Rwork0.2162 --
obs0.2185 22865 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.54 Å2 / Biso mean: 64.7208 Å2 / Biso min: 35.2 Å2
Refinement stepCycle: final / Resolution: 2.5→38.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 755 29 105 4489
Biso mean--68.86 58.37 -
Num. residues----488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084564
X-RAY DIFFRACTIONf_angle_d1.0546359
X-RAY DIFFRACTIONf_chiral_restr0.053719
X-RAY DIFFRACTIONf_plane_restr0.007681
X-RAY DIFFRACTIONf_dihedral_angle_d17.792612
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.61380.48331410.3505270099
2.6138-2.75160.39061330.31822715100
2.7516-2.92390.29881360.2898273099
2.9239-3.14960.38211530.2637270299
3.1496-3.46630.32281410.2416271599
3.4663-3.96740.25761640.1971270199
3.9674-4.99680.2071550.1701269798
4.9968-38.2270.19941640.1932271897

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