[English] 日本語
Yorodumi
- PDB-5yaa: Crystal structure of Marf1 NYN domain from Mus musculus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yaa
TitleCrystal structure of Marf1 NYN domain from Mus musculus
ComponentsMeiosis regulator and mRNA stability factor 1
KeywordsHYDROLASE / NYN domain / Marf1 / meiosis / nuclease
Function / homology
Function and homology information


CCR4-NOT complex binding / female meiotic nuclear division / oogenesis / mRNA base-pairing translational repressor activity / RNA nuclease activity / peroxisome / double-strand break repair / regulation of gene expression / intracellular membrane-bounded organelle / Golgi apparatus / cytoplasm
Similarity search - Function
Meiosis regulator and mRNA stability factor 1 / MARF1, RNA recognition motif 1 / MARF1, RNA recognition motif 2 / MARF1, first and second LOTUS domain / MARF1, RNA recognition motif 1 / MARF1 LOTUS domain / NYN domain, MARF1-type / NYN domain / OST-HTH/LOTUS domain / LOTUS-like domain ...Meiosis regulator and mRNA stability factor 1 / MARF1, RNA recognition motif 1 / MARF1, RNA recognition motif 2 / MARF1, first and second LOTUS domain / MARF1, RNA recognition motif 1 / MARF1 LOTUS domain / NYN domain, MARF1-type / NYN domain / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / 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
Meiosis regulator and mRNA stability factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsYao, Q.Q. / Wu, B.X. / Ma, J.B.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Ribonuclease activity of MARF1 controls oocyte RNA homeostasis and genome integrity in mice.
Authors: Yao, Q. / Cao, G. / Li, M. / Wu, B. / Zhang, X. / Zhang, T. / Guo, J. / Yin, H. / Shi, L. / Chen, J. / Yu, X. / Zheng, L. / Ma, J. / Su, Y.Q.
History
DepositionAug 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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: Meiosis regulator and mRNA stability factor 1
B: Meiosis regulator and mRNA stability factor 1
C: Meiosis regulator and mRNA stability factor 1
D: Meiosis regulator and mRNA stability factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,13617
Polymers73,9394
Non-polymers1,19713
Water4,990277
1
A: Meiosis regulator and mRNA stability factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7614
Polymers18,4851
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint0 kcal/mol
Surface area7590 Å2
MethodPISA
2
B: Meiosis regulator and mRNA stability factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7614
Polymers18,4851
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-1 kcal/mol
Surface area7730 Å2
MethodPISA
3
C: Meiosis regulator and mRNA stability factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0377
Polymers18,4851
Non-polymers5536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint1 kcal/mol
Surface area7720 Å2
MethodPISA
4
D: Meiosis regulator and mRNA stability factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5772
Polymers18,4851
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-1 kcal/mol
Surface area7720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.470, 163.470, 56.151
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein
Meiosis regulator and mRNA stability factor 1 / Limkain-b1 / Meiosis arrest female protein 1


Mass: 18484.684 Da / Num. of mol.: 4 / Fragment: NYN domain, UNP residues 337-499 / Mutation: L253M/L303M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Marf1, Kiaa0430, Lkap / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BJ34
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.07 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Li2SO4, 0.1M Tris-HCl pH 8.5, 22% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.75→81.74 Å / Num. obs: 56376 / % possible obs: 97.9 % / Redundancy: 4 % / Net I/σ(I): 2.152

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.75→29.941 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2827 2859 5.08 %
Rwork0.2319 --
obs0.2346 56259 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→29.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 78 277 5128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094947
X-RAY DIFFRACTIONf_angle_d1.0646675
X-RAY DIFFRACTIONf_dihedral_angle_d18.2782980
X-RAY DIFFRACTIONf_chiral_restr0.064756
X-RAY DIFFRACTIONf_plane_restr0.006870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.78020.33291460.2812640X-RAY DIFFRACTION100
1.7802-1.81260.29921490.26722690X-RAY DIFFRACTION100
1.8126-1.84750.32181480.24982629X-RAY DIFFRACTION100
1.8475-1.88520.2761260.24352701X-RAY DIFFRACTION100
1.8852-1.92620.32191260.24062715X-RAY DIFFRACTION100
1.9262-1.9710.3211640.23762606X-RAY DIFFRACTION100
1.971-2.02020.25561570.23052684X-RAY DIFFRACTION100
2.0202-2.07480.30151280.22822710X-RAY DIFFRACTION100
2.0748-2.13590.29071370.22732665X-RAY DIFFRACTION100
2.1359-2.20480.30171490.22652661X-RAY DIFFRACTION100
2.2048-2.28360.27721090.22812687X-RAY DIFFRACTION100
2.2836-2.3750.29621440.23932683X-RAY DIFFRACTION100
2.375-2.4830.31761570.24922664X-RAY DIFFRACTION100
2.483-2.61380.28461480.24062675X-RAY DIFFRACTION100
2.6138-2.77750.33411470.24012654X-RAY DIFFRACTION100
2.7775-2.99180.30781280.24682692X-RAY DIFFRACTION100
2.9918-3.29250.3181450.23632671X-RAY DIFFRACTION100
3.2925-3.76820.26511510.22522665X-RAY DIFFRACTION100
3.7682-4.74440.22451480.20282663X-RAY DIFFRACTION100
4.7444-29.94530.24141520.22442645X-RAY DIFFRACTION99

+
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