[English] 日本語
Yorodumi
- PDB-1q8y: The structure of the yeast SR protein kinase, Sky1p, with bound ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q8y
TitleThe structure of the yeast SR protein kinase, Sky1p, with bound ADP
ComponentsSR protein kinase
KeywordsTRANSFERASE / protein kinase
Function / homology
Function and homology information


intracellular monoatomic cation homeostasis / intracellular monoatomic ion homeostasis / regulation of mRNA processing / mRNA splice site recognition / stress granule disassembly / regulation of cell size / spliceosomal complex assembly / positive regulation of protein import into nucleus / cytoplasmic stress granule / non-specific serine/threonine protein kinase ...intracellular monoatomic cation homeostasis / intracellular monoatomic ion homeostasis / regulation of mRNA processing / mRNA splice site recognition / stress granule disassembly / regulation of cell size / spliceosomal complex assembly / positive regulation of protein import into nucleus / cytoplasmic stress granule / non-specific serine/threonine protein kinase / protein kinase activity / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENINE / ADENOSINE-5'-DIPHOSPHATE / Serine/threonine-protein kinase SKY1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsNolen, B. / Ngo, J. / Chakrabarti, S. / Vu, D. / Adams, J.A. / Ghosh, G.
CitationJournal: Biochemistry / Year: 2003
Title: Nucleotide-Induced Conformational Changes in the Saccharomyces cerevisiae SR Protein Kinase, Sky1p, Revealed by X-Ray Crystallography
Authors: Nolen, B. / Ngo, J. / Chakrabarti, S. / Vu, D. / Adams, J.A. / Ghosh, G.
History
DepositionAug 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE 137 amino acids truncated from N-terminus, RESIDUES 305-538 WERE DELETED AND REPLACED WITH VAL-ASP

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SR protein kinase
B: SR protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,40513
Polymers86,0502
Non-polymers1,35511
Water4,720262
1
A: SR protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7656
Polymers43,0251
Non-polymers7405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SR protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6417
Polymers43,0251
Non-polymers6156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.577, 88.653, 133.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein SR protein kinase


Mass: 43025.066 Da / Num. of mol.: 2 / Fragment: Sky1pdeltaN(137)deltaS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SKY1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLyS
References: UniProt: Q03656, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

-
Non-polymers , 5 types, 273 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 50.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.5M (NH4)2SO4, 100mM NaAcetate pH 4.5, 15% Ethylene Glycol. Crystals then dialyzed into 30% PEG 400 and 100mM NaAcetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Nolen, B., (2001) Nat.Struct.Biol., 8, 176.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
20.0066 mMATP1drop
30.0017 mM1dropMg2+
41.5 Mammonium sulfate1reservoir
515 %(v/v)ethylene glycol1reservoir
610 mMsodium acetate1reservoir

-
Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.54 Å
DetectorType: SBC-2 / Detector: CCD / Date: Nov 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→39.84 Å / Num. all: 54358 / Num. obs: 53312 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 9.7 Å2 / Limit h max: 34 / Limit h min: 0 / Limit k max: 43 / Limit k min: 0 / Limit l max: 65 / Limit l min: 0 / Observed criterion F max: 291752.06 / Observed criterion F min: 1.049
Reflection shellResolution: 2.05→2.15 Å / % possible all: 93.7
Reflection
*PLUS
Num. obs: 50520 / Num. measured all: 298198 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.2

-
Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
XTALVIEWrefinement
RefinementResolution: 2.05→19.92 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2337 5 %RANDOM
Rwork0.209 ---
all-54083 --
obs-47002 86.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 44.9792 Å2 / ksol: 0.372062 e/Å3
Displacement parametersBiso max: 84.01 Å2 / Biso mean: 27.08 Å2 / Biso min: 9.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2---3.63 Å20 Å2
3---2.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Luzzati d res high-2.05
Refinement stepCycle: LAST / Resolution: 2.05→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5702 0 78 262 6042
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_torsion_deg21.9
X-RAY DIFFRACTIONc_torsion_impr_deg0.74
LS refinement shellResolution: 2.05→2.14 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.261 230 5.1 %
Rwork0.212 4314 -
all-6681 -
obs-4544 93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ligand_2.paramligand_2.top
X-RAY DIFFRACTION4ion.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 37868 / % reflection Rfree: 5 % / Rfactor Rfree: 0.2446 / Rfactor Rwork: 0.2102
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.26

+
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