[English] 日本語
Yorodumi
- PDB-4dk6: Structure of Editosome protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dk6
TitleStructure of Editosome protein
Components
  • RNA-editing complex protein MP81
  • single domain antibody VHH
KeywordsRNA BINDING PROTEIN/IMMUNE SYSTEM / KREPA1 / VHH / Single domain antibody / PROTEIN BINDING / RNA BINDING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


RNA nucleotide insertion / RNA nucleotide deletion / mitochondrial RNA modification / alpha-catenin binding / mitochondrion
Similarity search - Function
RNA editing complex, structural subunit MP81 / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Nucleic acid-binding proteins / Zinc finger C2H2-type / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Immunoglobulins / Immunoglobulin-like / Beta Barrel ...RNA editing complex, structural subunit MP81 / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Nucleic acid-binding proteins / Zinc finger C2H2-type / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
RNA-editing complex protein MP81
Similarity search - Component
Biological speciesLama glama (llama)
Trypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsPark, Y.-J. / Hol, W.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The structure of the C-terminal domain of the largest editosome interaction protein and its role in promoting RNA binding by RNA-editing ligase L2.
Authors: Park, Y.J. / Budiarto, T. / Wu, M. / Pardon, E. / Steyaert, J. / Hol, W.G.
History
DepositionFeb 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Sep 18, 2013Group: Source and taxonomy
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: single domain antibody VHH
B: single domain antibody VHH
C: RNA-editing complex protein MP81
D: RNA-editing complex protein MP81


Theoretical massNumber of molelcules
Total (without water)52,4174
Polymers52,4174
Non-polymers00
Water0
1
A: single domain antibody VHH
D: RNA-editing complex protein MP81


Theoretical massNumber of molelcules
Total (without water)26,2092
Polymers26,2092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-11 kcal/mol
Surface area10990 Å2
MethodPISA
2
B: single domain antibody VHH
C: RNA-editing complex protein MP81


Theoretical massNumber of molelcules
Total (without water)26,2092
Polymers26,2092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-10 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.026, 40.882, 61.281
Angle α, β, γ (deg.)90.000, 92.550, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody single domain antibody VHH


Mass: 14769.310 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein RNA-editing complex protein MP81


Mass: 11439.330 Da / Num. of mol.: 2 / Mutation: deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95W15

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M magnesium chloride, 0.1M bis-tris, 25% w/v PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: M0 mirror: toroidal SiC
RadiationMonochromator: 6m spherical grating monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 12226 / % possible obs: 95.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.079 / Χ2: 1.01 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.65-2.72.30.3016241.002197.2
2.7-2.742.50.2756120.97196.2
2.74-2.82.40.2336000.978196
2.8-2.852.50.2146051.004196.3
2.85-2.922.60.1996221.001196.1
2.92-2.982.60.1815850.972195.9
2.98-3.062.60.1436200.997196.4
3.06-3.142.60.136051.031195.1
3.14-3.232.50.1046100.959196.5
3.23-3.342.60.0966041.035195.7
3.34-3.462.60.0866090.992195.8
3.46-3.62.60.0715911.016194.1
3.6-3.762.60.076180.975196.3
3.76-3.962.60.0695991.052194.5
3.96-4.212.60.0586231.043195.7
4.21-4.532.60.0546181.061196.4
4.53-4.992.60.0576211.024194.7
4.99-5.712.60.0616100.952194.1
5.71-7.192.50.0536101.061193
7.19-502.50.0436401.069192.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.81 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.65 Å48.94 Å
Translation2.65 Å48.94 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3K7U

3k7u


Resolution: 2.65→43.21 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.866 / WRfactor Rfree: 0.2708 / WRfactor Rwork: 0.2286 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.788 / SU B: 32.662 / SU ML: 0.303 / SU R Cruickshank DPI: 0.3164 / SU Rfree: 0.3846 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 585 4.8 %RANDOM
Rwork0.224 ---
obs0.226 12183 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 93.31 Å2 / Biso mean: 35.8094 Å2 / Biso min: 18.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.07 Å2
2---0.41 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.65→43.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 0 0 3278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193327
X-RAY DIFFRACTIONr_angle_refined_deg0.9091.9444484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9445413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06723.377151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33915572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6991528
X-RAY DIFFRACTIONr_chiral_restr0.0570.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022474
LS refinement shellResolution: 2.65→2.715 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 50 -
Rwork0.306 791 -
all-841 -
obs--94.18 %
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)
12.4293-1.0858-0.91692.86010.35941.7483-0.0639-0.01360.01320.14770.0032-0.2806-0.0890.34960.06070.08260.0164-0.01380.17040.02050.088137.2507-1.454912.663
28.6338-5.7293-1.16417.55341.02831.7020.04110.1164-0.07680.0084-0.0741-0.085-0.06720.23090.03310.1304-0.0267-0.01650.1016-0.0090.011536.3724-1.59076.9694
31.3810.34920.37395.45391.08782.32420.0043-0.37560.06730.5194-0.0133-0.06780.0674-0.0060.0090.1758-0.0483-0.02230.1855-0.02940.120419.8324-4.100233.0657
41.93851.31381.60597.93874.54894.3034-0.0164-0.17320.1120.4672-0.01450.03710.16070.04640.03090.1579-0.01620.07080.1719-0.03460.129514.0326-5.518234.2642
55.66464.5545-0.28019.10991.95552.7455-0.06240.18910.2022-0.01630.06511.01790.3147-0.3043-0.00260.11980.0102-0.04050.2223-0.00860.22653.3736-16.834917.1312
611.9298-1.9023-1.05852.6575-1.36882.86940.01670.36620.6765-0.3511-0.09570.21520.0982-0.21410.0790.1845-0.02120.00050.0633-0.06560.21318.4798-18.160712.5965
73.29481.2561-1.81711.8887-1.25595.4403-0.10270.52030.1188-0.2069-0.12080.1068-0.1973-0.91670.22360.16940.0285-0.02880.3107-0.0570.13715.76575.10983.3063
81.96780.2668-0.66934.34162.271114.39470.03790.5639-0.1117-0.211-0.01980.34550.3043-0.3547-0.01810.08740.05310.01460.1924-0.01210.222814.125110.12455.4759
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 86
2X-RAY DIFFRACTION2A87 - 127
3X-RAY DIFFRACTION3B1 - 87
4X-RAY DIFFRACTION4B88 - 127
5X-RAY DIFFRACTION5C627 - 718
6X-RAY DIFFRACTION6C719 - 761
7X-RAY DIFFRACTION7D627 - 650
8X-RAY DIFFRACTION8D651 - 762

+
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