[English] 日本語
Yorodumi
- PDB-2l5d: Solution Structures of human PIWI-like 1 PAZ domain with ssRNA (5... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l5d
TitleSolution Structures of human PIWI-like 1 PAZ domain with ssRNA (5'-pUGACA)
Components
  • 5'-R(*UP*GP*AP*CP*A)-3'
  • Piwi-like protein 1
KeywordsRNA binding protein/RNA / PIWI / PAZ / piRNA / ssRNA / RNA binding protein-RNA complex
Function / homology
Function and homology information


primary piRNA processing / mRNA cap binding complex binding / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / : / sperm DNA condensation / chromatoid body / dense body / P granule / regulatory ncRNA-mediated gene silencing ...primary piRNA processing / mRNA cap binding complex binding / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / : / sperm DNA condensation / chromatoid body / dense body / P granule / regulatory ncRNA-mediated gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / PIWI-interacting RNA (piRNA) biogenesis / spermatid development / RNA endonuclease activity / meiotic cell cycle / regulation of translation / spermatogenesis / single-stranded RNA binding / mRNA binding / protein kinase binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
GAGE / GAGE protein / GAGE / paz domain / paz domain / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain ...GAGE / GAGE protein / GAGE / paz domain / paz domain / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain / PAZ domain profile. / Beta Complex / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Mainly Beta
Similarity search - Domain/homology
RNA / Piwi-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsZeng, L. / Zhang, Q. / Yan, K. / Zhou, M.
CitationJournal: Proteins / Year: 2011
Title: Structural insights into piRNA recognition by the human PIWI-like 1 PAZ domain.
Authors: Zeng, L. / Zhang, Q. / Yan, K. / Zhou, M.M.
History
DepositionOct 29, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Piwi-like protein 1
B: 5'-R(*UP*GP*AP*CP*A)-3'


Theoretical massNumber of molelcules
Total (without water)17,2442
Polymers17,2442
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Piwi-like protein 1


Mass: 15673.758 Da / Num. of mol.: 1 / Fragment: PAZ domain, UNP residues 266-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIWIL1, HIWI / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96J94
#2: RNA chain 5'-R(*UP*GP*AP*CP*A)-3'


Mass: 1570.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HN(CA)CB
1223D HN(COCA)CB
1323D 1H-15N NOESY
1413D 1H-13C NOESY
1513D 13C-Edited-13C/15N-filtered NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
1100 mM sodium phosphate-1, 150 mM sodium chloride-2, 5 mM [U-100% 2H] DTT-3, 100% D2O100% D2O
2100 mM sodium phosphate-4, 150 mM sodium chloride-5, 5 mM [U-100% 2H] DTT-6, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMsodium phosphate-11
150 mMsodium chloride-21
5 mMDTT-3[U-100% 2H]1
100 mMsodium phosphate-42
150 mMsodium chloride-52
5 mMDTT-6[U-100% 2H]2
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker AvanceBrukerAvance6002
Bruker DRXBrukerDRX5003
Bruker AvanceBrukerAvance5004

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
NMRView5.04Johnson, One Moon Scientificpeak picking
NMRView5.04Johnson, One Moon Scientificchemical shift assignment
NMRView5.04Johnson, One Moon Scientificdata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: DGSA-distance geometry simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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