[English] 日本語
Yorodumi
- PDB-4ybg: Crystal structure of the MAEL domain of Drosophila melanogaster M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ybg
TitleCrystal structure of the MAEL domain of Drosophila melanogaster Maelstrom
ComponentsProtein maelstrom
KeywordsHYDROLASE / Transposons / Endoribonucleases / Gene Silencing / Ribonuclease H-like Fold / Zinc
Function / homology
Function and homology information


oocyte fate commitment / oocyte nucleus localization involved in oocyte dorsal/ventral axis specification / : / pole plasm mRNA localization / oocyte anterior/posterior axis specification / oocyte microtubule cytoskeleton organization / regulation of pole plasm oskar mRNA localization / regulation of miRNA-mediated gene silencing / dorsal appendage formation / piRNA processing ...oocyte fate commitment / oocyte nucleus localization involved in oocyte dorsal/ventral axis specification / : / pole plasm mRNA localization / oocyte anterior/posterior axis specification / oocyte microtubule cytoskeleton organization / regulation of pole plasm oskar mRNA localization / regulation of miRNA-mediated gene silencing / dorsal appendage formation / piRNA processing / microtubule organizing center organization / germ-line stem cell population maintenance / dorsal/ventral axis specification / male meiotic nuclear division / intracellular mRNA localization / miRNA metabolic process / regulatory ncRNA-mediated gene silencing / P granule / oogenesis / cytoskeleton organization / protein localization / spermatogenesis / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / nucleus / cytoplasm
Similarity search - Function
Maelstrom domain / Protein maelstrom / piRNA pathway germ-plasm component / High mobility group box domain superfamily
Similarity search - Domain/homology
ACETATE ION / Protein maelstrom
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 Å
AuthorsMatsumoto, N. / Ishitani, R. / Nishimasu, H. / Nureki, O.
CitationJournal: Cell Rep / Year: 2015
Title: Crystal Structure and Activity of the Endoribonuclease Domain of the piRNA Pathway Factor Maelstrom
Authors: Matsumoto, N. / Sato, K. / Nishimasu, H. / Namba, Y. / Miyakubi, K. / Dohmae, N. / Ishitani, R. / Siomi, H. / Siomi, M.C. / Nureki, O.
History
DepositionFeb 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein maelstrom
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2944
Polymers29,1071
Non-polymers1873
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.892, 71.892, 88.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

-
Components

#1: Protein Protein maelstrom


Mass: 29107.365 Da / Num. of mol.: 1 / Fragment: UNP residues 84-333 / Mutation: C228S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: mael, CG11254 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VNS0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 31077 / % possible obs: 99.8 % / Redundancy: 14.3 % / Rsym value: 0.09 / Net I/σ(I): 18.7
Reflection shellResolution: 1.6→1.7 Å

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SHARPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The MAEL domain solved by Zn-SAD

Resolution: 1.602→33.353 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 1556 5.01 %
Rwork0.1944 --
obs0.1955 31075 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.602→33.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 9 82 1984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111949
X-RAY DIFFRACTIONf_angle_d1.2892629
X-RAY DIFFRACTIONf_dihedral_angle_d13.508712
X-RAY DIFFRACTIONf_chiral_restr0.056297
X-RAY DIFFRACTIONf_plane_restr0.006331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6017-1.65340.29281370.25192605X-RAY DIFFRACTION99
1.6534-1.71250.25571390.22862640X-RAY DIFFRACTION100
1.7125-1.78110.2561400.22072653X-RAY DIFFRACTION100
1.7811-1.86210.23471380.20672622X-RAY DIFFRACTION100
1.8621-1.96030.25151410.19832681X-RAY DIFFRACTION100
1.9603-2.08310.21991390.19872650X-RAY DIFFRACTION100
2.0831-2.24390.21391410.18672673X-RAY DIFFRACTION100
2.2439-2.46960.22131410.20262684X-RAY DIFFRACTION100
2.4696-2.82690.21371430.19812698X-RAY DIFFRACTION100
2.8269-3.56090.20321440.19372751X-RAY DIFFRACTION100
3.5609-33.35990.20011530.17912862X-RAY DIFFRACTION99
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)
13.3122-1.03422.80863.5468-1.86175.243-0.15550.29790.2562-0.35060.04560.2469-0.3755-0.13480.09090.2067-0.01540.00110.25030.01690.150316.423429.792115.7455
24.8215-0.48411.66961.4474-0.79172.91-0.14350.17680.09010.0308-0.0467-0.0144-0.18110.32180.09240.1539-0.01520.00530.166-0.00050.138325.122919.606926.0878
34.1849-0.0735-1.16252.2945-0.99032.1812-0.0095-1.02-0.12410.46560.0627-0.37370.1060.9818-0.07940.24330.0151-0.04810.41180.03110.21133.210915.175738.0035
42.9958-1.82560.01723.20320.214.12940.15610.6186-0.1032-0.3646-0.2329-0.13080.20540.3360.08120.19-0.010.06110.27360.00650.158329.372220.18716.5408
54.67170.4344-1.6345.2329-1.03294.6235-0.15020.04170.0827-0.22130.1051-0.3134-0.45660.88670.03140.2372-0.1213-0.02120.32340.00260.147133.033827.663825.0379
64.9628-2.5812.4513.567-1.11493.7506-0.1746-0.01380.12150.00910.21110.4297-0.2914-0.4538-0.03570.18560.01130.01320.1810.0460.178911.861931.078519.5365
75.59731.79763.87434.34712.05257.0901-0.28990.08470.6983-0.30820.01780.6699-0.4531-0.43470.34460.2695-0.00990.06270.2612-0.01290.44013.587132.431925.818
85.9044-2.13671.39592.9242-0.00522.7237-0.0553-0.6023-0.71470.41840.15110.39810.2704-0.1721-0.10250.2619-0.03250.06780.21920.05230.276316.91812.099935.6089
95.2183-0.60420.5694.7076-0.04292.09950.11650.4608-0.633-0.5029-0.00950.97260.1689-0.299-0.11320.2186-0.0382-0.04130.2588-0.02510.34568.86817.12623.0638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 84 through 117 )
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 185 )
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 212 )
5X-RAY DIFFRACTION5chain 'A' and (resid 213 through 238 )
6X-RAY DIFFRACTION6chain 'A' and (resid 239 through 258 )
7X-RAY DIFFRACTION7chain 'A' and (resid 259 through 277 )
8X-RAY DIFFRACTION8chain 'A' and (resid 278 through 300 )
9X-RAY DIFFRACTION9chain 'A' and (resid 301 through 332 )

+
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