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- PDB-5guh: Crystal structure of silkworm PIWI-clade Argonaute Siwi bound to piRNA -

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Basic information

Entry
Database: PDB / ID: 5guh
TitleCrystal structure of silkworm PIWI-clade Argonaute Siwi bound to piRNA
Components
  • PIWI
  • RNA (28-MER)
KeywordsHYDROLASE/RNA / Nuclease / RNaseH / HYDROLASE-RNA complex
Function / homology
Function and homology information


PET complex / piRNA binding / piRNA processing / multicellular organism development / regulatory ncRNA-mediated gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA endonuclease activity / meiotic cell cycle / spermatogenesis / cell differentiation ...PET complex / piRNA binding / piRNA processing / multicellular organism development / regulatory ncRNA-mediated gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA endonuclease activity / meiotic cell cycle / spermatogenesis / cell differentiation / magnesium ion binding / cytoplasm
Similarity search - Function
Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain / PAZ domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Piwi-like protein Siwi
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMatsumoto, N. / Nishimasu, H. / Ishitani, R. / Nureki, O.
CitationJournal: Cell / Year: 2016
Title: Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA
Authors: Matsumoto, N. / Nishimasu, H. / Sakakibara, K. / Nishida, K.M. / Hirano, T. / Ishitani, R. / Siomi, H. / Siomi, M.C. / Nureki, O.
History
DepositionAug 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PIWI
B: RNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5584
Polymers110,5102
Non-polymers492
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-39 kcal/mol
Surface area33490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.899, 114.619, 136.718
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PIWI / / Piwi / Siwi / Uncharacterized protein


Mass: 101484.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The N-terminal region (residues 1-129) was truncated by thermolysin treatment.
Source: (natural) Bombyx mori (domestic silkworm) / References: UniProt: A8D8P8
#2: RNA chain RNA (28-MER)


Mass: 9025.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The bound RNAs are co-purified endogenous piRNAs, which have divergent sequences and lengths.
Source: (natural) Bombyx mori (domestic silkworm)
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50mM potassium phosphate monobasic, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→114.62 Å / Num. obs: 38755 / % possible obs: 99.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 8
Reflection shellResolution: 2.4→2.49 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.2data extraction
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OLB

4olb


Resolution: 2.4→87.835 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.68 / Phase error: 26.01
RfactorNum. reflection% reflection
Rfree0.2355 2000 5.17 %
Rwork0.2092 --
obs0.2106 38660 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 187.16 Å2 / Biso mean: 67.4326 Å2 / Biso min: 18.83 Å2
Refinement stepCycle: final / Resolution: 2.4→87.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5828 164 2 84 6078
Biso mean--45.49 47.39 -
Num. residues----767
LS refinement shellResolution: 2.4→2.46 Å / Rfactor Rfree: 0.3474 / Rfactor Rwork: 0.2988
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)
10.61860.3986-1.43751.1714-1.48133.3523-0.0812-0.1752-0.19420.23-0.0521-0.0436-0.25030.1790.12580.41470.0398-0.01580.45650.10420.562551.5816-1.7219102.9133
21.3458-0.5384-0.26371.52960.01880.687-0.0423-0.25120.14510.2508-0.0024-0.1365-0.0164-0.0040.02040.2833-0.0435-0.03610.359-0.00340.273140.052228.266987.0827
30.1033-0.41420.33112.6334-3.20315.93830.25930.0616-0.0941-1.2413-0.8874-0.51341.18660.41140.52910.5280.0189-0.12590.70180.03760.875549.898319.8274103.002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 130 through 449 )A130 - 449
2X-RAY DIFFRACTION2chain 'A' and (resid 450 through 899 )A450 - 899
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 28 )B1 - 28

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