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- PDB-2pn4: Crystal Structure of Hepatitis C Virus IRES Subdomain IIa -

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Basic information

Entry
Database: PDB / ID: 2pn4
TitleCrystal Structure of Hepatitis C Virus IRES Subdomain IIa
Components
  • 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*AP*CP*GP*CP*C)-3'
  • 5'-R(*GP*CP*GP*(5BU)P*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*(5BU)P*CP*CP*GP*G)-3'
KeywordsRNA / HCV / IRES / subdoamin IIa / Strontium / Hepatitis
Function / homologySTRONTIUM ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsZhao, Q. / Han, Q. / Kissinger, C.R. / Thompson, P.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of hepatitis C virus IRES subdomain IIa.
Authors: Zhao, Q. / Han, Q. / Kissinger, C.R. / Hermann, T. / Thompson, P.A.
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _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: 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*AP*CP*GP*CP*C)-3'
B: 5'-R(*GP*CP*GP*(5BU)P*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*(5BU)P*CP*CP*GP*G)-3'
C: 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*AP*CP*GP*CP*C)-3'
D: 5'-R(*GP*CP*GP*(5BU)P*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*(5BU)P*CP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,29514
Polymers28,4184
Non-polymers87610
Water1,20767
1
A: 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*AP*CP*GP*CP*C)-3'
B: 5'-R(*GP*CP*GP*(5BU)P*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*(5BU)P*CP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6477
Polymers14,2092
Non-polymers4385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-144.5 kcal/mol
Surface area7570 Å2
MethodPISA
2
C: 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*AP*CP*GP*CP*C)-3'
D: 5'-R(*GP*CP*GP*(5BU)P*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*(5BU)P*CP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6477
Polymers14,2092
Non-polymers4385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-144.5 kcal/mol
Surface area7570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.286, 48.730, 119.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is generated by applying the operation X, Y, Z to chains A, B or by applying the operation X, Y, Z to chains C, D.

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Components

#1: RNA chain 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*AP*CP*GP*CP*C)-3'


Mass: 7644.589 Da / Num. of mol.: 2 / Fragment: HCV IRES Subdomain IIa (residue 47-70) / Mutation: G47C,U48G,A70C / Source method: obtained synthetically
Details: This sequence of RNA naturally exists in hepatitis C virus
#2: RNA chain 5'-R(*GP*CP*GP*(5BU)P*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*(5BU)P*CP*CP*GP*G)-3'


Mass: 6564.623 Da / Num. of mol.: 2 / Fragment: HCV IRES Subdomain IIa (residue 98-117) / Mutation: A99C,A116G / Source method: obtained synthetically
Details: This sequence of RNA naturally exists in hepatitis C virus
#3: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 6.2
Details: 30% MPD, 80mM SrCl2, 25mM NaCl, 50mM Cacodylate equilibrated with 60%MPD, pH 6.2, EVAPORATION, temperature 290.0K
Components of the solutions
IDNameCrystal-IDSol-ID
130% MPD11
2SrCl211
3NaClSodium chloride11
4CacodylateCacodylic acid11
560%MPD12

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2006 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.32→59.98 Å / Num. all: 12751 / Num. obs: 12228 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 59.9 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 17.5
Reflection shellResolution: 2.32→2.43 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1247 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PN3

2pn3


Resolution: 2.32→59.98 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.872 / SU B: 16.579 / SU ML: 0.22 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.445 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: spare matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.32037 598 4.9 %RANDOM
Rwork0.26141 ---
all0.26515 12210 --
obs0.26405 11590 94.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.272 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å20 Å20 Å2
2---0.38 Å20 Å2
3---2.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.335 Å
Refinement stepCycle: LAST / Resolution: 2.32→59.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1860 10 67 1937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212072
X-RAY DIFFRACTIONr_angle_refined_deg1.83533224
X-RAY DIFFRACTIONr_chiral_restr0.0780.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02904
X-RAY DIFFRACTIONr_nbd_refined0.1650.2732
X-RAY DIFFRACTIONr_nbtor_refined0.2790.21250
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.294
X-RAY DIFFRACTIONr_metal_ion_refined0.2220.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3170.210
X-RAY DIFFRACTIONr_scbond_it1.40932562
X-RAY DIFFRACTIONr_scangle_it1.944.53224
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 36 -
Rwork0.301 752 -
obs-1247 86.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.85450.14860.4450.44170.28932.89510.0175-0.22780.2657-0.141-0.1201-0.242-0.20870.18550.1026-0.0837-0.04470.011-0.0901-0.0115-0.0066-9.5438-7.19414.8938
20.2019-0.10020.09572.8179-0.03312.0653-0.173-0.1624-0.1329-0.28270.05460.26170.2838-0.19080.1184-0.0229-0.0504-0.0022-0.10240.0186-0.017-29.1709-27.023915.1391
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA47 - 701 - 24
2X-RAY DIFFRACTION1BB98 - 1171 - 20
3X-RAY DIFFRACTION2CC47 - 701 - 24
4X-RAY DIFFRACTION2DD98 - 1171 - 20

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