[English] 日本語
Yorodumi
- PDB-3stb: A complex of two editosome proteins and two nanobodies -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3stb
TitleA complex of two editosome proteins and two nanobodies
Components
  • MP18 RNA editing complex protein
  • RNA-editing complex protein MP42
  • single domain antibody VHH
KeywordsRNA BINDING PROTEIN/IMMUNE SYSTEM / RNA EDITING / Editosome / Nanobody / Single domain antibody / VHH / KREPA3 / KREPA6 / RNA BINDING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


RNA endonuclease activity, producing 5'-phosphomonoesters / RNA modification / mitochondrial mRNA editing complex / mRNA modification / kinetoplast / response to metal ion / single-stranded DNA binding / 3'-5'-RNA exonuclease activity / endonuclease activity / mitochondrion ...RNA endonuclease activity, producing 5'-phosphomonoesters / RNA modification / mitochondrial mRNA editing complex / mRNA modification / kinetoplast / response to metal ion / single-stranded DNA binding / 3'-5'-RNA exonuclease activity / endonuclease activity / mitochondrion / RNA binding / zinc ion binding / nucleus
Similarity search - Function
RNA editing complex, nuclease subunit MP42 / RNA editing complex, subunit MP18 / Single-strand binding protein family / Primosome PriB/single-strand DNA-binding / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Nucleic acid-binding proteins ...RNA editing complex, nuclease subunit MP42 / RNA editing complex, subunit MP18 / Single-strand binding protein family / Primosome PriB/single-strand DNA-binding / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / 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
MP18 RNA editing complex protein / RNA-editing complex protein MP42
Similarity search - Component
Biological speciesLama glama (llama)
Trypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsPark, Y.-J. / Hol, W.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal structure of a heterodimer of editosome interaction proteins in complex with two copies of a cross-reacting nanobody.
Authors: Park, Y.J. / Pardon, E. / Wu, M. / Steyaert, J. / Hol, W.G.
History
DepositionJul 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Jan 11, 2012Group: Database references
Revision 1.3Mar 14, 2012Group: Database references
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

-
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 MP42
D: MP18 RNA editing complex protein


Theoretical massNumber of molelcules
Total (without water)61,2744
Polymers61,2744
Non-polymers00
Water1,06359
1
A: single domain antibody VHH
B: single domain antibody VHH
C: RNA-editing complex protein MP42
D: MP18 RNA editing complex protein

A: single domain antibody VHH
B: single domain antibody VHH
C: RNA-editing complex protein MP42
D: MP18 RNA editing complex protein


Theoretical massNumber of molelcules
Total (without water)122,5498
Polymers122,5498
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area18250 Å2
ΔGint-62 kcal/mol
Surface area38040 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-22 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.540, 74.540, 239.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Antibody single domain antibody VHH


Mass: 14270.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Gene: single domain antibody VHH / Plasmid: pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
#2: Protein RNA-editing complex protein MP42


Mass: 16889.070 Da / Num. of mol.: 1 / Fragment: UNP residues 247-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: KREPA3, Tb927.8.620 / Plasmid: pACYC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q95W13
#3: Protein MP18 RNA editing complex protein


Mass: 15843.716 Da / Num. of mol.: 1 / Fragment: UNP residues 20-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: KREPA6, Tb10.70.2090 / Plasmid: pACYC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q38B90
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 10% 2-propanol, 22% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.9792, 0.9794, 0.9116
2
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELJan 1, 2010Rh coated
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Liquid nitrogen-cooled double crystalMADMx-ray1
2Liquid nitrogen-cooled double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.91161
ReflectionResolution: 2.5→54.53 Å / Num. all: 232692 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 17.49
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2.333 / Rsym value: 0.361 / % possible all: 77.3

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALAdata scaling
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 2.5→54.53 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 21.425 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1244 5.1 %RANDOM
Rwork0.19891 ---
obs0.20069 23086 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.521 Å2
Baniso -1Baniso -2Baniso -3
1-3.5 Å20 Å20 Å2
2--3.5 Å20 Å2
3----7.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→54.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3593 0 0 59 3652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023673
X-RAY DIFFRACTIONr_bond_other_d0.0010.022458
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.944987
X-RAY DIFFRACTIONr_angle_other_deg0.8393.0015963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65123.636165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75515570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.451525
X-RAY DIFFRACTIONr_chiral_restr0.0810.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214152
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02777
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 91 -
Rwork0.373 1478 -
obs--99.94 %
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)
13.26791.41380.30692.6303-0.8216.4166-0.32160.14850.0772-0.4340.182-0.011-0.0749-0.15070.13970.3326-0.09630.0080.51760.02910.1558-0.4488-0.902214.9919
24.89341.51.44372.45951.32595.8554-0.1041-0.04790.0720.0005-0.05670.09130.0902-0.04930.16080.0455-0.00190.06740.3361-0.03450.1588-21.1618-17.365731.3578
312.3923-8.5514-11.167524.501117.040514.7557-1.9415-2.4388-1.53690.07711.6534-1.50181.19572.03080.28810.9580.310.32421.2280.45270.83617.7028-4.461754.178
48.57970.91551.292924.50381.63424.12780.1682-0.29790.12150.1695-0.1361.4922-0.2746-0.8429-0.03220.2230.05990.04520.7314-0.00650.1002-14.7789-6.4451.2246
54.89432.2899-1.28317.4936-2.40685.7335-0.11940.10.5631-0.26250.18610.3583-0.3753-0.4555-0.06670.22570.0734-0.05050.6127-0.13720.1202-10.86120.048246.5808
62.2878-0.4862-0.9594.03262.70056.2388-0.1289-0.53950.08890.76580.08290.14550.2231-0.17640.0460.18790.002-0.01480.5584-0.00680.2275-9.1037-6.898550.2567
74.5466-0.4463-0.15712.888-2.79382.8374-0.0968-0.6140.09210.0129-0.154-0.2952-0.12340.37330.25070.4021-0.1709-0.0640.5658-0.13670.22016.40863.624741.9903
83.86070.7638-0.846314.3553-2.00472.59240.0372-0.10580.02260.6325-0.1731-0.1823-0.67450.43180.13590.2219-0.0884-0.09590.5845-0.11650.13756.49790.900841.6294
96.1055-0.0940.49936.1062-1.01282.3707-0.19740.70060.68790.10330.0247-0.2816-0.61160.31010.17270.4242-0.0667-0.02810.6621-0.08040.16726.42775.214240.7717
103.85992.34413.03044.10120.80334.5453-0.3602-0.25380.70070.066-0.15830.1959-0.84250.09240.51850.3195-0.00130.04690.615-0.0910.242-0.11343.87639.167
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 128
2X-RAY DIFFRACTION2B3 - 128
3X-RAY DIFFRACTION3C283 - 292
4X-RAY DIFFRACTION4C293 - 307
5X-RAY DIFFRACTION5C308 - 338
6X-RAY DIFFRACTION6C339 - 393
7X-RAY DIFFRACTION7D20 - 38
8X-RAY DIFFRACTION8D39 - 81
9X-RAY DIFFRACTION9D82 - 106
10X-RAY DIFFRACTION10D107 - 132

+
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