[English] 日本語
Yorodumi
- PDB-8p5l: Kinase domain of mutant human ULK1 in complex with compound MRT67307 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p5l
TitleKinase domain of mutant human ULK1 in complex with compound MRT67307
ComponentsSerine/threonine-protein kinase ULK1
KeywordsTRANSFERASE / Autophagy / Unc-like 1 kinase / KCGS
Function / homology
Function and homology information


neuron projection regeneration / omegasome membrane / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of autophagosome assembly / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / phagophore assembly site ...neuron projection regeneration / omegasome membrane / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of autophagosome assembly / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / phagophore assembly site / axon extension / TBC/RABGAPs / reticulophagy / response to starvation / Receptor Mediated Mitophagy / Macroautophagy / cellular response to stress / autophagosome membrane / autophagosome assembly / regulation of macroautophagy / negative regulation of protein-containing complex assembly / cellular response to nutrient levels / mitophagy / positive regulation of autophagy / autophagosome / macroautophagy / Regulation of TNFR1 signaling / recycling endosome / peptidyl-serine phosphorylation / small GTPase binding / autophagy / neuron projection development / intracellular protein localization / protein autophosphorylation / GTPase binding / mitochondrial outer membrane / protein phosphorylation / non-specific serine/threonine protein kinase / regulation of autophagy / axon / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex binding / signal transduction / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase, Ulk1/Ulk2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / : / Atg1-like, MIT domain 1 / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Serine/threonine-protein kinase, Ulk1/Ulk2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / : / Atg1-like, MIT domain 1 / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like / 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
Similarity search - Domain/homology
Chem-1FV / Serine/threonine-protein kinase ULK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.836 Å
AuthorsBattista, T. / Semrau, M.S. / Heroux, A. / Lolli, G. / Storici, P.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Crystal structures of ULK1 in complex with KCGS compounds
Authors: Battista, T. / Semrau, M.S. / Lolli, G. / Storici, P.
History
DepositionMay 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase ULK1
B: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2698
Polymers64,2422
Non-polymers1,0266
Water8,035446
1
A: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6344
Polymers32,1211
Non-polymers5133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6344
Polymers32,1211
Non-polymers5133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.600, 152.600, 206.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

-
Components

#1: Protein Serine/threonine-protein kinase ULK1 / Autophagy-related protein 1 homolog / ATG1 / hATG1 / Unc-51-like kinase 1


Mass: 32121.098 Da / Num. of mol.: 2 / Mutation: R245A, E246A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ULK1, KIAA0722 / Production host: Escherichia coli (E. coli)
References: UniProt: O75385, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-1FV / N-{3-[(5-cyclopropyl-2-{[3-(morpholin-4-ylmethyl)phenyl]amino}pyrimidin-4-yl)amino]propyl}cyclobutanecarboxamide / MRT67307


Mass: 464.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H36N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.79 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.3-0.8 M NaAcetate pH 6, 20-26% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.836→111.255 Å / Num. obs: 79997 / % possible obs: 99.5 % / Redundancy: 18.4 % / CC1/2: 1 / Net I/σ(I): 20.2
Reflection shellResolution: 1.836→1.867 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3987 / CC1/2: 0.81

-
Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.836→111.255 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.611 / SU ML: 0.075 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.101
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2113 4146 5.183 %
Rwork0.1756 75851 -
all0.177 --
obs-79997 99.545 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.223 Å2
Baniso -1Baniso -2Baniso -3
1--0.235 Å2-0.118 Å2-0 Å2
2---0.235 Å2-0 Å2
3---0.762 Å2
Refinement stepCycle: LAST / Resolution: 1.836→111.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 72 446 4814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124628
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164548
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.6556282
X-RAY DIFFRACTIONr_angle_other_deg0.5541.57810500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.457529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95610850
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.16510205
X-RAY DIFFRACTIONr_chiral_restr0.0830.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021074
X-RAY DIFFRACTIONr_nbd_refined0.2220.2890
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24011
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22224
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.2347
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0770.214
X-RAY DIFFRACTIONr_nbd_other0.1890.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0970.226
X-RAY DIFFRACTIONr_mcbond_it3.4493.1182203
X-RAY DIFFRACTIONr_mcbond_other3.4493.1182203
X-RAY DIFFRACTIONr_mcangle_it4.7615.5692761
X-RAY DIFFRACTIONr_mcangle_other4.765.5712762
X-RAY DIFFRACTIONr_scbond_it4.6843.6672425
X-RAY DIFFRACTIONr_scbond_other4.6833.6692426
X-RAY DIFFRACTIONr_scangle_it7.2126.4623486
X-RAY DIFFRACTIONr_scangle_other7.2116.4643487
X-RAY DIFFRACTIONr_lrange_it9.19530.2025263
X-RAY DIFFRACTIONr_lrange_other9.11929.2355121
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.836-1.8830.3143390.27955340.28158770.9380.9599.93190.263
1.883-1.9350.3952820.38352560.38457550.9050.90296.22940.363
1.935-1.9910.2713040.23453280.23656360.950.96399.9290.205
1.991-2.0520.252450.20251460.20553920.960.97399.98150.175
2.052-2.1190.2532740.23649650.23752830.9530.95999.16710.201
2.119-2.1940.2272660.18148270.18450930.9660.9791000.155
2.194-2.2770.3152400.23946120.24249400.9320.9698.21860.199
2.277-2.3690.2022420.17544920.17747340.9740.9811000.151
2.369-2.4750.2132230.16443300.16745530.9710.9831000.143
2.475-2.5950.2042110.16241510.16443620.9770.9841000.142
2.595-2.7360.2182250.16739140.1741390.970.9831000.149
2.736-2.9020.2122190.1737060.17339250.9710.9821000.157
2.902-3.1020.1982040.16635040.16837080.9770.9841000.161
3.102-3.350.21900.17332530.17434430.9750.9841000.17
3.35-3.670.2031690.17530010.17731720.980.98699.9370.178
3.67-4.1020.1591460.1427520.14129020.9850.98999.86220.15
4.102-4.7360.151130.12224530.12325660.9870.9911000.139
4.736-5.7970.2151170.15620570.15921740.9830.991000.175
5.797-8.1880.196860.16716300.16917160.9810.9871000.188
8.188-111.2550.169510.1639400.1639930.980.98499.79860.201

+
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