[English] 日本語
Yorodumi
- PDB-7o6l: Crystal structure of C. elegans ERH-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o6l
TitleCrystal structure of C. elegans ERH-2
ComponentsEnhancer of rudimentary homolog 2
KeywordsPROTEIN BINDING / Enhancer of rudimentary ERH Homodimer
Function / homology
Function and homology information


21U-RNA metabolic process / positive regulation of chromosome segregation / RNA cap binding complex / piRNA processing / embryo development ending in birth or egg hatching / positive regulation of cell division / chromosome segregation / cell division / perinuclear region of cytoplasm / nucleus / cytoplasm
Similarity search - Function
Enhancer of rudimentary / Enhancer of rudimentary superfamily / Enhancer of rudimentary
Similarity search - Domain/homology
Enhancer of rudimentary homolog 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFalk, S. / Ketting, R.F.
CitationJournal: Genes Dev. / Year: 2021
Title: Structural basis of PETISCO complex assembly during piRNA biogenesis in C. elegans .
Authors: Perez-Borrajero, C. / Podvalnaya, N. / Holleis, K. / Lichtenberger, R. / Karaulanov, E. / Simon, B. / Basquin, J. / Hennig, J. / Ketting, R.F. / Falk, S.
History
DepositionApr 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_contact_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enhancer of rudimentary homolog 2
B: Enhancer of rudimentary homolog 2


Theoretical massNumber of molelcules
Total (without water)23,6872
Polymers23,6872
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, gel filtration and multi angle light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-16 kcal/mol
Surface area10200 Å2
Unit cell
Length a, b, c (Å)38.267, 54.053, 46.762
Angle α, β, γ (deg.)90.000, 93.417, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Enhancer of rudimentary homolog 2


Mass: 11843.388 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: erh-2, F35G12.11 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q20057
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Imidazole/MES pH 6.5, 0.03 M MgCl2, 0.03 M CaCl2, 20% (v/v) ethylene glycol, 10% (v/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Aug 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.5→35.35 Å / Num. obs: 30574 / % possible obs: 99.83 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.67 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 9.99
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 1.14 / Num. unique obs: 3039 / CC1/2: 0.558 / CC star: 0.846 / % possible all: 99.47

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2nml

2nml


Resolution: 1.5→31.2 Å / SU ML: 0.1803 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7078
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2156 1502 4.92 %
Rwork0.2006 29051 -
obs0.2014 30553 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 1 102 1536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961459
X-RAY DIFFRACTIONf_angle_d1.04181969
X-RAY DIFFRACTIONf_chiral_restr0.087217
X-RAY DIFFRACTIONf_plane_restr0.0083249
X-RAY DIFFRACTIONf_dihedral_angle_d4.8055196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.32311330.30732591X-RAY DIFFRACTION98.66
1.55-1.60.27441210.27562640X-RAY DIFFRACTION99.75
1.6-1.670.27681300.26812643X-RAY DIFFRACTION99.75
1.67-1.740.28751380.25422651X-RAY DIFFRACTION99.86
1.74-1.830.26081420.24012609X-RAY DIFFRACTION99.93
1.84-1.950.25021330.21022644X-RAY DIFFRACTION100
1.95-2.10.23271380.21112630X-RAY DIFFRACTION100
2.1-2.310.21931360.20512636X-RAY DIFFRACTION99.96
2.31-2.650.21711470.19812652X-RAY DIFFRACTION99.96
2.65-3.330.22941440.20312655X-RAY DIFFRACTION99.96
3.33-31.20.18311400.17742700X-RAY DIFFRACTION99.65
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)
12.06279264799-0.188915810949-1.107727954771.764430904760.3590949818922.13604381494-0.001829152224020.0472583667547-0.009317893081330.005512455148870.0952750363951-0.02221906148120.04499997809680.2502394217940.07366840433480.3531299888250.03323124713430.08542746695080.34076809511-0.01466934290850.1207900376784.86296648968-7.2024606266817.281382465
21.01504376716-0.1930105097760.4323968453441.64688278931-0.0167651685586.289369915360.02926991927970.153050415957-0.2300297704350.0226815486804-0.03269745930330.1366979135350.3872130736170.1091541183750.06758578287140.314255207371-0.009838899943560.0890997965480.341452759065-0.03092219854610.166147938044.21203350605-12.779528045520.5084372274
32.31892166255-1.715945291460.02740538250534.88485707034-0.01189163880612.47200643555-0.05356269213970.22664731488-0.03751966524310.389971028643-0.100089918647-0.01377150748340.07677894877130.03961756830720.1375245868120.303046651174-0.02317128586610.07764552933550.328257711037-0.02000941584630.15013638767511.1797735338-7.5451731086422.3810063559
43.783608219280.740118809999-2.640450618637.08587514352-5.925592870558.34934996977-0.192900428122-0.232316224258-0.2613495911170.319454801439-0.203777383663-0.4680910715710.05551128858930.48562147450.3681911835450.271471366329-0.01129314714750.05112738932230.373057682183-0.03557926020440.26348582059514.9051597491-10.160503883628.8795690026
55.318411128751.99269321879-0.4654444813345.88262331505-0.9630795290692.550685924870.141399322160.332400527869-0.323964887208-0.395543074284-0.0788716218745-0.0110891217920.1322298389030.1473914311030.03871080777940.2911384446530.01451792200370.06804929875430.326417251352-0.02340417363140.138006611143-0.664572118149-1.9102929478610.33773788
61.81539182532-0.0216403621461-0.3498246096591.371224196940.3015198371964.99260624991-0.09274132208140.440187341578-0.129885923571-0.390053554681-0.0166461781346-0.04293908814330.330640523176-0.2395751219020.1061361890510.535958786773-0.02569328696730.1700701174260.5864451704780.03591044368590.217803961108-4.469926531094.775835020240.84445555671
74.192889276192.055098810090.1282140112064.22575747433-0.1415265477740.53501720066-0.1786049510970.3756925878510.286046049045-0.4604780251060.1412584987140.422222599041-0.0018152191367-0.006714410029480.004427458889530.296578723048-0.01865632142170.02828478357860.3486339335580.03509104277340.180613982403-9.577342701955.599609009027.14155942053
82.15168176916-0.5613032589991.034742188021.84714516826-0.8562217226223.85854584057-0.1697227080820.2725458664530.115877888108-0.09378170240580.0821741113725-0.159198488739-0.207584394552-0.1060170946060.03757431735050.318691852558-0.03987997443470.08782215667360.3302099997680.01556467529710.165819027524-3.1521494285112.184372149812.2438797695
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 16 )AA3 - 161 - 14
22chain 'A' and (resid 17 through 43 )AA17 - 4315 - 41
33chain 'A' and (resid 44 through 84 )AA44 - 8442 - 76
44chain 'A' and (resid 85 through 99 )AA85 - 9977 - 91
55chain 'B' and (resid 4 through 27 )BC4 - 271 - 24
66chain 'B' and (resid 28 through 42 )BC28 - 4225 - 39
77chain 'B' and (resid 43 through 74 )BC43 - 7440 - 63
88chain 'B' and (resid 75 through 97 )BC75 - 9764 - 86

+
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