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- PDB-1ytu: Structural basis for 5'-end-specific recognition of the guide RNA... -

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Basic information

Entry
Database: PDB / ID: 1ytu
TitleStructural basis for 5'-end-specific recognition of the guide RNA strand by the A. fulgidus PIWI protein
Components
  • 5'-R(P*AP*GP*AP*CP*AP*G)-3'
  • 5'-R(P*UP*GP*UP*C)-3'
  • hypothetical protein AF1318Hypothesis
KeywordsRNA binding Protein/RNA / Protein-RNA complex / RNA duplex / RNA binding Protein-RNA COMPLEX
Function / homology
Function and homology information


DNA binding / RNA binding / metal ion binding
Similarity search - Function
Piwi domain / Piwi domain profile. / Piwi domain / Piwi / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold ...Piwi domain / Piwi domain profile. / Piwi domain / Piwi / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMa, J.B. / Yuan, Y.R. / Meister, G. / Pei, Y. / Tuschl, T. / Patel, D.J.
CitationJournal: Nature / Year: 2005
Title: Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein.
Authors: Ma, J.B. / Yuan, Y.R. / Meister, G. / Pei, Y. / Tuschl, T. / Patel, D.J.
History
DepositionFeb 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-R(P*AP*GP*AP*CP*AP*G)-3'
D: 5'-R(P*UP*GP*UP*C)-3'
E: 5'-R(P*AP*GP*AP*CP*AP*G)-3'
F: 5'-R(P*UP*GP*UP*C)-3'
A: hypothetical protein AF1318
B: hypothetical protein AF1318
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9978
Polymers105,9496
Non-polymers492
Water1,02757
1
C: 5'-R(P*AP*GP*AP*CP*AP*G)-3'
D: 5'-R(P*UP*GP*UP*C)-3'
A: hypothetical protein AF1318
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9994
Polymers52,9743
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-R(P*AP*GP*AP*CP*AP*G)-3'
F: 5'-R(P*UP*GP*UP*C)-3'
B: hypothetical protein AF1318
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9994
Polymers52,9743
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)238.747, 238.747, 52.042
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsMonomer. There are two copies at one asymmetric unit related by NCS 2-fold axis

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Components

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


Mass: 1938.253 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: RNA chain 5'-R(P*UP*GP*UP*C)-3'


Mass: 1217.762 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein hypothetical protein AF1318 / Hypothesis / PIWI


Mass: 49818.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O28951
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.88 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4K, potassium chloride, magnisium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 4K11
2potassium chloride11
3magnisium chloride11
4cacodylateCacodylic acid11
5H2O11
6potassium chloride12
7magnisium chloride12
8PEG 4K12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9776 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 38254 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.279 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1w9H

1w9h


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.907 / SU B: 20.95 / SU ML: 0.22 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.533 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26623 1904 5 %RANDOM
Rwork0.20392 ---
obs0.20689 36055 99.19 %-
all-36055 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.463 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å2-0.44 Å20 Å2
2---0.87 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6814 409 2 57 7282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227439
X-RAY DIFFRACTIONr_angle_refined_deg1.7922.03310179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2215833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.74924.62316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.923151247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2491528
X-RAY DIFFRACTIONr_chiral_restr0.1180.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025425
X-RAY DIFFRACTIONr_nbd_refined0.2420.23341
X-RAY DIFFRACTIONr_nbtor_refined0.320.24960
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2276
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.28
X-RAY DIFFRACTIONr_mcbond_it1.2081.54282
X-RAY DIFFRACTIONr_mcangle_it1.83426832
X-RAY DIFFRACTIONr_scbond_it2.21633771
X-RAY DIFFRACTIONr_scangle_it3.3094.53347
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 163 -
Rwork0.242 2652 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: 120.0854 Å / Origin y: -0.4952 Å / Origin z: 33.6794 Å
111213212223313233
T-0.1831 Å2-0.0308 Å20.0131 Å2--0.093 Å20.0227 Å2---0.1906 Å2
L1.0159 °2-1.3671 °20.1567 °2-1.8404 °2-0.1965 °2--0.328 °2
S0.0831 Å °0.0469 Å °-0.0948 Å °-0.1154 Å °-0.0391 Å °0.0305 Å °0.1584 Å °-0.0152 Å °-0.0439 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AE2 - 4272 - 427
2X-RAY DIFFRACTION1BF2 - 4272 - 427
3X-RAY DIFFRACTION1CA1 - 51 - 5
4X-RAY DIFFRACTION1DB15 - 181 - 4
5X-RAY DIFFRACTION1EC1 - 61 - 6
6X-RAY DIFFRACTION1FD15 - 181 - 4

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