[English] 日本語
Yorodumi
- PDB-5guh: Crystal structure of silkworm PIWI-clade Argonaute Siwi bound to piRNA -

+
Open data


ID or keywords:

Loading...

-
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


female sex determination / PET complex / secondary piRNA processing / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / piRNA processing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA endonuclease activity / meiotic cell cycle / spermatogenesis ...female sex determination / PET complex / secondary piRNA processing / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / piRNA processing / 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, N-terminal domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain ...Piwi, N-terminal domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more