[English] 日本語
Yorodumi
- PDB-4ili: Crystal structure of an Aar2p S253E phosphomimetic mutant protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ili
TitleCrystal structure of an Aar2p S253E phosphomimetic mutant protein
ComponentsA1 cistron-splicing factor AAR2
KeywordsSPLICING / U5 snRNP assembly / Aar2 / Prp8
Function / homology
Function and homology information


spliceosomal tri-snRNP complex assembly / U5 snRNP / spliceosomal snRNP assembly / cytoplasm
Similarity search - Function
Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Aar2, C-terminal domain-like / 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 ...Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Aar2, C-terminal domain-like / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
A1 cistron-splicing factor AAR2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2046 Å
AuthorsWeber, G. / Heroven, C. / Santos, K.F. / Wahl, M.C.
CitationJournal: Genes Dev. / Year: 2013
Title: Structural basis for dual roles of Aar2p in U5 snRNP assembly.
Authors: Weber, G. / Cristao, V.F. / Santos, K.F. / Jovin, S.M. / Heroven, A.C. / Holton, N. / Luhrmann, R. / Beggs, J.D. / Wahl, M.C.
History
DepositionDec 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: A1 cistron-splicing factor AAR2
B: A1 cistron-splicing factor AAR2


Theoretical massNumber of molelcules
Total (without water)74,0992
Polymers74,0992
Non-polymers00
Water00
1
A: A1 cistron-splicing factor AAR2


Theoretical massNumber of molelcules
Total (without water)37,0501
Polymers37,0501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: A1 cistron-splicing factor AAR2


Theoretical massNumber of molelcules
Total (without water)37,0501
Polymers37,0501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.820, 62.820, 326.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein A1 cistron-splicing factor AAR2


Mass: 37049.664 Da / Num. of mol.: 2 / Mutation: S253E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: AAR2, YBL074C, YBL06.06, YBL0611 / Production host: Escherichia coli (E. coli) / References: UniProt: P32357
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.75
Details: 40 mM imidazole, pH 7.75, 0.95 M sodium potassium tartrate and 0.2 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 13, 2012
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 13156 / Num. obs: 13092 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.113 / Rsym value: 0.099 / Net I/σ(I): 14
Reflection shellResolution: 3.2→3.29 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 2 / Rsym value: 0.8 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SBT

3sbt


Resolution: 3.2046→45.259 Å / SU ML: 0.44 / σ(F): 1.99 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3054 663 5.06 %
Rwork0.2604 --
obs0.2627 13090 99.61 %
all-13156 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2046→45.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4831 0 0 0 4831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024960
X-RAY DIFFRACTIONf_angle_d0.5846699
X-RAY DIFFRACTIONf_dihedral_angle_d11.7321826
X-RAY DIFFRACTIONf_chiral_restr0.044695
X-RAY DIFFRACTIONf_plane_restr0.002865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2046-3.4520.37121270.32722392X-RAY DIFFRACTION99
3.452-3.79920.3361370.29222424X-RAY DIFFRACTION100
3.7992-4.34860.29961280.24912466X-RAY DIFFRACTION100
4.3486-5.47720.2811330.24392495X-RAY DIFFRACTION100
5.4772-45.26330.29011380.24642650X-RAY DIFFRACTION99
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)
13.7297-0.6684-2.50665.04232.03637.0976-0.4669-2.06340.19481.0064-0.24530.93180.4729-0.57780.62950.82530.13860.25881.7229-0.24141.0934-32.389118.546424.2596
22.64842.3966-3.02983.9616-2.01277.7350.21370.04110.4759-0.59390.07540.1742-0.7833-0.8145-0.32230.94260.4615-0.07580.9315-0.16861.1169-27.242327.64171.2404
37.60291.04520.10518.097-1.78734.8927-0.08460.13990.086-0.7504-0.1499-0.6505-0.3168-0.13370.21120.51030.22420.03020.4839-0.13150.569-13.443719.35223.9159
42.4087-3.5671.7438.5637-2.88065.42670.30931.1954-1.6814-0.4647-0.03290.12890.0979-0.4156-0.05270.64170.18690.14570.8121-0.14370.9631-11.58265.69760.6368
59.19981.3851-2.65893.5821-3.33493.5125-0.2822-0.34450.35660.2426-0.3207-1.5912-0.23841.18330.561.0634-0.039-0.00441.66820.00891.09223.583230.819229.3869
64.41362.6815-2.66337.9412-2.72822.93510.3427-0.0606-0.05580.2428-0.4036-0.0847-0.3171-0.04160.14121.0413-0.022-0.21.376-0.04670.8462-4.74530.074126.8335
73.04-1.3788-5.42150.49262.60489.33120.2609-0.9751-0.24550.4309-0.03680.1542-0.93730.7207-0.59081.19990.1445-0.02621.60450.01410.8959-13.718434.031952.7895
86.3018-0.2262-2.0555.787-2.20922.2484-0.8895-1.2395-0.97321.54670.72030.13820.47950.25490.35461.84480.51240.06871.81880.08480.8716-8.175119.972350.9351
97.67-1.0818-5.19292.8934-2.24656.65220.014-0.8908-1.99891.0517-1.9449-1.4812-0.7819-1.55472.0431.62010.17030.03162.87870.13041.7783-0.532915.042557.8055
105.79215.54265.46465.37825.22425.10121.3379-0.2479-2.2111-1.8535-2.4413-4.6735-0.3023-0.49341.4091.98830.2996-0.1942.3510.56532.31233.18479.107254.1233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:122)
2X-RAY DIFFRACTION2chain 'A' and (resseq 123:204)
3X-RAY DIFFRACTION3chain 'A' and (resseq 205:273)
4X-RAY DIFFRACTION4chain 'A' and (resseq 274:318)
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:55)
6X-RAY DIFFRACTION6chain 'B' and (resseq 56:122)
7X-RAY DIFFRACTION7chain 'B' and (resseq 123:217)
8X-RAY DIFFRACTION8chain 'B' and (resseq 218:273)
9X-RAY DIFFRACTION9chain 'B' and (resseq 274:302)
10X-RAY DIFFRACTION10chain 'B' and (resseq 303:316)

+
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