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- PDB-4dka: Structure of Editosome protein -

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Basic information

Entry
Database: PDB / ID: 4dka
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: 1.97 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8066
Polymers50,7604
Non-polymers462
Water4,288238
1
A: single domain antibody VHH
D: RNA-editing complex protein MP81
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4033
Polymers25,3802
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-22 kcal/mol
Surface area10720 Å2
MethodPISA
2
B: single domain antibody VHH
hetero molecules

C: RNA-editing complex protein MP81


Theoretical massNumber of molelcules
Total (without water)25,4033
Polymers25,3802
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x+1/2,y-1/2,-z1
Buried area1620 Å2
ΔGint-21 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.653, 105.912, 40.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-381-

HOH

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Components

#1: Antibody single domain antibody VHH


Mass: 13940.430 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
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.39 %
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, 0.2 M sodium thiocyanate, 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: 8.2.1 / Wavelength: 0.9999 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: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.97→105.91 Å / Num. obs: 31254 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.366
Reflection shellResolution: 1.97→2.03 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.333 / Num. unique all: 1496 / % possible all: 95.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.06 Å
Translation2.5 Å47.06 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3K7U

3k7u


Resolution: 1.97→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2452 / WRfactor Rwork: 0.1974 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.862 / SU B: 7.138 / SU ML: 0.103 / SU R Cruickshank DPI: 0.1349 / SU Rfree: 0.1593 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 1587 5.1 %RANDOM
Rwork0.1868 ---
obs0.189 31254 97.9 %-
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: 99.34 Å2 / Biso mean: 33.9452 Å2 / Biso min: 13.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2---0.54 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 2 238 3511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193323
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.9444480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5275414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50623.377151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73615573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8071528
X-RAY DIFFRACTIONr_chiral_restr0.0640.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022474
X-RAY DIFFRACTIONr_rigid_bond_restr2.44233319
X-RAY DIFFRACTIONr_sphericity_bonded14.93853270
LS refinement shellResolution: 1.97→2.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 93 -
Rwork0.19 1629 -
all-1722 -
obs--78.27 %
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)
10.5352-0.09720.29190.29420.21120.5115-0.0045-0.0090.00970.01870.0381-0.04320.00350.0414-0.03360.03360.01030.00150.0407-0.00610.039637.33537.87982.9534
20.1322-0.1294-0.10050.40920.15690.40690.0004-0.01090.00420.00530.014-0.0016-0.0351-0.0054-0.01440.0484-0.0012-0.00060.03480.00260.03131.2688-20.4987-5.7396
31.1318-0.6061-0.69360.40830.12281.1772-0.03830.0214-0.10470.02890.00580.0641-0.0226-0.07280.03260.02870.00680.00320.019-0.00310.04554.975416.71915.2556
44.0804-1.67070.66032.84341.01712.9995-0.1384-0.1048-0.05990.11520.03520.2167-0.0498-0.23340.10320.03770.00650.01370.02910.01320.05253.807117.285822.2667
51.7111-0.1188-0.24930.543-0.00760.17420.03180.0695-0.07130.0041-0.00440.08950.0009-0.0079-0.02740.0460.0038-0.00450.04950.00940.028310.317513.56919.7308
610.4409-1.11641.78540.69340.13260.8706-0.0125-0.0009-0.3899-0.0248-0.00370.1647-0.0288-0.08560.01620.0465-0.0025-0.00570.03330.00030.04717.258310.799618.8812
72.28280.03852.72071.8031-0.82163.66750.0790.1504-0.0179-0.44020.20840.61980.27540.0676-0.28750.1376-0.0066-0.18110.08350.01080.28629.3841-1.788-11.5068
80.7618-0.33680.34480.78090.13881.44340.0257-0.0379-0.0764-0.05670.00630.05820.0665-0.025-0.0320.02050.0139-0.00110.02120.00440.049417.41631.845-4.5392
90.09140.1045-0.01793.0535-0.94180.30060.0241-0.0034-0.02770.00090.02860.133-0.00740.0027-0.05270.03610.0016-0.00240.0528-0.00910.022215.92038.1963-9.9277
101.44280.8714-0.27496.165-2.23540.81340.0528-0.0467-0.1252-0.01810.11210.45820.006-0.0376-0.1650.0337-0.0018-0.01130.06010.01360.071310.78743.8788-6.7401
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 127
2X-RAY DIFFRACTION2B1 - 127
3X-RAY DIFFRACTION3C627 - 653
4X-RAY DIFFRACTION4C654 - 717
5X-RAY DIFFRACTION5C718 - 741
6X-RAY DIFFRACTION6C742 - 761
7X-RAY DIFFRACTION7D627 - 636
8X-RAY DIFFRACTION8D637 - 718
9X-RAY DIFFRACTION9D719 - 742
10X-RAY DIFFRACTION10D743 - 762

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