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- PDB-4qpx: NV polymerase post-incorporation-like complex -

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Basic information

Entry
Database: PDB / ID: 4qpx
TitleNV polymerase post-incorporation-like complex
Components
  • PolyproteinProteolysis
  • RNA (5'-R(*U*AP*CP*CP*CP*GP*GP*G)-3')
  • RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')
KeywordsHydrolase/RNA / RNA-depedent RNA polymerase / Hydrolase-RNA complex
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Helix non-globular / Special ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Helix non-globular / Special / 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. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RNA / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsZamyatkin, D.F. / Parra, F. / Grochulski, P. / Ng, K.K.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of a backtracked state reveals conformational changes similar to the state following nucleotide incorporation in human norovirus polymerase.
Authors: Zamyatkin, D. / Rao, C. / Hoffarth, E. / Jurca, G. / Rho, H. / Parra, F. / Grochulski, P. / Ng, K.K.
History
DepositionJun 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyprotein
P: RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')
T: RNA (5'-R(*U*AP*CP*CP*CP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2928
Polymers61,9433
Non-polymers3495
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-53 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.220, 81.220, 188.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polyprotein / Proteolysis / polyprotein


Mass: 56843.574 Da / Num. of mol.: 1 / Fragment: unp residues 331-838
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q70ET3, RNA-directed RNA polymerase

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RNA chain , 2 types, 2 molecules PT

#2: RNA chain RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')


Mass: 2557.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA oligonucleotide
#3: RNA chain RNA (5'-R(*U*AP*CP*CP*CP*GP*GP*G)-3')


Mass: 2541.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA oligonucleotide

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Non-polymers , 3 types, 330 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 19 % PEG 8000, 25% glycerol, 100 mM Tris-HCl, pH 7.0, 50 mM KCl, 10 mM MnCl2 and 0.1% 2-mecaptoethanol , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 22, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.86→40 Å / Num. obs: 73009 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 15.6
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 1.82 / Rsym value: 0.849 / % possible all: 72

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3BSO

3bso


Resolution: 1.86→19.7 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.714 / SU ML: 0.114 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25278 2684 5 %RANDOM
Rwork0.20492 ---
obs0.20725 50992 100 %-
all-50992 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--0.96 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 1.86→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 317 15 325 4541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224357
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1192.0685964
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.365493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2823.795166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19315687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3261525
X-RAY DIFFRACTIONr_chiral_restr0.0740.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213166
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.70422478
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6632.54012
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8853.51879
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0444.51952
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 192 -
Rwork0.325 3660 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -14.9678 Å / Origin y: 30.2401 Å / Origin z: -2.373 Å
111213212223313233
T0.0652 Å2-0.0011 Å2-0.0372 Å2-0.0749 Å20.0434 Å2--0.1084 Å2
L0.1526 °2-0.0705 °20.063 °2-1.2357 °2-0.3225 °2--0.868 °2
S0.0813 Å °-0.0254 Å °-0.0155 Å °-0.1818 Å °0.0048 Å °0.1368 Å °0.0598 Å °-0.0317 Å °-0.0861 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T101 - 126
2X-RAY DIFFRACTION1P201 - 221
3X-RAY DIFFRACTION1A701 - 978
4X-RAY DIFFRACTION1P101
5X-RAY DIFFRACTION1A601 - 604
6X-RAY DIFFRACTION1T2 - 8
7X-RAY DIFFRACTION1P1 - 8
8X-RAY DIFFRACTION1A4 - 505

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