[English] 日本語
Yorodumi
- PDB-3wws: Crystal structure of Serine/threonine-protein kinase 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wws
TitleCrystal structure of Serine/threonine-protein kinase 3
Components(Serine/threonine-protein kinase 3Serine/threonine-specific protein kinase) x 2
KeywordsTRANSFERASE / WW45 / Hippo pathway / Homodimerization / Heterodomerization / SARAH domain / SAV1 / RASSF / LATS
Function / homology
Function and homology information


cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / protein localization to centrosome ...cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / protein localization to centrosome / organ growth / hepatocyte apoptotic process / regulation of MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of fat cell differentiation / canonical Wnt signaling pathway / JNK cascade / protein serine/threonine kinase activator activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / epithelial cell proliferation / central nervous system development / protein tetramerization / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / protein import into nucleus / negative regulation of epithelial cell proliferation / positive regulation of protein binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / magnesium ion binding / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53, subunit A / p53-like tetramerisation domain / p53-like tetramerisation domain superfamily / Few Secondary Structures / Irregular ...: / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53, subunit A / p53-like tetramerisation domain / p53-like tetramerisation domain superfamily / Few Secondary Structures / Irregular / 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
Similarity search - Domain/homology
Serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsLee, S.J. / Song, J. / Yamashita, E.
CitationJournal: To be Published
Title: Crystal structure of Serine/threonine-protein kinase 3
Authors: Lee, S.J. / Song, J. / Yamashita, E.
History
DepositionJun 27, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Structure summary

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase 3
D: Serine/threonine-protein kinase 3
C: Serine/threonine-protein kinase 3
B: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)24,6924
Polymers24,6924
Non-polymers00
Water64936
1
A: Serine/threonine-protein kinase 3
B: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)12,4172
Polymers12,4172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-32 kcal/mol
Surface area7200 Å2
MethodPISA
2
D: Serine/threonine-protein kinase 3
C: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)12,2752
Polymers12,2752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-31 kcal/mol
Surface area7490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.831, 32.678, 55.830
Angle α, β, γ (deg.)90.00, 109.63, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Serine/threonine-protein kinase 3 / Serine/threonine-specific protein kinase / Mammalian STE20-like protein kinase 2 / MST-2 / STE20-like kinase MST2 / Serine/threonine-protein ...Mammalian STE20-like protein kinase 2 / MST-2 / STE20-like kinase MST2 / Serine/threonine-protein kinase Krs-1 / Serine/threonine-protein kinase 3 36kDa subunit / MST2/N / Serine/threonine-protein kinase 3 20kDa subunit / MST2/C


Mass: 6279.653 Da / Num. of mol.: 1 / Fragment: UNP residues 436-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK3, KRS1, MST2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13188, non-specific serine/threonine protein kinase
#2: Protein/peptide Serine/threonine-protein kinase 3 / Serine/threonine-specific protein kinase / Mammalian STE20-like protein kinase 2 / MST-2 / STE20-like kinase MST2 / Serine/threonine-protein ...Mammalian STE20-like protein kinase 2 / MST-2 / STE20-like kinase MST2 / Serine/threonine-protein kinase Krs-1 / Serine/threonine-protein kinase 3 36kDa subunit / MST2/N / Serine/threonine-protein kinase 3 20kDa subunit / MST2/C


Mass: 6137.498 Da / Num. of mol.: 3 / Fragment: UNP residues 436-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK3, KRS1, MST2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13188, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M Tris-HCl pH 7.4. 10%(m/v) PEG3350, 0.1M (NH4)3PO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Apr 15, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→60.67 Å / Num. all: 49626 / Num. obs: 43771 / % possible obs: 58.55 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXAutoSolmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→60 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.895 / SU B: 11.634 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31141 736 5.1 %RANDOM
Rwork0.269 ---
obs0.27108 13815 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.248 Å2
Baniso -1Baniso -2Baniso -3
1--5.05 Å20 Å2-0.29 Å2
2--3.65 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.01→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 0 0 36 1681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221661
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.12.0172214
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6045194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22924.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23315357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8231520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211224
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7911.5992
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5521583
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6143669
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.184.5631
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.20631661
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.006→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 54 -
Rwork0.355 977 -
obs--94.07 %
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)
14.5109-0.23511.43430.1127-0.18830.66220.17-0.0339-0.24790.0004-0.03410.04710.00560.0795-0.13590.09280.01840.00160.0827-0.00790.076913.743919.151844.7861
28.7025-3.02450.65061.2043-0.23310.08950.16220.0838-0.3331-0.1417-0.06440.13750.02520.0334-0.09780.10230.0649-0.01630.0728-0.02750.119853.633911.247932.0475
310.5753-2.71540.80280.7647-0.17330.21630.1015-0.04260.7065-0.0653-0.0483-0.19170.019-0.0092-0.05320.04450.04610.02040.05580.01090.168163.892516.274932.3427
413.00880.34532.61570.12580.01850.5689-0.016-0.71560.31740.0603-0.0079-0.0013-0.0401-0.13670.02390.10120.03240.01170.1411-0.05890.06553.357923.305749.5093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A434 - 484
2X-RAY DIFFRACTION2D436 - 484
3X-RAY DIFFRACTION3C436 - 484
4X-RAY DIFFRACTION4B436 - 484

+
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