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- PDB-6c9d: Crystal structure of KA1-autoinhibited MARK1 kinase -

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Basic information

Entry
Database: PDB / ID: 6c9d
TitleCrystal structure of KA1-autoinhibited MARK1 kinase
ComponentsSerine/threonine-protein kinase MARK1,Serine/threonine-protein kinase MARK1
KeywordsTRANSFERASE / Kinase / CAMKL / KA1 domain / autoinhibition
Function / homology
Function and homology information


establishment of mitochondrion localization / regulation of dendrite development / phosphatidic acid binding / tau-protein kinase / negative regulation of epithelial to mesenchymal transition / tau-protein kinase activity / phosphatidylserine binding / regulation of neuron projection development / regulation of postsynapse assembly / phosphatidylinositol-4,5-bisphosphate binding ...establishment of mitochondrion localization / regulation of dendrite development / phosphatidic acid binding / tau-protein kinase / negative regulation of epithelial to mesenchymal transition / tau-protein kinase activity / phosphatidylserine binding / regulation of neuron projection development / regulation of postsynapse assembly / phosphatidylinositol-4,5-bisphosphate binding / cytoskeleton organization / tau protein binding / microtubule cytoskeleton organization / Wnt signaling pathway / neuron migration / microtubule cytoskeleton / eukaryotic translation initiation factor 2alpha kinase activity / cytoskeleton / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / postsynapse / intracellular signal transduction / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / positive regulation of gene expression / glutamatergic synapse / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
: / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Transferase(Phosphotransferase) domain 1 ...: / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein kinase MARK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsEmptage, R.P. / Marmorstein, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM115098 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)5P01CA114046 United States
CitationJournal: Structure / Year: 2018
Title: Structural Basis for MARK1 Kinase Autoinhibition by Its KA1 Domain.
Authors: Emptage, R.P. / Lemmon, M.A. / Ferguson, K.M. / Marmorstein, R.
History
DepositionJan 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase MARK1,Serine/threonine-protein kinase MARK1
B: Serine/threonine-protein kinase MARK1,Serine/threonine-protein kinase MARK1


Theoretical massNumber of molelcules
Total (without water)105,8732
Polymers105,8732
Non-polymers00
Water1,22568
1
A: Serine/threonine-protein kinase MARK1,Serine/threonine-protein kinase MARK1


Theoretical massNumber of molelcules
Total (without water)52,9371
Polymers52,9371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase MARK1,Serine/threonine-protein kinase MARK1


Theoretical massNumber of molelcules
Total (without water)52,9371
Polymers52,9371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.993, 69.578, 103.999
Angle α, β, γ (deg.)90.000, 124.300, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 53 through 54 and (name N...
21(chain B and (resid 53 through 67 or (resid 68...
12(chain A and (resid 696 through 764 or (resid 765...
22(chain B and (resid 696 through 718 or (resid 719...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUGLNGLN(chain A and ((resid 53 through 54 and (name N...AA53 - 5416 - 17
121GLUGLUGLYGLY(chain A and ((resid 53 through 54 and (name N...AA53 - 37716 - 340
131GLUGLUGLYGLY(chain A and ((resid 53 through 54 and (name N...AA53 - 37716 - 340
141GLUGLUGLYGLY(chain A and ((resid 53 through 54 and (name N...AA53 - 37716 - 340
151GLUGLUGLYGLY(chain A and ((resid 53 through 54 and (name N...AA53 - 37716 - 340
211GLUGLUGLYGLY(chain B and (resid 53 through 67 or (resid 68...BB53 - 6716 - 30
221LYSLYSLYSLYS(chain B and (resid 53 through 67 or (resid 68...BB6831
231GLUGLUPROPRO(chain B and (resid 53 through 67 or (resid 68...BB53 - 37316 - 336
241GLUGLUPROPRO(chain B and (resid 53 through 67 or (resid 68...BB53 - 37316 - 336
251GLUGLUPROPRO(chain B and (resid 53 through 67 or (resid 68...BB53 - 37316 - 336
261GLUGLUPROPRO(chain B and (resid 53 through 67 or (resid 68...BB53 - 37316 - 336
271GLUGLUPROPRO(chain B and (resid 53 through 67 or (resid 68...BB53 - 37316 - 336
112LYSLYSSERSER(chain A and (resid 696 through 764 or (resid 765...AA696 - 764360 - 428
122LEULEULEULEU(chain A and (resid 696 through 764 or (resid 765...AA765429
132LYSLYSLEULEU(chain A and (resid 696 through 764 or (resid 765...AA696 - 795360 - 459
142LYSLYSLEULEU(chain A and (resid 696 through 764 or (resid 765...AA696 - 795360 - 459
152LYSLYSLEULEU(chain A and (resid 696 through 764 or (resid 765...AA696 - 795360 - 459
162LYSLYSLEULEU(chain A and (resid 696 through 764 or (resid 765...AA696 - 795360 - 459
212LYSLYSMETMET(chain B and (resid 696 through 718 or (resid 719...BB696 - 718360 - 382
222ARGARGARGARG(chain B and (resid 696 through 718 or (resid 719...BB719383
232SERSERLEULEU(chain B and (resid 696 through 718 or (resid 719...BB695 - 795359 - 459
242SERSERLEULEU(chain B and (resid 696 through 718 or (resid 719...BB695 - 795359 - 459
252SERSERLEULEU(chain B and (resid 696 through 718 or (resid 719...BB695 - 795359 - 459
262SERSERLEULEU(chain B and (resid 696 through 718 or (resid 719...BB695 - 795359 - 459

