[English] 日本語
Yorodumi
- PDB-7d1l: complex structure of two RRM domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d1l
Titlecomplex structure of two RRM domains
Components
  • Embryonic developmental protein tofu-6
  • Uncharacterized protein
KeywordsPROTEIN BINDING / RRM / protein complex / RNA
Function / homology
Function and homology information


21U-RNA metabolic process / positive regulation of chromosome segregation / RNA cap binding complex / piRNA processing / mitotic sister chromatid separation / embryonic cleavage / embryo development ending in birth or egg hatching / positive regulation of cell division / chromosome segregation / DNA replication ...21U-RNA metabolic process / positive regulation of chromosome segregation / RNA cap binding complex / piRNA processing / mitotic sister chromatid separation / embryonic cleavage / embryo development ending in birth or egg hatching / positive regulation of cell division / chromosome segregation / DNA replication / cell division / perinuclear region of cytoplasm / RNA binding / nucleus / cytoplasm
Similarity search - Function
RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Protein pid-3 / Embryonic developmental protein tofu-6
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsWang, X. / Liao, S. / Xu, C.
CitationJournal: Nat Commun / Year: 2021
Title: Molecular basis for PICS-mediated piRNA biogenesis and cell division.
Authors: Wang, X. / Zeng, C. / Liao, S. / Zhu, Z. / Zhang, J. / Tu, X. / Yao, X. / Feng, X. / Guang, S. / Xu, C.
History
DepositionSep 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Embryonic developmental protein tofu-6
B: Embryonic developmental protein tofu-6
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)41,5704
Polymers41,5704
Non-polymers00
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-22 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.686, 86.908, 92.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Embryonic developmental protein tofu-6 / 21U-RNA biogenesis fouled up protein 6 / Maternal effect lethal protein 47


Mass: 10761.389 Da / Num. of mol.: 2 / Fragment: RRM1 domain / Mutation: LEU23MSE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: tofu-6, mel-47, EEED8.1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q09293
#2: Protein Uncharacterized protein


Mass: 10023.728 Da / Num. of mol.: 2 / Fragment: RRM2 domain / Mutation: ILE233MSE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: pid-3, CELE_Y23H5A.3, Y23H5A.3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O76616
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2% v/v 1, 4-Dioxane 0.1M Tris pH 8.0 15% w/v PEG3350 0.01 M Nickel(II) Chloride hexahydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 58993 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.143 / Net I/σ(I): 19.2
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 1.075 / Num. unique obs: 3258 / CC1/2: 0.722

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→27.653 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.81 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2247 3627 6.15 %
Rwork0.1843 55366 -
obs0.1868 58993 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.36 Å2 / Biso mean: 25.6598 Å2 / Biso min: 8.51 Å2
Refinement stepCycle: final / Resolution: 1.95→27.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 0 317 2874
Biso mean---35.37 -
Num. residues----328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9502-1.97590.27461080.2656140863
1.9759-2.0030.24941000.2421162773
2.003-2.03160.26491040.2354170275
2.0316-2.06190.22631320.2341183982
2.0619-2.09410.29361230.2152196286
2.0941-2.12840.27491430.2083201692
2.1284-2.16510.28731240.203217296
2.1651-2.20450.23561530.2054223199
2.2045-2.24680.24641320.19922229100
2.2468-2.29270.21251410.19922284100
2.2927-2.34250.21741600.20022214100
2.3425-2.3970.27951440.2032266100
2.397-2.45690.2911370.20482225100
2.4569-2.52330.23621470.19262256100
2.5233-2.59750.27891530.19942240100
2.5975-2.68120.26691440.18942248100
2.6812-2.7770.21541530.18362250100
2.777-2.8880.20711340.18252292100
2.888-3.01930.22311440.17412213100
3.0193-3.17830.27421570.18112241100
3.1783-3.37710.18771380.17472263100
3.3771-3.63730.17441460.15872269100
3.6373-4.00240.22091600.14822216100
4.0024-4.57930.18721490.14542239100
4.5793-5.76080.1851470.17312251100
5.7608-27.6530.22271540.2105221399
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)
11.0867-0.099-0.62380.6470.28991.7438-0.0183-0.10230.02870.07370.0523-0.0742-0.00730.2065-0.00020.16910.0255-0.01070.17660.00630.142625.486821.67128.0925
21.85990.2905-0.23871.68490.38161.2395-0.04910.0906-0.2683-0.16570.0374-0.05360.044-0.01410.00030.1991-0.00660.02190.13-0.00280.1638-6.1229-6.43011.708
31.07280.0990.27620.4830.43150.5598-0.13860.0821-0.14-0.02360.1192-0.0811-0.0020.1047-0.03040.12620.01320.04540.14160.00040.136421.683312.38096.6568
40.80620.37260.26770.47790.40610.3994-0.1031-0.06440.1141-0.0535-0.01020.08980.06080.0235-0.01930.10860.03010.00380.0994-0.01250.1109-2.046215.58839.7286
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 9 through 92)A9 - 92
2X-RAY DIFFRACTION2(chain 'B' and resid 8 through 92)B8 - 92
3X-RAY DIFFRACTION3(chain 'C' and resid 200 through 282)C200 - 282
4X-RAY DIFFRACTION4(chain 'D' and resid 200 through 282)D200 - 282

+
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