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- PDB-6u7y: RNA hairpin structure containing one TNA nucleotide as template -

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Basic information

Entry
Database: PDB / ID: 6u7y
TitleRNA hairpin structure containing one TNA nucleotide as template
Components
  • RNA (5'-R(*CP*UP*AP*UP*GP*CP*CP*UP*GP*CP*UP*G)-3')
  • RNA (5'-R(*CP*UP*GP*CP*UP*GP*GP*CP*UP*AP*AP*GP*GP*(TG)P*CP*CP*GP*AP*AP*AP*GP*G)-3')
KeywordsRNA
Function / homologyCYTIDINE-5'-MONOPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSzostak, J.W. / Zhang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization.
Authors: Zhang, W. / Kim, S.C. / Tam, C.P. / Lelyveld, V.S. / Bala, S. / Chaput, J.C. / Szostak, J.W.
History
DepositionSep 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Jul 3, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity_poly / entity_poly_seq / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*UP*GP*CP*UP*GP*GP*CP*UP*AP*AP*GP*GP*(TG)P*CP*CP*GP*AP*AP*AP*GP*G)-3')
B: RNA (5'-R(*CP*UP*AP*UP*GP*CP*CP*UP*GP*CP*UP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2103
Polymers10,8872
Non-polymers3231
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-5 kcal/mol
Surface area6130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.766, 68.766, 69.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 7121.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(*CP*UP*AP*UP*GP*CP*CP*UP*GP*CP*UP*G)-3')


Mass: 3765.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 2599 / % possible obs: 98.5 % / Redundancy: 6 % / CC1/2: 1 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.079 / Rrim(I) all: 0.141 / Χ2: 1.149 / Net I/σ(I): 10.3
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 263 / CC1/2: 0.956 / Rpim(I) all: 0.243 / Rrim(I) all: 0.413 / Χ2: 1.15 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VCI

5vci


Resolution: 2.95→45.35 Å / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.422
RfactorNum. reflection% reflectionSelection details
Rfree0.256 136 5.2 %random
Rwork0.182 ---
obs0.186 2463 99.27 %-
Displacement parametersBiso mean: 62.634 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.95→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 720 21 1 742
LS refinement shellResolution: 2.95→3.02 Å
RfactorNum. reflection% reflection
Rfree0.38 15 -
Rwork0.405 171 -
obs--93 %

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