[English] 日本語
Yorodumi
- PDB-6s2w: Structure of S. pombe Erh1, a protein important for meiotic mRNA ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s2w
TitleStructure of S. pombe Erh1, a protein important for meiotic mRNA decay in mitosis and meiosis progression.
ComponentsEnhancer of rudimentary-like protein
KeywordsCELL CYCLE / Meiosis / mRNA degradation
Function / homology
Function and homology information


ascospore-type prospore nucleus / regulation of siRNA-independent facultative heterochromatin formation / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / nuclear exosome focus / heterochromatin island / termination of RNA polymerase II transcription, poly(A)-coupled / rDNA heterochromatin / molecular function inhibitor activity / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Enhancer of rudimentary / Enhancer of rudimentary superfamily / Enhancer of rudimentary
Similarity search - Domain/homology
ACETIC ACID / Enhancer of rudimentary homolog 1 / Enhancer of rudimentary homolog 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHazra, D. / Graille, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Sci Rep / Year: 2020
Title: Formation of S. pombe Erh1 homodimer mediates gametogenic gene silencing and meiosis progression.
Authors: Hazra, D. / Andric, V. / Palancade, B. / Rougemaille, M. / Graille, M.
History
DepositionJun 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enhancer of rudimentary-like protein
B: Enhancer of rudimentary-like protein
C: Enhancer of rudimentary-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,47911
Polymers37,8913
Non-polymers5898
Water1,31573
1
A: Enhancer of rudimentary-like protein
hetero molecules

A: Enhancer of rudimentary-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3854
Polymers25,2602
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area1600 Å2
ΔGint-7 kcal/mol
Surface area10490 Å2
MethodPISA
2
B: Enhancer of rudimentary-like protein
C: Enhancer of rudimentary-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7879
Polymers25,2602
Non-polymers5277
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-19 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.845, 123.847, 68.144
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Enhancer of rudimentary-like protein


Mass: 12630.225 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: Erh1 / Production host: Escherichia coli (E. coli) / References: UniProt: K7PD52, UniProt: G2TRN4*PLUS

-
Non-polymers , 5 types, 81 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.3M Ammonium sulfate, 0.1M Sodium Acetate pH 3.8

-
Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2018 / Details: bimorph mirrors Kirkpatrick-Baez (KB)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→45.918 Å / Num. obs: 22390 / % possible obs: 99.6 % / Redundancy: 7.891 % / Biso Wilson estimate: 48.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.083 / Χ2: 1.088 / Net I/σ(I): 14.26 / Num. measured all: 176672
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.95-2.077.5491.9081.0226429357435010.5042.04998
2.07-2.218.0361.0342.1627064336833680.8211.106100
2.21-2.398.0610.5833.9725329314231420.9370.624100
2.39-2.628.250.3176.9823875289528940.980.338100
2.62-2.937.9990.16112.3521134264226420.9930.172100
2.93-3.388.0920.08222.4418968234423440.9970.087100
3.38-4.137.6990.04836.1915337199219920.9980.051100
4.13-5.827.5670.03746.7911948158015790.9990.0499.9
5.82-45.9187.0990.03447.8465889399280.9990.03698.8

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W9G

1w9g


Resolution: 1.95→45.918 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.17 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.149
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1120 5 %RANDOM
Rwork0.2 ---
obs0.202 22390 99.2 %-
Displacement parametersBiso max: 172.97 Å2 / Biso mean: 61.25 Å2 / Biso min: 32.09 Å2
Baniso -1Baniso -2Baniso -3
1--2.6642 Å20 Å20 Å2
2--12.6163 Å20 Å2
3----9.9521 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.95→45.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 37 73 2374
Biso mean--80.02 58.64 -
Num. residues----269
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d804SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes349HARMONIC5
X-RAY DIFFRACTIONt_it2412HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion302SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2727SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2412HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3275HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion20.16
LS refinement shellResolution: 1.95→2.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.338 140 5 %
Rwork0.285 2658 -
all0.288 2798 -
obs--94.53 %
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)
10.4802-0.76280.31285.193-1.80882.17610.06570.0936-0.095-0.41350.02640.51810.0788-0.2883-0.0921-0.08320.0275-0.0342-0.0817-0.0081-0.018325.2803-49.230713.0267
23.0667-2.7281.60064.0167-2.13852.3412-0.1464-0.2345-0.25250.0710.10420.09810.1612-0.07120.0423-0.08410.03430.0279-0.07020.0092-0.075513.4092-27.671319.1588
32.9332-0.14560.25190.8991-1.15141.8705-0.02980.27750.3628-0.1373-0.1741-0.3160.02350.32670.204-0.1111-0.00670.0188-0.05170.0685-0.009223.683-12.00589.9459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A6 - 100
2X-RAY DIFFRACTION2{ B|* }B-3 - 98
3X-RAY DIFFRACTION3{ C|* }C1 - 98

+
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