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- PDB-4peh: Dbr1 in complex with synthetic linear RNA -

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Basic information

Entry
Database: PDB / ID: 4peh
TitleDbr1 in complex with synthetic linear RNA
Components
  • RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')
  • RNA lariat debranching enzyme, putative
KeywordsHYDROLASE/RNA / NUCLEASE / PHOSPHODIESTERASE / METALLOHYDROLASE / METALLOPHOSPHOESTERASE / LARIAT RNA / HYDROLASE / METALLOENZYME / HYDROLASE-RNA complex
Function / homology
Function and homology information


RNA lariat debranching enzyme activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / RNA splicing, via transesterification reactions / mRNA splicing, via spliceosome / manganese ion binding / iron ion binding / perinuclear region of cytoplasm / RNA binding / zinc ion binding / nucleus
Similarity search - Function
Lariat debranching enzyme, N-terminal metallophosphatase domain / : / Dbr1, C-terminal domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / RNA / Lariat debranching enzyme
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMontemayor, E.J. / Katolik, A. / Clark, N.E. / Taylor, A.B. / Schuermann, J.P. / Combs, D.J. / Johnsson, R. / Holloway, S.P. / Stevens, S.W. / Damha, M.J. / Hart, P.J.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural basis of lariat RNA recognition by the intron debranching enzyme Dbr1.
Authors: Montemayor, E.J. / Katolik, A. / Clark, N.E. / Taylor, A.B. / Schuermann, J.P. / Combs, D.J. / Johnsson, R. / Holloway, S.P. / Stevens, S.W. / Damha, M.J. / Hart, P.J.
History
DepositionApr 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / refine_hist / struct_conn / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA lariat debranching enzyme, putative
V: RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')
B: RNA lariat debranching enzyme, putative
W: RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')
C: RNA lariat debranching enzyme, putative
X: RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')
D: RNA lariat debranching enzyme, putative
Y: RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')
E: RNA lariat debranching enzyme, putative
Z: RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,46324
Polymers217,32810
Non-polymers1,13514
Water18,1411007
1
A: RNA lariat debranching enzyme, putative
V: RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7095
Polymers43,4662
Non-polymers2433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA lariat debranching enzyme, putative
W: RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7135
Polymers43,4662
Non-polymers2473
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA lariat debranching enzyme, putative
X: RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8096
Polymers43,4662
Non-polymers3434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA lariat debranching enzyme, putative
Y: RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6174
Polymers43,4662
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RNA lariat debranching enzyme, putative
Z: RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6174
Polymers43,4662
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.021, 141.936, 212.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / RNA chain , 2 types, 10 molecules ABCDEVWXYZ

#1: Protein
RNA lariat debranching enzyme, putative


Mass: 41197.199 Da / Num. of mol.: 5 / Mutation: C14S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_062730 / Plasmid: YEp351 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: C4M1P9
#2: RNA chain
RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')


Mass: 2268.375 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 1021 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1007 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M lithium sulfate, 0.1 M bis-tris, 25% PEG 3350, 8.5 % glycerol, 3.0 mM manganese sulfate, 1.45 mM AK65

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→47.98 Å / Num. obs: 129196 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 36.6 Å2 / Rsym value: 0.081 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.8 / % possible all: 99.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39.033 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 6446 4.99 %
Rwork0.2034 --
obs0.2056 129111 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14285 397 51 1007 15740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515176
X-RAY DIFFRACTIONf_angle_d0.90720605
X-RAY DIFFRACTIONf_dihedral_angle_d14.1165656
X-RAY DIFFRACTIONf_chiral_restr0.0642176
X-RAY DIFFRACTIONf_plane_restr0.0042516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.11730.34161800.28413338X-RAY DIFFRACTION82
2.1173-2.14220.3332130.27734069X-RAY DIFFRACTION99
2.1422-2.16830.32132150.26144063X-RAY DIFFRACTION99
2.1683-2.19580.29991870.25324107X-RAY DIFFRACTION99
2.1958-2.22470.30232350.24894036X-RAY DIFFRACTION99
2.2247-2.25510.29392070.25774071X-RAY DIFFRACTION99
2.2551-2.28730.2922030.25164133X-RAY DIFFRACTION99
2.2873-2.32150.30482270.24894015X-RAY DIFFRACTION100
2.3215-2.35780.31672230.2434120X-RAY DIFFRACTION99
2.3578-2.39640.32922090.24384080X-RAY DIFFRACTION99
2.3964-2.43770.32592280.24854072X-RAY DIFFRACTION99
2.4377-2.4820.31182320.24484065X-RAY DIFFRACTION100
2.482-2.52980.281880.23954129X-RAY DIFFRACTION100
2.5298-2.58140.28362270.22854061X-RAY DIFFRACTION99
2.5814-2.63750.29052090.22144118X-RAY DIFFRACTION100
2.6375-2.69890.2822090.22594112X-RAY DIFFRACTION100
2.6989-2.76630.29332080.23064100X-RAY DIFFRACTION100
2.7663-2.84110.28522440.2314096X-RAY DIFFRACTION99
2.8411-2.92470.27312270.22264103X-RAY DIFFRACTION100
2.9247-3.0190.28132070.21594111X-RAY DIFFRACTION99
3.019-3.12690.24912080.21224124X-RAY DIFFRACTION99
3.1269-3.2520.23462150.20694101X-RAY DIFFRACTION99
3.252-3.40.2572090.19824139X-RAY DIFFRACTION99
3.4-3.57910.25952080.20044121X-RAY DIFFRACTION99
3.5791-3.80320.21412130.19014148X-RAY DIFFRACTION99
3.8032-4.09650.20982340.17384117X-RAY DIFFRACTION99
4.0965-4.50820.17762260.16454114X-RAY DIFFRACTION98
4.5082-5.15930.20112190.15834154X-RAY DIFFRACTION98
5.1593-6.49530.23472010.18684258X-RAY DIFFRACTION99
6.4953-39.04010.2022350.17924390X-RAY DIFFRACTION99

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