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- PDB-4dk3: Structure of Editosome protein -

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Basic information

Entry
Database: PDB / ID: 4dk3
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 / zinc ion binding
Similarity search - Function
RNA editing complex, structural subunit MP81 / Zinc finger C2H2 type domain profile. / Nucleic acid-binding proteins / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like ...RNA editing complex, structural subunit MP81 / Zinc finger C2H2 type domain profile. / Nucleic acid-binding proteins / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / 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: 2.76 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 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
1
A: 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 area1360 Å2
ΔGint-9 kcal/mol
Surface area11440 Å2
MethodPISA
2
B: 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
crystal symmetry operation4_555x,-y,-z1
Buried area1400 Å2
ΔGint-9 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.790, 105.310, 94.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.05 M ammonium sulfate, 0.05M sodium acetate trihydrate, 30% w/v PEG 2000 MME, 5% v/v jeffamine M600, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / 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: 2.75→94.03 Å / Num. obs: 12360 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.75-2.85.20.484193.7
2.8-2.855.80.483197.5
2.85-2.96.60.468199.3
2.9-2.9670.4111100
2.96-3.037.30.3281100
3.03-3.17.30.2591100
3.1-3.177.40.251100
3.17-3.267.30.2141100
3.26-3.367.30.1691100
3.36-3.467.30.151100
3.46-3.597.40.131100
3.59-3.737.30.1131100
3.73-3.97.40.1051100
3.9-4.117.20.0891100
4.11-4.367.20.0821100
4.36-4.77.20.0831100
4.7-5.177.10.0831100
5.17-5.9270.0821100
5.92-7.466.80.0661100
7.46-506.40.056199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.65 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.76 Å45.94 Å
Translation2.76 Å45.94 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→94.03 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.889 / Occupancy max: 1 / Occupancy min: 1 / SU B: 38.423 / SU ML: 0.334 / SU R Cruickshank DPI: 0.7969 / Cross valid method: THROUGHOUT / ESU R: 0.805 / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 601 4.9 %RANDOM
Rwork0.22428 ---
obs0.2264 11720 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.269 Å2
Baniso -1Baniso -2Baniso -3
1--3.08 Å20 Å20 Å2
2--3.63 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.76→94.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 0 0 3238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193285
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9171.9434424
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.945405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79923.243148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73215567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7771528
X-RAY DIFFRACTIONr_chiral_restr0.0620.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022430
X-RAY DIFFRACTIONr_gen_planes_other
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: 2.76→2.833 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 35 -
Rwork0.337 652 -
obs--78.87 %
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)
15.39730.1005-1.41723.9658-1.52816.138-0.0232-0.07750.45350.16560.10960.1674-0.3202-0.2404-0.08640.12020.04520.00410.0263-0.00970.0518-12.961610.7283-42.8275
25.12550.5461-4.26883.2355-2.04627.8866-0.03170.090.43850.06730.24610.2785-0.2068-0.4256-0.21440.20330.12850.00140.0990.01590.0777-14.604713.9187-43.7487
37.61271.09150.03764.4174-1.23457.38190.1592-0.122-0.3724-0.21020.0232-0.48540.14520.3414-0.18240.135-0.00870.03730.3254-0.09790.2455-12.661115.82371.8137
46.86033.382-2.90774.6282-3.25989.18260.2096-0.03840.1594-0.51410.4122-0.13730.04630.2545-0.62190.1848-0.01360.02840.4524-0.03640.3123-15.442218.92870.4907
513.20881.5808-4.05076.2523-2.69148.6349-0.06870.12650.16790.09540.25530.7928-0.506-1.0602-0.18660.26280.25310.20650.30210.21370.3906-33.497910.0576-28.3106
67.0793-5.57191.476112.00321.2794.29190.12830.2062-0.5199-0.35950.10840.6991-0.0864-0.0967-0.23670.34860.14830.29550.55370.29760.4526-33.56454.571-26.6515
75.4242-2.06582.40226.5559-2.95266.53930.19280.0838-0.02250.40610.62480.7708-0.2291-1.0003-0.81760.16210.08680.16820.5740.41030.6185-34.9051-9.4722-11.5887
84.41891.1391-4.02328.255-3.50647.81720.343-0.21880.36250.44140.48390.7511-0.8466-0.5879-0.82690.33990.24010.07890.62280.35420.463-33.2556-3.0086-14.5488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 78
2X-RAY DIFFRACTION2A79 - 127
3X-RAY DIFFRACTION3B1 - 81
4X-RAY DIFFRACTION4B82 - 127
5X-RAY DIFFRACTION5C627 - 716
6X-RAY DIFFRACTION6C717 - 761
7X-RAY DIFFRACTION7D627 - 719
8X-RAY DIFFRACTION8D720 - 762

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