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- PDB-3t4b: Crystal Structure of the HCV IRES pseudoknot domain -

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Basic information

Entry
Database: PDB / ID: 3t4b
TitleCrystal Structure of the HCV IRES pseudoknot domain
ComponentsHCV IRES pseudoknot domain plus crystallization module
KeywordsRNA / Pseudoknot / four-way junction / HCV IRES central domain
Function / homologyNICKEL (II) ION / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
Hepatitis C virus ED43
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.55 Å
AuthorsBerry, K.E. / Waghray, S. / Mortimer, S.A. / Bai, Y. / Doudna, J.A.
CitationJournal: Structure / Year: 2011
Title: Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning.
Authors: Berry, K.E. / Waghray, S. / Mortimer, S.A. / Bai, Y. / Doudna, J.A.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Nov 23, 2011Group: Other
Revision 1.3Jun 28, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / pdbx_entity_src_syn ...entity / pdbx_entity_src_syn / struct / struct_conn / struct_ref / struct_ref_seq
Item: _entity.pdbx_fragment / _struct.pdbx_descriptor ..._entity.pdbx_fragment / _struct.pdbx_descriptor / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.4Feb 28, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: HCV IRES pseudoknot domain plus crystallization module
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,26718
Polymers27,2691
Non-polymers99817
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.390, 113.390, 88.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsAS PER THE AUTHORS THERE IS ABSOLUTELY NO EVIDENCE TO SUGGEST THAT THE HCV IRES FUNCTIONS AS A DIMER

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Components

#1: RNA chain HCV IRES pseudoknot domain plus crystallization module


Mass: 27269.125 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This portion of RNA sequence was inserted to facilitate crystallization
Source: (synth.) synthetic construct (others), (synth.) Hepatitis C virus ED43
References: GenBank: 2252489
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Ni

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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: 5.2 Å3/Da / Density % sol: 76.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: RNA was mixed in a 1:1 ratio with well solution (0.5-0.6 M Li2SO4, 30-37 mM MgCl2, 1-2 mM spermine, 50 mM MES, pH 6.5) with an additional 10 mM NiCl2 added to the drop before equilibration, ...Details: RNA was mixed in a 1:1 ratio with well solution (0.5-0.6 M Li2SO4, 30-37 mM MgCl2, 1-2 mM spermine, 50 mM MES, pH 6.5) with an additional 10 mM NiCl2 added to the drop before equilibration, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159, 1.4855, 1.4370
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2011
RadiationMonochromator: KHOZU Double flat crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11591
21.48551
31.4371
ReflectionResolution: 3.55→100 Å / Num. all: 7384 / Num. obs: 7348 / % possible obs: 99.5 % / Observed criterion σ(I): -3
Reflection shellResolution: 3.55→3.64 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 3.02 / Num. unique all: 515 / Rsym value: 0.757 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.55→40.089 Å / SU ML: 0.33 / σ(F): 1.99 / Phase error: 28.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 366 5 %RANDOM
Rwork0.2211 ---
obs0.2227 7317 99.65 %-
all-7319 --
Solvent computationShrinkage radii: 1.13 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.231 Å2 / ksol: 0.258 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.0892 Å2-0 Å20 Å2
2---11.0892 Å2-0 Å2
3---22.1785 Å2
Refinement stepCycle: LAST / Resolution: 3.55→40.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1796 17 0 1813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082026
X-RAY DIFFRACTIONf_angle_d0.7693166
X-RAY DIFFRACTIONf_dihedral_angle_d19.4231003
X-RAY DIFFRACTIONf_chiral_restr0.054419
X-RAY DIFFRACTIONf_plane_restr0.00599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3.55-4.06390.34591190.349622572258
4.0639-5.11840.28661180.268722812281
5.1184-40.0920.22391290.178524132414
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)
11.4364-0.50770.73340.40640.7151.8301-0.1158-1.47080.6490.58620.86630.1850.34350.8936-0.00452.17740.560.25732.5250.28241.9369-28.6437-71.5451101.3591
21.3968-0.7281-0.66811.19840.47550.29030.22960.1042-0.8442-0.09430.35730.85290.2115-0.83550.00061.21640.15440.18221.73380.26481.3549-22.7683-62.395381.5445
30.9405-1.01850.88971.4335-1.57921.53980.68450.669-0.1755-0.31550.6591.05981.2569-0.93080.00371.3806-0.2168-0.0231.39210.07531.1346-12.5683-59.464659.5791
40.49990.1540.7510.31930.36221.2031-0.2907-0.5236-1.084-0.37220.76960.44460.17-0.3686-0.0021.17370.1760.04961.630.50282.3606-41.5074-63.359978.5335
51.59191.77391.40736.74434.86323.50480.95941.05180.57680.72240.6657-0.03810.3441-0.82850.73860.3960.40350.43811.74570.96662.1074-42.6219-62.457995.3513
60.9604-0.53771.49081.0452-0.78892.22410.14841.05320.13970.0877-0.3697-0.11041.01060.47740.05421.52430.20020.49171.50870.28972.7194-49.7469-53.653106.0719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 125:133 OR RESID 315:324 ) )A125 - 133
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 125:133 OR RESID 315:324 ) )A315 - 324
3X-RAY DIFFRACTION2( CHAIN A AND ( RESID 134:139 OR RESID 285:290 ) )A134 - 139
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 134:139 OR RESID 285:290 ) )A285 - 290
5X-RAY DIFFRACTION3( CHAIN A AND RESID 1:21 )A1 - 21
6X-RAY DIFFRACTION4( CHAIN A AND RESID 291:302 )A291 - 302
7X-RAY DIFFRACTION5( CHAIN A AND ( RESID 303:305 OR RESID 312:314 ) )A303 - 305
8X-RAY DIFFRACTION5( CHAIN A AND ( RESID 303:305 OR RESID 312:314 ) )A312 - 314
9X-RAY DIFFRACTION6( CHAIN A AND ( RESID 306:311 OR RESID 325:331 OR RESID 332:332 ) )A306 - 311
10X-RAY DIFFRACTION6( CHAIN A AND ( RESID 306:311 OR RESID 325:331 OR RESID 332:332 ) )A325 - 331
11X-RAY DIFFRACTION6( CHAIN A AND ( RESID 306:311 OR RESID 325:331 OR RESID 332:332 ) )A332

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