[English] 日本語
Yorodumi
- PDB-5r10: PanDDA analysis group deposition -- Auto-refined data of Aar2/RNa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5r10
TitlePanDDA analysis group deposition -- Auto-refined data of Aar2/RNaseH for ground state model 14, DMSO-free
Components
  • A1 cistron-splicing factor AAR2
  • Pre-mRNA-splicing factor 8
KeywordsSPLICING / FragMAX / FragMAXapp / fragment screening / RNaseH like domain / VHS like domain / U5 snRNP assembly
Function / homology
Function and homology information


generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding ...generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / mRNA binding / nucleus / cytoplasm
Similarity search - Function
Aar2, C-terminal domain-like / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / A1 cistron-splicing factor, AAR2 / AAR2, N-terminal / AAR2, C-terminal / AAR2, C-terminal domain superfamily / AAR2, N-terminal domain superfamily / AAR2 C-terminal repeat region / AAR2 N-terminal domain ...Aar2, C-terminal domain-like / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / A1 cistron-splicing factor, AAR2 / AAR2, N-terminal / AAR2, C-terminal / AAR2, C-terminal domain superfamily / AAR2, N-terminal domain superfamily / AAR2 C-terminal repeat region / AAR2 N-terminal domain / 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. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Ribonuclease H-like superfamily / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
A1 cistron-splicing factor AAR2 / Pre-mRNA-splicing factor 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsWollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G. / Weiss, M.S.
CitationJournal: Structure / Year: 2020
Title: F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening.
Authors: Wollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G. / Weiss, M.S.
History
DepositionFeb 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 10, 2021Group: Data collection
Category: diffrn_detector / diffrn_radiation / diffrn_source
Item: _diffrn_detector.pdbx_collection_date / _diffrn_detector.type ..._diffrn_detector.pdbx_collection_date / _diffrn_detector.type / _diffrn_radiation.monochromator / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.3Mar 6, 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-splicing factor 8
B: A1 cistron-splicing factor AAR2


Theoretical massNumber of molelcules
Total (without water)65,7112
Polymers65,7112
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.683, 82.655, 93.072
Angle α, β, γ (deg.)90.000, 107.990, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Pre-mRNA-splicing factor 8


Mass: 29501.113 Da / Num. of mol.: 1 / Fragment: yPrp8 RNaseH (UNP Residues 1836-2096)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Production host: Escherichia coli (E. coli) / References: UniProt: P33334
#2: Protein A1 cistron-splicing factor AAR2


Mass: 36209.836 Da / Num. of mol.: 1 / Fragment: GAMA - Aar2(1-152) - SSSSS - Aar2(171-317) / Mutation: L153_D170delinsSSSSS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: AAR2, YBL074C, YBL06.06, YBL0611 / Production host: Escherichia coli (E. coli) / References: UniProt: P32357
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.827 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.7→22.42 Å / Num. obs: 70265 / % possible obs: 99.7 % / Redundancy: 6.844 % / Biso Wilson estimate: 47.793 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.046 / Χ2: 1.057 / Net I/σ(I): 18.54 / Num. measured all: 481553
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obsCC1/2Rrim(I) allRejects% possible all
1.7-1.86.92.9470.527851211372112400.3233.185750.988
1.8-1.926.961.3421.237408810648106370.6891.451390.999
1.92-2.086.610.5642.9765907996899570.9190.612240.999
2.08-2.286.370.2366.9158288915191400.980.25710.999
2.28-2.547.260.11215.5160410831683060.9950.12100.999
2.54-2.947.140.05828.952136729772950.9990.06231
2.94-3.596.640.03149.4841451623862270.9990.03300.998
3.59-5.066.370.02268.5830822483848300.9990.02400.998
5.06-507.280.02578.5219939273827230.9990.02700.995

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMAC5.8.0238phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→22.42 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 2093 2.98 %
Rwork0.2035 68168 -
obs0.205 70265 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 284.34 Å2 / Biso mean: 74.696 Å2 / Biso min: 33.42 Å2
Refinement stepCycle: final / Resolution: 1.7→22.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 16 110 4528
Biso mean--95.1 52.85 -
Num. residues----537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.740.49891360.48714435457197
1.74-1.780.4941400.463745484688100
1.78-1.830.3931390.385645074646100
1.83-1.880.3881400.356445324672100
1.88-1.940.4031380.34345184656100
1.94-2.010.35271400.292445574697100
2.01-2.090.31391390.266545104649100
2.09-2.190.2931390.248145334672100
2.19-2.30.27291400.236845574697100
2.3-2.450.28871400.240745374677100
2.45-2.640.30671410.243945764717100
2.64-2.90.28831400.241545644704100
2.9-3.320.28531410.230345724713100
3.32-4.180.22761400.167145594699100
4.18-22.420.18991440.145946634807100
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)
12.1315-0.5988-0.280.36590.47361.39510.0460.0397-0.0941-0.0892-0.0919-0.0591-0.0532-0.04400.4291-0.01060.01840.37880.08660.413638.00847.998625.8288
21.3449-0.18960.61481.5255-0.33080.8288-0.01910.1685-0.1436-0.2731-0.0510.01660.1916-0.0834-00.48950.01970.00640.46310.04640.355428.076211.984320.931
31.3224-0.57010.25851.10650.31341.6801-0.0201-0.16480.23560.07590.0546-0.2129-0.05130.118-00.3755-0.0110.02450.43870.06450.476142.917916.69335.5371
40.7043-0.4654-0.01290.17160.05850.87020.1547-0.240.4175-0.0554-0.0045-0.2961-0.2140.3862-0.00020.4612-0.08190.02880.525-0.00150.647151.425324.751136.6444
50.6032-0.47980.44770.3387-0.28810.9917-0.08190.0870.064-0.2629-0.01550.10860.0805-0.12330.00010.5845-0.0047-0.05640.5151-0.10880.561411.963411.6588-29.7183
60.93380.40010.2811.02860.05582.3856-0.0354-0.07570.0314-0.3479-0.0790.33050.1382-0.455-0.00030.4406-0.0456-0.06610.5374-0.12370.53176.49137.3468-27.8154
70.13660.0587-0.03590.6720.56752.2636-0.0847-0.22270.11850.0593-0.12610.0765-0.0033-0.45140.00020.4811-0.0390.00080.5657-0.11840.460117.05854.5383-2.6667
80.6631-0.31780.37760.59230.96831.5732-0.0311-0.0870.0724-0.10770.0843-0.07280.26810.2566-0.00010.502-0.02260.01660.514-0.06360.477931.057-0.8595-10.89
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1833:1904)A1833 - 1904
2X-RAY DIFFRACTION2(chain A and resid 1905:1964)A1905 - 1964
3X-RAY DIFFRACTION3(chain A and resid 1965:2027)A1965 - 2027
4X-RAY DIFFRACTION4(chain A and resid 2028:2069)A2028 - 2069
5X-RAY DIFFRACTION5(chain B and resid 1:66)B1 - 66
6X-RAY DIFFRACTION6(chain B and resid 67:137)B67 - 137
7X-RAY DIFFRACTION7(chain B and resid 138:251)B138 - 251
8X-RAY DIFFRACTION8(chain B and resid 252:317)B252 - 317

+
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