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- PDB-6nqi: Prp8 RH domain from C. merolae -

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Basic information

Entry
Database: PDB / ID: 6nqi
TitlePrp8 RH domain from C. merolae
ComponentsPre-mRNA splicing factor PRP8
KeywordsSPLICING / Spliceosome / RNase H
Function / homology
Function and homology information


U5 snRNA binding / U6 snRNA binding / spliceosomal complex / mRNA splicing, via spliceosome
Similarity search - Function
Prp8 RNase H domain, palm region / 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 ...Prp8 RNase H domain, palm region / 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 / Nucleotidyltransferase; domain 5 / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Pre-mRNA splicing factor PRP8
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsGarside, E.L. / MacMillan, A.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Prp8 in a Reduced Spliceosome Lacks a Conserved Toggle that Correlates with Splicing Complexity across Diverse Taxa.
Authors: Garside, E.L. / Whelan, T.A. / Stark, M.R. / Rader, S.D. / Fast, N.M. / MacMillan, A.M.
History
DepositionJan 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA splicing factor PRP8
B: Pre-mRNA splicing factor PRP8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7874
Polymers49,6312
Non-polymers1562
Water0
1
A: Pre-mRNA splicing factor PRP8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8942
Polymers24,8161
Non-polymers781
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pre-mRNA splicing factor PRP8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8942
Polymers24,8161
Non-polymers781
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.516, 67.508, 58.859
Angle α, β, γ (deg.)90.000, 101.640, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1853 through 1897 or resid 1902 through 2025 or resid 2041 through 2058))
21chain B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLYGLY(chain A and (resid 1853 through 1897 or resid 1902 through 2025 or resid 2041 through 2058))AA1853 - 18976 - 50
12ALAALATRPTRP(chain A and (resid 1853 through 1897 or resid 1902 through 2025 or resid 2041 through 2058))AA1902 - 202555 - 178
13TRPTRPLEULEU(chain A and (resid 1853 through 1897 or resid 1902 through 2025 or resid 2041 through 2058))AA2041 - 2058194 - 211
21LEULEULEULEUchain BBB1853 - 20586 - 211

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Components

#1: Protein Pre-mRNA splicing factor PRP8


Mass: 24815.578 Da / Num. of mol.: 2 / Fragment: RH domain (UNP residues 1848-2065)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / Gene: CYME_CMH168C / Production host: Escherichia coli (E. coli) / References: UniProt: M1V7K2
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS

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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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, pH 8.5, 100-150 mM magnesium chloride, 10-12% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 14, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 15227 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 58.83 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.044 / Rrim(I) all: 0.109 / Χ2: 1.03 / Net I/σ(I): 9.7 / Num. measured all: 97205
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.5-2.575.711160.8620.4970.87495.6
2.57-2.646.411500.9450.3550.9911000.8440.917
2.64-2.736.311710.9320.3131.0791000.7320.797
2.73-2.836.511810.9730.2251.0341000.5350.581
2.83-2.946.511750.9670.1841.0251000.440.478
2.94-3.076.511670.9840.1331.031000.3180.346
3.07-3.236.611570.9910.0851.0161000.2040.222
3.23-3.446.511780.9930.0630.9941000.150.163
3.44-3.7611670.9830.0741.08899.70.1680.184
3.7-4.086.411810.9920.0491.0791000.1160.126
4.08-4.666.611770.9970.0291.0821000.0690.075
4.66-5.886.511980.9980.0231.0691000.0540.058
5.88-506.412090.9990.0181.00899.30.0420.046

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.49 Å36.42 Å
Translation2.49 Å36.42 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4JK7

4jk7


Resolution: 2.75→36.425 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 562 4.94 %
Rwork0.2116 10808 -
obs0.2143 11370 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.32 Å2 / Biso mean: 77.9701 Å2 / Biso min: 30.96 Å2
Refinement stepCycle: final / Resolution: 2.75→36.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 8 0 3135
Biso mean--55 --
Num. residues----383
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1749X-RAY DIFFRACTION10.456TORSIONAL
12B1749X-RAY DIFFRACTION10.456TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7501-3.02670.36031300.268726812811100
3.0267-3.46440.32051430.26626952838100
3.4644-4.36360.30271380.22132682282099
4.3636-36.42770.20251510.174327502901100
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)
18.0205-2.4712-5.27215.88892.66295.41070.20651.82510.2358-1.15490.7296-0.6664-0.40950.2651-0.56180.6841-0.1805-0.07530.62840.06030.5123-31.0831-9.539-12.2735
26.3770.6920.1291.7847-1.33339.073-0.2223-0.37110.19250.08290.04010.17320.0863-0.70830.24320.3924-0.0024-0.07230.3149-0.04590.4237-30.922-11.10852.9704
38.20511.1095-0.15693.31280.667.3921-0.51620.54910.17690.04010.384-0.2349-0.36681.7921-0.00990.4972-0.0968-0.09720.61550.01150.497-15.6803-8.1518-7.5754
43.65320.04610.19820.2226-0.73114.0001-0.16181.72480.5343-0.01910.7177-0.2379-0.08451.5851-0.84210.8103-0.10580.1051.7434-0.03690.6856-9.5391-10.1468-20.8669
54.59851.47770.43084.7786-0.88411.0430.07940.1186-0.2101-0.0599-0.3240.1741-0.0059-1.7555-0.10670.4789-0.072-0.03211.2439-0.13930.505-37.6509-3.1773-38.156
60.90870.2073-0.01857.60652.9766.41690.276-0.19130.00630.2343-0.4251-0.02040.36-0.13460.22490.4155-0.12940.01670.84740.05230.4283-25.6944-6.3103-38.61
75.5549-3.7042-1.5154.36222.80662.9407-0.4282-0.7628-0.33841.6018-0.16451.20571.6204-0.9491-0.13240.2448-0.41680.14551.6653-0.2070.5195-39.3495-5.1702-30.948
81.34960.71750.83672.21473.33045.4068-0.14950.27310.3499-0.6413-0.67970.2987-1.3636-1.45870.8490.72390.1972-0.13541.1718-0.17970.6466-42.47637.6605-38.3959
95.0484-3.13424.1782.2459-1.6077.5531-0.0894-0.89950.1183-0.7232-0.2970.64190.099-2.71640.42530.6279-0.0975-0.02391.5559-0.28150.6366-47.94436.1424-27.1385
102.98214.2245-0.56256.7798-1.48150.91110.459-0.02681.59661.01330.77962.274-1.4255-2.00110.16290.77640.31410.1712.1788-0.46210.789-50.49212.5936-20.1129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1851 through 1862 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1863 through 1957 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1958 through 2047 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 2048 through 2059 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1853 through 1902 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1903 through 1952 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1953 through 1969 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1970 through 1998 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1999 through 2047 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 2048 through 2058 )B0

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