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- PDB-5k77: Dbr1 in complex with 7-mer branched RNA -

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Basic information

Entry
Database: PDB / ID: 5k77
TitleDbr1 in complex with 7-mer branched RNA
Components
  • RNA lariat debranching enzyme, putative
  • branch 1 of branched RNA 5'-UAA(-2'GU)CA-3'
  • brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'
KeywordsHYDROLASE/RNA / metalloenzyme / complex / branched RNA / 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
: / HYDROXIDE ION / RNA / Lariat debranching enzyme
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.17 Å
AuthorsClark, N.E. / Taylor, A.B. / Hart, P.J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1.
Authors: Clark, N.E. / Katolik, A. / Roberts, K.M. / Taylor, A.B. / Holloway, S.P. / Schuermann, J.P. / Montemayor, E.J. / Stevens, S.W. / Fitzpatrick, P.F. / Damha, M.J. / Hart, P.J.
History
DepositionMay 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 27, 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_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
B: RNA lariat debranching enzyme, putative
C: RNA lariat debranching enzyme, putative
D: RNA lariat debranching enzyme, putative
E: RNA lariat debranching enzyme, putative
V: branch 1 of branched RNA 5'-UAA(-2'GU)CA-3'
v: brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'
W: branch 1 of branched RNA 5'-UAA(-2'GU)CA-3'
w: brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'
X: branch 1 of branched RNA 5'-UAA(-2'GU)CA-3'
x: brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'
Y: branch 1 of branched RNA 5'-UAA(-2'GU)CA-3'
y: brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'
Z: branch 1 of branched RNA 5'-UAA(-2'GU)CA-3'
z: brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,13055
Polymers220,03715
Non-polymers3,09340
Water9,332518
1
A: RNA lariat debranching enzyme, putative
V: branch 1 of branched RNA 5'-UAA(-2'GU)CA-3'
v: brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,62611
Polymers44,0073
Non-polymers6198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA lariat debranching enzyme, putative
W: branch 1 of branched RNA 5'-UAA(-2'GU)CA-3'
w: brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,53010
Polymers44,0073
Non-polymers5237
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA lariat debranching enzyme, putative
X: branch 1 of branched RNA 5'-UAA(-2'GU)CA-3'
x: brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,81813
Polymers44,0073
Non-polymers81110
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA lariat debranching enzyme, putative
Y: branch 1 of branched RNA 5'-UAA(-2'GU)CA-3'
y: brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,62611
Polymers44,0073
Non-polymers6198
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RNA lariat debranching enzyme, putative
Z: branch 1 of branched RNA 5'-UAA(-2'GU)CA-3'
z: brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,53010
Polymers44,0073
Non-polymers5237
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.151, 141.892, 212.511
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 , 1 types, 5 molecules ABCDE

#1: Protein
RNA lariat debranching enzyme, putative


Mass: 41846.934 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_062730 / Production host: Escherichia coli (E. coli) / References: UniProt: C4M1P9

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RNA chain , 2 types, 10 molecules VWXYZvwxyz

#2: RNA chain
branch 1 of branched RNA 5'-UAA(-2'GU)CA-3'


Mass: 1554.008 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: This is a 2' branched RNA 5'-UAA(-2'GU)CA-3' / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: RNA chain
brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'


Mass: 606.414 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: This is a 2' branched RNA 5'-UAA(-2'GU)CA-3' / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Non-polymers , 5 types, 558 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe
#6: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: HO
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, lithium sulfate, glycerol, bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.17→118.005 Å / Num. obs: 220944 / % possible obs: 99.7 % / Redundancy: 4.6 % / CC1/2: 0.984 / Rmerge(I) obs: 0.118 / Net I/σ(I): 10.5
Reflection shellResolution: 2.17→2.29 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4PEF

4pef


Resolution: 2.17→118.005 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 23.4
RfactorNum. reflection% reflection
Rfree0.2229 11066 5.01 %
Rwork0.1819 --
obs0.1839 220944 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.17→118.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14260 460 140 518 15378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215431
X-RAY DIFFRACTIONf_angle_d0.48421021
X-RAY DIFFRACTIONf_dihedral_angle_d11.099048
X-RAY DIFFRACTIONf_chiral_restr0.0432219
X-RAY DIFFRACTIONf_plane_restr0.0032555
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)
11.9717-0.3558-0.03411.77340.10871.2130.1012-0.11060.02270.0066-0.03620.08170.011-0.1484-0.06470.308-0.0296-0.00770.29920.01780.29760.6664-38.217-23.7944
21.8120.54730.20582.14630.04791.09240.1543-0.08090.11330.0788-0.1737-0.1543-0.16840.26890.02040.3258-0.0756-0.03110.38040.04120.231634.1763-68.1516-19.2762
31.09180.0413-0.25192.52820.96491.5877-0.05250.0763-0.06650.0196-0.05440.05990.07980.00210.10910.2216-0.0087-0.06580.24070.01260.25453.0229-88.84939.8645
41.89510.3973-1.09711.80170.06452.29910.09-0.22030.04950.17050.00850.1379-0.127-0.0098-0.08770.22-0.0060.02280.30130.02330.280941.6142-81.6626-65.2754
51.6309-0.26760.35512.6994-0.79652.8188-0.01680.07570.0259-0.3138-0.05790.26340.3521-0.27250.09490.29-0.0379-0.0170.2898-0.01460.2638.1596-95.3897-43.977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 511)
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 511)
3X-RAY DIFFRACTION3(chain 'C' and resid 5 through 511)
4X-RAY DIFFRACTION4(chain 'D' and resid 5 through 511)
5X-RAY DIFFRACTION5(chain 'E' and resid 5 through 511)

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