[English] 日本語
Yorodumi
- PDB-6y75: BIL2 domain from T.thermophila BUBL1 locus (C1A-N143A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y75
TitleBIL2 domain from T.thermophila BUBL1 locus (C1A-N143A)
Components(NAD(P)(+)--arginine ADP- ...) x 2
KeywordsSPLICING / intein / PTM / ubiquitin
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / intein-mediated protein splicing / nucleotidyltransferase activity / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Vint domain / Hint-domain / NAD:arginine ADP-ribosyltransferase, ART / NAD:arginine ADP-ribosyltransferase / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region ...Vint domain / Hint-domain / NAD:arginine ADP-ribosyltransferase, ART / NAD:arginine ADP-ribosyltransferase / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / : / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / NAD(P)(+)--arginine ADP-ribosyltransferase
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIlari, A. / Chiarini, V.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationPRIN20154JRJPP Italy
Citation
Journal: Biochim Biophys Acta Gen Subj / Year: 2021
Title: Structural basis of ubiquitination mediated by protein splicing in early Eukarya.
Authors: Chiarini, V. / Fiorillo, A. / Camerini, S. / Crescenzi, M. / Nakamura, S. / Battista, T. / Guidoni, L. / Colotti, G. / Ilari, A.
#1: Journal: Biochim.Biophys.Acta / Year: 2021
Title: Structural basis of ubiquitination mediated by protein splicing in early Eukarya
Authors: Chiarini, V. / Fiorillo, A. / Camerini, S. / Crescenzi, M. / Nakamura, S. / Battista, T. / Guidoni, L. / Colotti, G. / Ilari, A.
History
DepositionFeb 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jan 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD(P)(+)--arginine ADP-ribosyltransferase
B: NAD(P)(+)--arginine ADP-ribosyltransferase
C: NAD(P)(+)--arginine ADP-ribosyltransferase
D: NAD(P)(+)--arginine ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,97812
Polymers69,4124
Non-polymers5668
Water4,828268
1
A: NAD(P)(+)--arginine ADP-ribosyltransferase
B: NAD(P)(+)--arginine ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1418
Polymers34,7062
Non-polymers4356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: NAD(P)(+)--arginine ADP-ribosyltransferase
D: NAD(P)(+)--arginine ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8374
Polymers34,7062
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.821, 67.605, 82.445
Angle α, β, γ (deg.)90.000, 114.580, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A78 - 230
2114B78 - 230
3114C78 - 230
4114D78 - 230

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.197352, -0.968334, -0.152911), (-0.969996, 0.17029, 0.173517), (-0.141983, 0.182567, -0.972887)-8.75422, -21.03252, 89.479698
3given(-0.028602, 0.990995, -0.130806), (-0.988579, -0.047414, -0.143052), (-0.147965, 0.125221, 0.981033)0.15792, 3.27812, -50.942791
4given(0.986437, -0.161483, 0.029403), (-0.162964, -0.942149, 0.292913), (-0.019599, -0.293732, -0.955687)-5.62386, -31.33918, 139.14238

-
Components

-
NAD(P)(+)--arginine ADP- ... , 2 types, 4 molecules ACBD

#1: Protein NAD(P)(+)--arginine ADP-ribosyltransferase / Mono(ADP-ribosyl)transferase


Mass: 17502.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (strain SB210) (eukaryote)
Gene: TTHERM_00085190 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q236S9, NAD+-protein-arginine ADP-ribosyltransferase
#2: Protein NAD(P)(+)--arginine ADP-ribosyltransferase / Mono(ADP-ribosyl)transferase


Mass: 17203.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (strain SB210) (eukaryote)
Gene: TTHERM_00085190 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q236S9, NAD+-protein-arginine ADP-ribosyltransferase

-
Non-polymers , 4 types, 276 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: Mg formate 0.1M, PEG3350 19%, Tris 50mM, NaCl 250 mM.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 34430 / % possible obs: 99.1 % / Redundancy: 3.36 % / Biso Wilson estimate: 40.902 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.15 / Net I/σ(I): 7.23
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 3.41 % / Num. unique obs: 10795 / CC1/2: 0.83 / % possible all: 99

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TMM

6tmm


Resolution: 2.3→47.57 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.867 / SU B: 9.649 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.391 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3018 1662 4.8 %RANDOM
Rwork0.2538 ---
obs0.256 32698 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.68 Å2 / Biso mean: 34.514 Å2 / Biso min: 11.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.05 Å2
2---0.12 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 2.3→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4886 0 24 268 5178
Biso mean--55.41 32.64 -
Num. residues----606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125018
X-RAY DIFFRACTIONr_angle_refined_deg0.9431.636769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9735602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46124.776268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10715885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9891512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023800
Refine LS restraints NCS

Ens-ID: 1 / Number: 1211 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.210.5
2BMEDIUM POSITIONAL0.230.5
3CMEDIUM POSITIONAL0.250.5
4DMEDIUM POSITIONAL0.280.5
1AMEDIUM THERMAL4.942
2BMEDIUM THERMAL4.842
3CMEDIUM THERMAL4.032
4DMEDIUM THERMAL9.22
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.378 133 -
Rwork0.338 2384 -
obs--99.21 %

+
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