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- PDB-4jkf: Open and closed forms of T1791P+R1865A human PRP8 RNase H-like do... -

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Basic information

Entry
Database: PDB / ID: 4jkf
TitleOpen and closed forms of T1791P+R1865A human PRP8 RNase H-like domain with bound Mg ion
ComponentsPre-mRNA-processing-splicing factor 8
KeywordsRNA BINDING PROTEIN / metalloprotein / conformational change
Function / homology
Function and homology information


RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding ...RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / mRNA processing / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / nuclear speck / RNA binding / nucleoplasm / nucleus / membrane
Similarity search - Function
Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding ...Prp8 RNase H domain, fingers region / Prp8 RNase H domain, palm region / Acyl-CoA Binding Protein / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H-like superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Pre-mRNA-processing-splicing factor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSchellenberg, M.J. / Wu, T. / Ritchie, D.B. / Atta, K.A. / MacMillan, A.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: A conformational switch in PRP8 mediates metal ion coordination that promotes pre-mRNA exon ligation.
Authors: Schellenberg, M.J. / Wu, T. / Ritchie, D.B. / Fica, S. / Staley, J.P. / Atta, K.A. / Lapointe, P. / Macmillan, A.M.
History
DepositionMar 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Sep 20, 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_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_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_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_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: Pre-mRNA-processing-splicing factor 8
B: Pre-mRNA-processing-splicing factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9223
Polymers50,8972
Non-polymers241
Water7,819434
1
A: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)25,4491
Polymers25,4491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pre-mRNA-processing-splicing factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4732
Polymers25,4491
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.171, 77.253, 93.601
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 25448.682 Da / Num. of mol.: 2 / Fragment: PRP8 RNase H-like domain, UNP residues 1769-1990' / Mutation: T1791P R1865A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRP8, PRPC8, PRPF8 / Plasmid: pMalC2-E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta2 / References: UniProt: Q6P2Q9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 15% PEG 4000, 300mM MgCl2, 100mM Tris, pH 7.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 38416 / % possible obs: 94.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.054 / Χ2: 1.02 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.024.10.52840051.006199.8
2.02-2.140.34640001.141199.7
2.1-2.24.10.23940121.06199.9
2.2-2.313.80.21524941.041161.9
2.31-2.464.10.11740430.9771100
2.46-2.654.10.08940300.9831100
2.65-2.914.10.05740550.998199.9
2.91-3.334.10.04340870.996199.8
3.33-4.23.80.0434200.997182.8
4.2-503.90.01842701.008198.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
REFMAC5.6.0117phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ENB

3enb


Resolution: 1.95→40.03 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2115 / WRfactor Rwork: 0.1745 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8293 / SU B: 3.988 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1665 / SU Rfree: 0.1515 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2016 5.3 %RANDOM
Rwork0.1865 ---
obs0.1886 38311 93.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.7 Å2 / Biso mean: 32.0608 Å2 / Biso min: 14.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 1 434 3925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023605
X-RAY DIFFRACTIONr_bond_other_d0.0010.023685
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9664908
X-RAY DIFFRACTIONr_angle_other_deg0.76138415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.27424.57151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89315664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4651516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02788
LS refinement shellResolution: 1.95→2.004 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 147 -
Rwork0.321 2544 -
all-2691 -
obs--97.08 %

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