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- PDB-1xr6: Crystal Structure of RNA-dependent RNA Polymerase 3D from human r... -

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Basic information

Entry
Database: PDB / ID: 1xr6
TitleCrystal Structure of RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 1B
ComponentsGenome polyprotein
KeywordsTRANSFERASE / RNA-DEPENDENT RNA POLYMERASE
Function / homology
Function and homology information


: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / : / 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 genome entry into host cell via pore formation in plasma membrane / picornain 3C ...: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / : / 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 genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell 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 / 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 / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / 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 ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / 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
: / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 1B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLove, R.A. / Maegley, K.A. / Yu, X. / Ferre, R.A. / Lingardo, L.K. / Diehl, W. / Parge, H.E. / Dragovich, P.S. / Fuhrman, S.A.
CitationJournal: Structure / Year: 2004
Title: The Crystal Structure of the RNA-Dependent RNA Polymerase from Human Rhinovirus: A Dual-Function Target for Common Cold Antiviral Therapy
Authors: Love, R.A. / Maegley, K.A. / Yu, X. / Ferre, R.A. / Lingardo, L.K. / Diehl, W. / Parge, H.E. / Dragovich, P.S. / Fuhrman, S.A.
History
DepositionOct 13, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionOct 26, 2004ID: 1TE8
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONFLICTS LISTED IN THE SEQADV RECORDS REPRESENT NORMAL VARIATION WITHIN THE ...SEQUENCE THE CONFLICTS LISTED IN THE SEQADV RECORDS REPRESENT NORMAL VARIATION WITHIN THE RHINOVIRUS SEROTYPE SOURCE OF THIS PROTEIN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4082
Polymers52,3691
Non-polymers391
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.395, 88.395, 186.198
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Genome polyprotein


Mass: 52368.984 Da / Num. of mol.: 1 / Fragment: RNA-DIRECTED RNA POLYMERASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 1B / Genus: Rhinovirus / Species: Human rhinovirus A / Description: T7 promoter / Gene: P3D / Plasmid: PET24A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12916, RNA-directed RNA polymerase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 4.01 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium potassium tartrate, ADA, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 30009 / Num. obs: 30009 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 17
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 7 % / Rmerge(I) obs: 0.055 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.055 / % possible all: 99

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.453 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 1520 5.1 %RANDOM
Rwork0.22859 ---
obs0.23031 28456 99.94 %-
all-28454 --
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: 31.391 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20.89 Å20 Å2
2--1.79 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 1 251 3940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223776
X-RAY DIFFRACTIONr_bond_other_d0.0020.023396
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.9575104
X-RAY DIFFRACTIONr_angle_other_deg0.77937962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4725459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33124.512164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9531513
X-RAY DIFFRACTIONr_chiral_restr0.0670.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024121
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02751
X-RAY DIFFRACTIONr_nbd_refined0.1940.2786
X-RAY DIFFRACTIONr_nbd_other0.2170.23809
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22204
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4811.52294
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92923726
X-RAY DIFFRACTIONr_scbond_it1.09631482
X-RAY DIFFRACTIONr_scangle_it1.954.51378
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.496→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 135
Rwork0.304 2014

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