NCS ensembles :
ID
1
2

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Components

#1: Protein Serine/threonine-protein kinase MARK1,Serine/threonine-protein kinase MARK1 / MAP/microtubule affinity-regulating kinase 1 / PAR1 homolog c / Par1c


Mass: 52936.715 Da / Num. of mol.: 2
Fragment: kinase and UBA domain (UNP residues 45-381), KA1 domain (UNP residues 681-795)
Mutation: T215E, K761S, R764S
Source method: isolated from a genetically manipulated source
Details: This arrangement of chains is most probable based on spatial considerations and experimental evidence, though there is a possibility that the kinase and UBA domains of chain A may be part of ...Details: This arrangement of chains is most probable based on spatial considerations and experimental evidence, though there is a possibility that the kinase and UBA domains of chain A may be part of the same polymer chain as the KA1 domain of chain B, and vice versa.
Source: (gene. exp.) Homo sapiens (human) / Gene: MARK1, KIAA1477, MARK / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P0L2, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 6-8% PEG8000, 0.2-0.3 M imidazole, pH 8.0-8.5 / PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2017
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.499→50 Å / Num. obs: 34570 / % possible obs: 98.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 24
Reflection shellResolution: 2.499→2.54 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.317 / Num. unique obs: 1660 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3OSE & 2HAK

