[English] 日本語
Yorodumi
- PDB-4p1z: Structure of the MID domain from MIWI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p1z
TitleStructure of the MID domain from MIWI
ComponentsPiwi-like protein 1
KeywordsRNA BINDING PROTEIN / MID domain / MIWI / piRNA biogenesis
Function / homology
Function and homology information


primary piRNA processing / mRNA cap binding complex binding / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / regulation of cytoplasmic translation / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing / sperm DNA condensation / chromatoid body / dense body ...primary piRNA processing / mRNA cap binding complex binding / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / regulation of cytoplasmic translation / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing / sperm DNA condensation / chromatoid body / dense body / regulatory ncRNA-mediated gene silencing / P granule / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / spermatid development / RNA endonuclease activity / meiotic cell cycle / spermatogenesis / single-stranded RNA binding / hydrolase activity / mRNA binding / protein kinase binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
GAGE / GAGE protein / GAGE / Piwi, N-terminal domain / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi ...GAGE / GAGE protein / GAGE / Piwi, N-terminal domain / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Response regulator / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsCora, E. / McCarthy, A.A. / Pillai, R.S.
CitationJournal: Rna / Year: 2014
Title: The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs.
Authors: Cora, E. / Pandey, R.R. / Xiol, J. / Taylor, J. / Sachidanandam, R. / McCarthy, A.A. / Pillai, R.S.
History
DepositionFeb 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 23, 2015Group: Data collection
Revision 1.3Sep 30, 2015Group: Data collection
Revision 1.4Dec 27, 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_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Piwi-like protein 1
B: Piwi-like protein 1
C: Piwi-like protein 1
D: Piwi-like protein 1


Theoretical massNumber of molelcules
Total (without water)57,6044
Polymers57,6044
Non-polymers00
Water23413
1
A: Piwi-like protein 1
C: Piwi-like protein 1


Theoretical massNumber of molelcules
Total (without water)28,8022
Polymers28,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-13 kcal/mol
Surface area14420 Å2
MethodPISA
2
B: Piwi-like protein 1
D: Piwi-like protein 1


Theoretical massNumber of molelcules
Total (without water)28,8022
Polymers28,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-10 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.860, 101.290, 146.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 3

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ALAALALYSLYSAA486 - 6122 - 128
2ALAALAASNASNBB486 - 6102 - 126
3ALAALAASNASNCC486 - 6102 - 126
4LYSLYSASNASNDD492 - 6108 - 126

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.965592, -0.067046, -0.25127), (0.105364, 0.984202, 0.142286), (0.23776, -0.163865, 0.957402)13.48526, -5.53824, -33.34134
3given(-0.857315, 0.187907, -0.479273), (-0.285076, -0.94851, 0.138061), (-0.428652, 0.254991, 0.866739)-17.21182, -2.0516, -6.33293
4given(-0.979324, -0.019536, 0.201352), (0.02304, -0.999621, 0.015074), (0.200981, 0.019402, 0.979403)-38.23595, 3.04141, -33.95143

-
Components

#1: Protein
Piwi-like protein 1


Mass: 14400.985 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Piwil1, Miwi / Plasmid: pProExHtb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Rosetta / References: UniProt: Q9JMB7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.73 % / Description: Plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 26-32% PEG 4000, 100mM Tris-HCl, 100-200mM MgCl2 / PH range: 7.8-8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 24331 / % possible obs: 98.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 16
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.3 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
SHARPphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
SHARPphasing
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 34.58 / SU ML: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1245 5.1 %RANDOM
Rwork0.242 23086 --
obs0.2437 24331 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.11 Å2 / Biso mean: 79.951 Å2 / Biso min: 46.32 Å2
Baniso -1Baniso -2Baniso -3
1-4.71 Å20 Å2-0 Å2
2---2.62 Å20 Å2
3----2.09 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3876 0 0 13 3889
Biso mean---62.64 -
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023933
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9835323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18625.135148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61615773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7191522
X-RAY DIFFRACTIONr_chiral_restr0.1030.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212774
X-RAY DIFFRACTIONr_mcbond_it3.2593.7021981
X-RAY DIFFRACTIONr_mcangle_it5.1625.5342468
X-RAY DIFFRACTIONr_scbond_it4.5684.1721952
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A443LOOSE POSITIONAL0.085
2B443LOOSE POSITIONAL0.075
3C443LOOSE POSITIONAL0.085
4D443LOOSE POSITIONAL0.075
1A471TIGHT THERMAL5.340.5
2B471TIGHT THERMAL5.260.5
3C471TIGHT THERMAL7.260.5
4D471TIGHT THERMAL11.350.5
1A443LOOSE THERMAL6.6310
2B443LOOSE THERMAL6.710
3C443LOOSE THERMAL10.3910
4D443LOOSE THERMAL11.2510
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 76 -
Rwork0.455 1604 -
all-1680 -
obs--93.23 %
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)
11.66110.5728-1.00860.2006-0.31426.71090.2422-0.1664-0.03720.0492-0.0473-0.0244-0.1195-0.1329-0.19490.7019-0.07-0.03040.2234-0.03410.1366-13.641-11.7598.624
20.87520.98740.07581.1872-0.38244.4657-0.0770.1363-0.0002-0.04840.22760.0452-0.0899-0.0469-0.15060.8092-0.06190.02950.22430.06770.0892-16.965-11.26146.122
30.4050.7777-0.42232.19861.08396.07760.0747-0.00660.02810.2016-0.09950.06290.03040.03910.02480.9729-0.00280.0420.1819-0.02610.0418-6.64813.7819.765
41.46731.4741.20151.68212.1367.5359-0.23970.3287-0.529-0.43660.3917-0.4692-1.1322-0.321-0.15210.9939-0.04110.07920.4012-0.09430.2129-14.71615.35846.993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A486 - 612
2X-RAY DIFFRACTION2B486 - 610
3X-RAY DIFFRACTION3C485 - 610
4X-RAY DIFFRACTION4D492 - 610

+
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