[English] 日本語
Yorodumi
- PDB-3enb: Crystal Structure of PRP8 core domain IV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3enb
TitleCrystal Structure of PRP8 core domain IV
ComponentsPre-mRNA-processing-splicing factor 8
KeywordsRNA BINDING PROTEIN / PRP8 domain IV / beta finger / RNase H / spliceosome / U5-220K / Disease mutation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / Retinitis pigmentosa / RNA-binding / Sensory transduction / Vision
Function / homology
Function and homology information


U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / 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 ...U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / 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 / membrane / nucleus
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 / MAD / Resolution: 1.85 Å
AuthorsSchellenberg, M.J. / Ritchie, D.B. / MacMillan, A.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural elucidation of a PRP8 core domain from the heart of the spliceosome.
Authors: Ritchie, D.B. / Schellenberg, M.J. / Gesner, E.M. / Raithatha, S.A. / Stuart, D.T. / Macmillan, A.M.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pre-mRNA-processing-splicing factor 8
B: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)51,0782
Polymers51,0782
Non-polymers00
Water6,828379
1
A: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)25,5391
Polymers25,5391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)25,5391
Polymers25,5391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.397, 78.062, 93.575
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 25538.787 Da / Num. of mol.: 2 / Fragment: UNP residues 1769-1990
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPF8, PRPC8 / Plasmid: pMALC2X / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6P2Q9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.5 M NaCl, 100 mM Tris-HCl pH 7.0, 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872, 0.9796, 1.0200, 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2006
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.1158721
20.97961
31.021
40.97971
ReflectionRedundancy: 2.9 % / Av σ(I) over netI: 27.88 / Number: 138717 / Rmerge(I) obs: 0.051 / Χ2: 1.01 / D res high: 2.3 Å / D res low: 100 Å / Num. obs: 47374 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.961009810.0281.0192.9
3.934.9699.510.031.0363
3.443.9399.710.0380.983
3.123.4499.610.051.0073
2.93.1299.610.0721.0353
2.732.999.510.0961.053
2.592.7399.210.1361.0183
2.482.599910.1870.9792.9
2.382.4898.610.2240.9642.9
2.32.389810.2640.9812.8
ReflectionResolution: 1.85→100 Å / Num. obs: 47833 / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.044 / Χ2: 1.023 / Net I/σ(I): 27.879
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.923.50.40846871.186199.6
1.92-1.993.90.29247401.121199.8
1.99-2.0840.19947001.062199.8
2.08-2.194.10.12347360.9931100
2.19-2.3340.11247321.017199.7
2.33-2.514.10.06747910.9441100
2.51-2.764.10.05347680.9471100
2.76-3.164.10.03748220.9631100
3.16-3.9940.02948431.045199.8
3.99-1003.80.02150140.994198.8

-
Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.36 Å / D res low: 30 Å / FOM : 0.47 / Reflection: 23362
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97963.85-8.32
13 wavelength21.020.54-2.84
13 wavelength30.97970.5-8.05
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se14.6310.8010.240.2160.629
2Se600.140.4940.1350.837
3Se600.160.5820.1860.761
4Se41.4410.1010.3240.030.711
Phasing MAD shell
Resolution (Å)FOM Reflection
8.39-300.691192
5.33-8.390.661961
4.18-5.330.582503
3.54-4.180.542884
3.13-3.540.513266
2.84-3.130.453565
2.61-2.840.383843
2.43-2.610.284148

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 1.85→59.98 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.294 / WRfactor Rwork: 0.242 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.854 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2414 5.1 %RANDOM
Rwork0.206 ---
obs0.208 47768 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.75 Å2 / Biso mean: 27.164 Å2 / Biso min: 12.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.85→59.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 0 379 3818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223520
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9634787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1625419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37124.564149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54515648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8051516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022554
X-RAY DIFFRACTIONr_nbd_refined0.20.21637
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2304
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.225
X-RAY DIFFRACTIONr_mcbond_it0.8761.52184
X-RAY DIFFRACTIONr_mcangle_it1.46423470
X-RAY DIFFRACTIONr_scbond_it2.13831534
X-RAY DIFFRACTIONr_scangle_it3.3344.51317
LS refinement shellResolution: 1.85→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 175 -
Rwork0.242 3013 -
all-3188 -
obs--97.03 %
Refinement TLS params.Method: refined / Origin x: 49.68 Å / Origin y: 2.484 Å / Origin z: 17.129 Å
111213212223313233
T0.3102 Å20.0043 Å20.0033 Å2-0.306 Å20.0008 Å2--0.3036 Å2
L0.1663 °20.079 °20.0273 °2-0.1702 °20.016 °2--0.1467 °2
S0.0034 Å °-0.0116 Å °-0.0001 Å °0.0063 Å °-0.0021 Å °0.0166 Å °0.0044 Å °-0.0164 Å °-0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1774 - 1988
2X-RAY DIFFRACTION1A1771 - 1989

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more