[English] 日本語
Yorodumi
- PDB-4q5w: Crystal structure of extended-Tudor 9 of Drosophila melanogaster -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q5w
TitleCrystal structure of extended-Tudor 9 of Drosophila melanogaster
ComponentsMaternal protein tudor
KeywordsTRANSCRIPTION / tudor domain / recognize sDMA of Aubergine / sDMA of Aubergine / nucleus
Function / homology
Function and homology information


pole cell development / positive regulation of post-transcriptional gene silencing by RNA / P granule assembly / methylation-dependent protein binding / pole plasm / secondary piRNA processing / pole plasm assembly / P granule organization / pole cell formation / piRNA processing ...pole cell development / positive regulation of post-transcriptional gene silencing by RNA / P granule assembly / methylation-dependent protein binding / pole plasm / secondary piRNA processing / pole plasm assembly / P granule organization / pole cell formation / piRNA processing / intracellular mRNA localization / P granule / oogenesis / germ cell development / spermatogenesis / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / SH3 type barrels. - #140 / SNase-like, OB-fold superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Maternal protein tudor
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsRen, R. / Liu, H. / Wang, W. / Wang, M. / Yang, N. / Dong, Y. / Gong, W. / Lehmann, R. / Xu, R.M.
CitationJournal: Cell Res. / Year: 2014
Title: Structure and domain organization of Drosophila Tudor
Authors: Ren, R. / Liu, H. / Wang, W. / Wang, M. / Yang, N. / Dong, Y.H. / Gong, W. / Lehmann, R. / Xu, R.M.
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maternal protein tudor
B: Maternal protein tudor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8193
Polymers41,5802
Non-polymers2381
Water9,350519
1
A: Maternal protein tudor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0282
Polymers20,7901
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maternal protein tudor


Theoretical massNumber of molelcules
Total (without water)20,7901
Polymers20,7901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.230, 105.678, 52.603
Angle α, β, γ (deg.)90.00, 100.57, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Maternal protein tudor


Mass: 20790.104 Da / Num. of mol.: 2 / Fragment: extended-Tudor 9, UNP residues 1978-2160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG9450, tud, tudor / Plasmid: pET28-smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: P25823
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.04M ammonium sulphate, 0.1M HEPES, pH 7.5, 22.5% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 19, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 36917 / Num. obs: 36887 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.092
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3693 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.801→36.957 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 1860 5.05 %RANDOM
Rwork0.18 ---
obs0.1824 36854 99.63 %-
all-36917 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→36.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 15 519 3429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063028
X-RAY DIFFRACTIONf_angle_d0.9764118
X-RAY DIFFRACTIONf_dihedral_angle_d12.9461189
X-RAY DIFFRACTIONf_chiral_restr0.068502
X-RAY DIFFRACTIONf_plane_restr0.004517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8006-1.84920.27681530.2215258296
1.8492-1.90360.271240.21312712100
1.9036-1.96510.25181430.20852723100
1.9651-2.03530.25771350.19712690100
2.0353-2.11680.23251390.18872691100
2.1168-2.21310.24961440.18312663100
2.2131-2.32980.2341460.19072731100
2.3298-2.47570.24741450.18942672100
2.4757-2.66680.26191480.19872701100
2.6668-2.93510.26421280.1992724100
2.9351-3.35960.2171480.18412678100
3.3596-4.23170.19581530.15592693100
4.2317-36.9650.18831540.15222734100
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)
11.139-1.22230.08542.1189-0.21870.37890.0062-0.0466-0.0568-0.04870.01530.05120.0267-0.005-0.01970.0802-0.02260.00370.13290.00440.1002-0.05080.22531.5035
20.57240.3241-0.18181.7025-1.11431.57690.0233-0.02070.06910.03710.02910.0739-0.08650.0022-0.03820.12180.0051-0.01040.1284-0.01550.114112.6878-42.377524.6003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

+
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://pdbjlvh1.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