3ose

2hak


Resolution: 2.499→45.352 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.47
RfactorNum. reflection% reflection
Rfree0.2514 1995 5.78 %
Rwork0.2033 --
obs0.2061 34499 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.9 Å2 / Biso mean: 77.8037 Å2 / Biso min: 53.17 Å2
Refinement stepCycle: final / Resolution: 2.499→45.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6600 0 0 68 6668
Biso mean---67.46 -
Num. residues----847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096772
X-RAY DIFFRACTIONf_angle_d1.2639171
X-RAY DIFFRACTIONf_chiral_restr0.0731030
X-RAY DIFFRACTIONf_plane_restr0.0091187
X-RAY DIFFRACTIONf_dihedral_angle_d27.242520
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2836X-RAY DIFFRACTION11.395TORSIONAL
12B2836X-RAY DIFFRACTION11.395TORSIONAL
21A852X-RAY DIFFRACTION11.395TORSIONAL
22B852X-RAY DIFFRACTION11.395TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4995-2.5620.39461320.32122197232994
2.562-2.63130.33271450.30072304244999
2.6313-2.70870.30851370.27872341247899
2.7087-2.79610.35151430.26622291243499
2.7961-2.8960.2671280.25882333246199
2.896-3.01190.30061520.27392288244099
3.0119-3.1490.35021430.26932331247499
3.149-3.3150.25641380.24722327246599
3.315-3.52260.31821430.24142335247899
3.5226-3.79440.29691440.21592317246199
3.7944-4.1760.23431490.185323572506100
4.176-4.77980.21321430.162327247099
4.7798-6.01980.231460.17932357250399
6.0198-45.35920.19261520.16372399255198
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)
12.46710.7742.06291.50631.54643.3351-0.1976-0.38610.6613-0.0793-0.06750.208-0.4021-0.296800.87710.01790.01180.8018-0.09790.8938-4.196794.089626.5553
20.4390.63980.17351.49070.17911.47220.23690.1648-0.169-0.3903-0.13860.16370.1062-0.1653-00.7972-0.0337-0.02990.79120.0880.7539-15.14472.84943.1559
30.08740.089-0.37490.4417-0.19250.11810.20580.8042-0.51-0.1177-0.2530.23490.58880.2082-00.95640.02140.03481.081-0.11141.006218.815971.389620.4748
40.5743-0.2014-0.09970.6673-0.32870.14480.304-0.3913-1.3948-0.0117-0.0533-0.14060.2480.0484-00.9447-0.0148-0.04460.94330.16251.155513.222662.490431.4008
5-0.00970.00960.0069-0.02870.00030.0099-0.0026-0.43730.05120.7966-0.240.0835-0.34450.2414-01.07220.0159-0.07491.5636-0.25861.07440.658572.151543.3912
61.09080.57950.92752.3964-0.60551.03080.21870.0254-0.1339-0.12130.0382-0.23620.02260.3300.8202-0.05790.02540.8909-0.00870.721112.662572.082728.4063
73.49950.0481-0.38932.1499-0.2152.57330.0937-0.11040.27620.004-0.04210.09-0.01770.0039-00.8384-0.16930.04080.8710.03440.7407-53.957152.802524.2824
81.5108-0.6405-0.16721.898-0.26520.31540.0505-0.6595-0.05080.2267-0.0876-0.3010.14120.070500.8075-0.121-0.06210.92620.07820.7612-37.530452.246722.7769
92.59050.7732-0.72152.90520.33622.9025-0.05730.1189-0.944-0.08290.0047-0.76510.42890.060900.839-0.0467-0.03080.79320.06661.1197-30.398743.246213.1543
100.5733-0.2165-0.19080.5244-1.22390.53830.6505-1.60870.22970.5262-0.2366-0.3266-0.168-0.049901.1814-0.19380.02011.55350.05240.8927-51.244847.966841.217
110.0283-0.01630.0703-0.01430.05420.17740.2063-0.64810.04221.6977-0.32410.2425-0.07110.0441-01.079-0.12270.04131.0031-0.2051.2383-36.219773.299827.4896
12-0.0682-0.014-0.0809-0.02990.18270.00480.3366-0.76330.7844-0.2089-0.21170.2935-0.38310.320700.8698-0.01970.03361.0284-0.18111.1199-29.894579.84719.9805
130.02980.2395-0.0240.2726-0.28870.1491-0.11450.10871.7875-0.3383-0.402-0.0522-0.95-0.167100.81310.06840.04450.84620.04561.3294-39.386682.265112.5376
140.0996-0.03050.01070.4349-0.09570.0513-0.123-0.31540.50070.11950.1360.52470.0163-0.20600.89010.0376-0.0030.926-0.0541.2308-47.760976.114112.2229
150.14130.1324-0.1250.2808-0.33550.1827-0.128-0.81020.8602-0.26490.19260.0873-0.3172-0.1901-00.7185-0.0645-0.03260.9372-0.0091.0742-45.27574.168614.7232
16-0.00460.011-0.00770.00870.0270.02460.19750.2599-0.6581-0.79460.0587-0.29190.7171-0.159601.05650.1078-0.0691.10510.16411.3088-44.6661.93070.9084
170.2079-0.156-0.25620.2490.02480.16790.3117-0.30150.32340.79710.3051-0.12960.2990.262900.8975-0.04250.03960.868-0.05811.1353-37.75374.417321.7706
180.5705-0.08350.09280.4401-0.22151.05750.3124-0.08130.244-0.07070.2531-0.1246-0.0568-0.0437-00.77350.02870.0160.71420.06240.8553-36.155169.491612.7328
190.58760.12670.13180.592-0.58830.3422-0.1382-0.9103-0.56320.5427-0.37340.0680.2645-0.526200.8515-0.05-0.01530.89170.03390.9088-8.539564.794520.9566
201.45190.97240.7652.94390.86771.09310.0943-0.46030.19180.2236-0.08560.0713-0.1175-0.225300.7401-0.05110.00120.8294-0.01820.6404-14.33974.90420.3778
211.45270.84570.63341.28320.62380.5731-0.1137-0.1850.2983-0.0880.00290.0563-0.1686-0.0202-00.812-0.05910.01150.6987-0.03470.6476-0.248686.023221.9864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 196 through 342 )A196 - 342
2X-RAY DIFFRACTION2chain 'A' and (resid 343 through 377 )A343 - 377
3X-RAY DIFFRACTION3chain 'A' and (resid 696 through 713 )A696 - 713
4X-RAY DIFFRACTION4chain 'A' and (resid 714 through 744 )A714 - 744
5X-RAY DIFFRACTION5chain 'A' and (resid 745 through 752 )A745 - 752
6X-RAY DIFFRACTION6chain 'A' and (resid 753 through 795 )A753 - 795
7X-RAY DIFFRACTION7chain 'B' and (resid 53 through 127 )B53 - 127
8X-RAY DIFFRACTION8chain 'B' and (resid 128 through 195 )B128 - 195
9X-RAY DIFFRACTION9chain 'B' and (resid 196 through 317 )B196 - 317
10X-RAY DIFFRACTION10chain 'B' and (resid 318 through 373 )B318 - 373
11X-RAY DIFFRACTION11chain 'B' and (resid 695 through 704 )B695 - 704
12X-RAY DIFFRACTION12chain 'B' and (resid 705 through 713 )B705 - 713
13X-RAY DIFFRACTION13chain 'B' and (resid 714 through 728 )B714 - 728
14X-RAY DIFFRACTION14chain 'B' and (resid 729 through 736 )B729 - 736
15X-RAY DIFFRACTION15chain 'B' and (resid 737 through 744 )B737 - 744
16X-RAY DIFFRACTION16chain 'B' and (resid 745 through 752 )B745 - 752
17X-RAY DIFFRACTION17chain 'B' and (resid 753 through 767 )B753 - 767
18X-RAY DIFFRACTION18chain 'B' and (resid 768 through 795 )B768 - 795
19X-RAY DIFFRACTION19chain 'A' and (resid 53 through 71 )A53 - 71
20X-RAY DIFFRACTION20chain 'A' and (resid 72 through 130 )A72 - 130
21X-RAY DIFFRACTION21chain 'A' and (resid 131 through 195 )A131 - 195

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