[English] 日本語
Yorodumi
- PDB-9eyh: Ubiquitin conjugating enzyme Ubc6 UBC domain with isopeptide-link... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9eyh
TitleUbiquitin conjugating enzyme Ubc6 UBC domain with isopeptide-linked ubiquitin
Components
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-conjugating enzyme E2 6
KeywordsTRANSFERASE / ubiquitin / Endoplasmic Reticulum Associated Degradation
Function / homology
Function and homology information


maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues ...S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / Ubiquitin-ribosomal protein eS31 fusion protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSwarnkar, A. / Stein, A.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)677770European Union
German Research Foundation (DFG)SFB1190 Germany
CitationJournal: Embo J. / Year: 2024
Title: Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes.
Authors: Swarnkar, A. / Leidner, F. / Rout, A.K. / Ainatzi, S. / Schmidt, C.C. / Becker, S. / Urlaub, H. / Griesinger, C. / Grubmuller, H. / Stein, A.
History
DepositionApr 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 25, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 6
B: Ubiquitin-conjugating enzyme E2 6
C: Ubiquitin-40S ribosomal protein S31
D000: Ubiquitin-40S ribosomal protein S31


Theoretical massNumber of molelcules
Total (without water)57,8844
Polymers57,8844
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.753, 53.490, 111.798
Angle α, β, γ (deg.)90.000, 103.152, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

-
Components

#1: Protein Ubiquitin-conjugating enzyme E2 6 / E2 ubiquitin-conjugating enzyme 6 / Ubiquitin carrier protein UBC6 / Ubiquitin-protein ligase UBC6


Mass: 20373.053 Da / Num. of mol.: 2 / Mutation: C87K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBC6, GI527_G0001907 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A8H8ULW7, E2 ubiquitin-conjugating enzyme
#2: Protein Ubiquitin-40S ribosomal protein S31


Mass: 8568.769 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPS31, RPS37, UBI3, YLR167W, L9470.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P05759
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG smear, sodium acetate, sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.01 Å / Num. obs: 19017 / % possible obs: 99.67 % / Redundancy: 12.1 % / Biso Wilson estimate: 63.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0848 / Net I/σ(I): 17.41
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 11.8 % / Num. unique obs: 1903 / CC1/2: 0.945 / % possible all: 99.53

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.01 Å / SU ML: 0.3587 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6574
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2656 895 4.72 %
Rwork0.2341 18073 -
obs0.2356 18968 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.87 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 0 0 3937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224031
X-RAY DIFFRACTIONf_angle_d0.50625472
X-RAY DIFFRACTIONf_chiral_restr0.0368611
X-RAY DIFFRACTIONf_plane_restr0.0039704
X-RAY DIFFRACTIONf_dihedral_angle_d12.4141544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.760.34781600.31922962X-RAY DIFFRACTION99.49
2.76-2.980.3321700.31882970X-RAY DIFFRACTION99.59
2.98-3.280.35271300.28682982X-RAY DIFFRACTION99.65
3.28-3.750.30041420.2593019X-RAY DIFFRACTION99.62
3.75-4.720.22721420.20913024X-RAY DIFFRACTION99.81
4.72-48.010.23211510.23116X-RAY DIFFRACTION99.97
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)
11.00271406623-0.08379544244020.1311288614511.046953061850.1764620568251.33473193209-0.2000348185670.7495525982990.0899494308492-0.2057498914930.164657492209-0.103284073298-0.420764709693-0.161437029643-7.05240795896E-50.751207002913-0.1189034115380.009596018631750.888626180586-0.05234841317440.725433051676-33.0960043904-14.5998892573-12.1004991454
22.737183438480.49933318602-0.3392071434651.358170321390.9697612269932.36691131575-0.4438493012150.2349961075250.391212357376-0.2812633331810.305979104562-0.264150984352-0.569170300599-0.0658712331837-0.0002031417341250.755383819711-0.118535695095-0.09625825673280.6292064555570.01727124939250.75476785756-28.462069693-7.68177532765-1.45791545737
31.238806287182.268353778120.1984020341281.601388679690.2988531838280.9301900081960.1252677543520.4704649461310.1108323680530.155502973360.277251326744-0.290410766827-0.2265741519631.277116729550.001139654640210.772406405488-0.0605195776356-0.04704397881940.721444961974-0.04361018451520.699294235794-21.7751213628-9.510436816990.410991061478
41.154870493271.0262461190.1118375007990.988730893621-0.7837428237990.739943105553-0.002839680818930.130274858626-0.333597055999-0.07473329512460.07405123360620.1157710435560.289769047536-0.04764099402284.44029140296E-50.676265920404-0.06354938995310.008403659727290.653674651917-0.07497808297910.750708913591-35.4621640736-25.5842788415.96155397027
52.70769783379-1.405545869741.485840311011.80704488593-0.7378335700624.42568163111-0.185120842125-0.2583638568620.2511241044870.1480467086760.183084799022-0.227707042761-0.5654574278-0.3636327912718.91334980181E-50.6839613902350.0410389160306-0.02307596989890.623382888050.06517788928990.729437036597-43.2262740736-23.485730261124.6791780487
61.14473055868-1.530264445571.463956819581.8272570835-1.509630970921.523020490971.556150600531.562765441470.363337810138-1.567113554980.06506591913350.04570048407411.04473525004-1.142169562930.1693415348291.138324144770.360223238660.02805981323270.9773022928180.2255883195331.12153121744-42.5052185617-6.7084004071630.7762068822
73.169002177360.805508960266-0.59741999832.57857174037-1.123429062994.3394805875-0.0263450200768-0.227163107743-0.5802604534770.2609730988830.502397945050.4318467931240.482438030216-1.409144866142.27032051335E-50.836434522814-0.0298165568502-0.1600191307110.9247299809870.1765604275930.777979603436-54.2120163361-30.197521807320.0122552495
80.2246350990550.273761253826-0.199791190790.988774255878-0.05751570607780.170832924676-0.3316638887181.33168185257-0.684274177656-0.5653125302390.777432643524-0.478797798393-0.3081835248771.21544349010.0004483998431980.95204809572-0.05966881036270.1668667334461.40291163029-0.17942692880.989568555653-7.95041736848-16.3917552343-15.6928079718
9-0.00731926741709-0.0246924439356-0.11718086978-0.01040686052250.007135597273120.05668401699720.244635724146-0.1314469923381.139212409610.188744680884-0.453506622191-0.496108908295-1.112712003120.63604299468-0.001160427716461.47232339628-0.391571990989-0.1235529528691.319191176980.05167724802181.34988401199-6.23216844652-6.81292491941-15.1103159291
100.5268632509120.351103722820.1257697744840.2502716620370.1380975297690.180036298972-0.881575696141-0.527791267430.496471299725-0.123804120290.61839779939-0.806509676151-0.756123110334-0.2414792831690.0004010935245030.683944769944-0.03866751130710.1006638089350.952069188019-0.08993374704240.972850492734-8.07546939597-15.4715978219-3.98064720073
111.521076158430.945996312194-0.5925517143660.945077158863-1.089791051121.23978303693-0.60797575103-0.01886981853760.3622056398090.890761173460.505232135925-1.138068637960.117839753040.7401714000090.001780224153380.860381876103-0.0833965645878-0.03846613948911.13956496001-0.05359545774960.804407120043-12.0825598995-14.1925161377-8.58027240723
120.5131810342540.518272600086-0.08783632130670.329366155657-0.09663147542140.0514224891258-0.368187762406-0.6858479645050.7654868757291.105121667910.953843753247-0.210612489462-0.41049078492-0.972618204569-9.94573326332E-51.817206044510.4586315193960.09407213681561.400653772220.2187996213350.983622050456-52.0835026617-14.731839562349.8884720268
130.366240930390.0670119042577-0.4473956853870.1499245064030.2307621941630.632278947325-0.789376847259-0.9264078210.814112137976-0.8473405685320.2951633548740.878684583018-1.62706648899-1.22769847599-0.001028075995591.718604637780.6586398365970.05830207539161.300176204570.04686997301111.19916398922-52.2393520318-10.380704573642.2502872891
140.0697420426975-0.0923461928282-0.05866575015190.07455059122170.05414306365140.0287590207299-0.0270942361198-0.7186865087331.08097818097-0.0637210693297-1.052301686521.45001754872-0.5044684320690.0403850172265-0.001304908966652.118692585850.2919621372970.2587604354491.844391405570.3572904146761.68507762325-63.3955364276-9.6829463468342.8545772538
150.3340884145170.1185597856990.1875027071070.01203440666810.2299022596730.387345511698-0.168960528366-1.138086968320.128431634165-0.44518736010.2970493157870.4835434445050.720962314454-0.8190301461240.000643783872371.564976216330.3142854665840.02508208277511.344902944350.2503894053910.78996386775-55.451921956-15.750439895841.4507168637
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 2:44)AA2 - 441 - 43
22(chain A and resid 45:98)AA45 - 9844 - 97
33(chain A and resid 99:130)AA99 - 13098 - 129
44(chain A and resid 131:170)AA131 - 170130 - 169
55(chain B and resid 2:88)BB3 - 881 - 86
66(chain B and resid 89:103)BB89 - 10387 - 101
77(chain B and resid 104:171)BB104 - 171102 - 169
88(chain C and resid 1:24)CC1 - 241 - 24
99(chain C and resid 25:40)CC25 - 4025 - 40
1010(chain C and resid 41:59)CC41 - 5941 - 59
1111(chain C and resid 60:76)CC60 - 7660 - 76
1212(chain D and resid 1:22)D000D2 - 221 - 21
1313(chain D and resid 23:49)D000D23 - 4922 - 48
1414(chain D and resid 50:59)D000D50 - 5949 - 58
1515(chain D and resid 60:76)D000D60 - 7659 - 75

+
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