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- PDB-4nr2: Crystal structure of STK4 (MST1) SARAH domain -

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Basic information

Entry
Database: PDB / ID: 4nr2
TitleCrystal structure of STK4 (MST1) SARAH domain
ComponentsSerine/threonine-protein kinase 4
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / SARAH domain / STK3 / MST2 / heptad repeat / STK4 / MST1
Function / homology
Function and homology information


positive regulation of hepatocyte apoptotic process / 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 / positive regulation of substrate-dependent cell migration, cell attachment to substrate / endocardium development / negative regulation of organ growth / hippo signaling ...positive regulation of hepatocyte apoptotic process / 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 / positive regulation of substrate-dependent cell migration, cell attachment to substrate / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / organ growth / branching involved in blood vessel morphogenesis / 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 / keratinocyte differentiation / protein serine/threonine kinase activator activity / epithelial cell proliferation / central nervous system development / protein tetramerization / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / protein import into nucleus / negative regulation of epithelial cell proliferation / positive regulation of protein binding / positive regulation of peptidyl-serine phosphorylation / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / protein autophosphorylation / nuclear body / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / magnesium ion binding / signal transduction / protein homodimerization activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
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 / Protein kinase domain ...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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsChaikuad, A. / Krojer, T. / Kopec, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of STK4 (MST1) SARAH domain
Authors: Chaikuad, A. / Krojer, T. / Kopec, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionNov 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 4
B: Serine/threonine-protein kinase 4
C: Serine/threonine-protein kinase 4
D: Serine/threonine-protein kinase 4
E: Serine/threonine-protein kinase 4
F: Serine/threonine-protein kinase 4
G: Serine/threonine-protein kinase 4
H: Serine/threonine-protein kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,17418
Polymers49,5538
Non-polymers62110
Water4,017223
1
A: Serine/threonine-protein kinase 4
B: Serine/threonine-protein kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6997
Polymers12,3882
Non-polymers3105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-21 kcal/mol
Surface area7300 Å2
MethodPISA
2
C: Serine/threonine-protein kinase 4
D: Serine/threonine-protein kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4503
Polymers12,3882
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-25 kcal/mol
Surface area7480 Å2
MethodPISA
3
E: Serine/threonine-protein kinase 4
F: Serine/threonine-protein kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5124
Polymers12,3882
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-25 kcal/mol
Surface area7320 Å2
MethodPISA
4
G: Serine/threonine-protein kinase 4
H: Serine/threonine-protein kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5124
Polymers12,3882
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-25 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.260, 63.750, 144.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALAAA434 - 4795 - 50
21GLUGLUALAALABB434 - 4795 - 50
12SERSERLYSLYSAA-1 - 4801 - 51
22SERSERLYSLYSCC-1 - 4801 - 51
13ASPASPALAALAAA432 - 4793 - 50
23ASPASPALAALADD432 - 4793 - 50
14SERSERLYSLYSAA-1 - 4801 - 51
24SERSERLYSLYSEE-1 - 4801 - 51
15GLUGLUALAALAAA434 - 4795 - 50
25GLUGLUALAALAFF434 - 4795 - 50
16SERSERLYSLYSAA-1 - 4801 - 51
26SERSERLYSLYSGG-1 - 4801 - 51
17SERSERLYSLYSAA-1 - 4801 - 51
27SERSERLYSLYSHH-1 - 4801 - 51
18GLUGLUALAALABB434 - 4795 - 50
28GLUGLUALAALACC434 - 4795 - 50
19GLUGLUALAALABB434 - 4795 - 50
29GLUGLUALAALADD434 - 4795 - 50
110GLUGLUALAALABB434 - 4795 - 50
210GLUGLUALAALAEE434 - 4795 - 50
111GLUGLULYSLYSBB434 - 4805 - 51
211GLUGLULYSLYSFF434 - 4805 - 51
112GLUGLUALAALABB434 - 4795 - 50
212GLUGLUALAALAGG434 - 4795 - 50
113GLUGLUALAALABB434 - 4795 - 50
213GLUGLUALAALAHH434 - 4795 - 50
114ASPASPALAALACC432 - 4793 - 50
214ASPASPALAALADD432 - 4793 - 50
115SERSERLYSLYSCC-1 - 4801 - 51
215SERSERLYSLYSEE-1 - 4801 - 51
116GLUGLUALAALACC434 - 4795 - 50
216GLUGLUALAALAFF434 - 4795 - 50
117SERSERLYSLYSCC-1 - 4801 - 51
217SERSERLYSLYSGG-1 - 4801 - 51
118SERSERLYSLYSCC-1 - 4801 - 51
218SERSERLYSLYSHH-1 - 4801 - 51
119ASPASPALAALADD432 - 4793 - 50
219ASPASPALAALAEE432 - 4793 - 50
120GLUGLUALAALADD434 - 4795 - 50
220GLUGLUALAALAFF434 - 4795 - 50
121ASPASPALAALADD432 - 4793 - 50
221ASPASPALAALAGG432 - 4793 - 50
122ASPASPALAALADD432 - 4793 - 50
222ASPASPALAALAHH432 - 4793 - 50
123GLUGLUALAALAEE434 - 4795 - 50
223GLUGLUALAALAFF434 - 4795 - 50
124SERSERLYSLYSEE-1 - 4801 - 51
224SERSERLYSLYSGG-1 - 4801 - 51
125SERSERLYSLYSEE-1 - 4801 - 51
225SERSERLYSLYSHH-1 - 4801 - 51
126GLUGLUALAALAFF434 - 4795 - 50
226GLUGLUALAALAGG434 - 4795 - 50
127GLUGLUALAALAFF434 - 4795 - 50
227GLUGLUALAALAHH434 - 4795 - 50
128SERSERLYSLYSGG-1 - 4801 - 51
228SERSERLYSLYSHH-1 - 4801 - 51

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
Detailsthe asymmetric unit consists of four dimers

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Components

#1: Protein
Serine/threonine-protein kinase 4 / Mammalian STE20-like protein kinase 1 / MST-1 / STE20-like kinase MST1 / Serine/threonine-protein ...Mammalian STE20-like protein kinase 1 / MST-1 / STE20-like kinase MST1 / Serine/threonine-protein kinase Krs-2 / Serine/threonine-protein kinase 4 37kDa subunit / MST1/N / Serine/threonine-protein kinase 4 18kDa subunit / MST1/C


Mass: 6194.113 Da / Num. of mol.: 8 / Fragment: SARAH domain, UNP residues 432-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRS2, MST1, STK4 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: Q13043, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2.3M sodium formate, 0.1M acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2013
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→63.75 Å / Num. all: 34708 / Num. obs: 34702 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4951 / % possible all: 98

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Processing

Software
NameVersionClassification
GDAdata collection
SHARPphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2→55.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.132 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.192 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24033 1736 5 %RANDOM
Rwork0.2069 ---
all0.264 34702 --
obs0.20866 32937 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.839 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å20 Å2-0 Å2
2--0.77 Å2-0 Å2
3----3.66 Å2
Refine analyzeLuzzati coordinate error obs: 0.295 Å
Refinement stepCycle: LAST / Resolution: 2→55.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 40 223 3621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023527
X-RAY DIFFRACTIONr_bond_other_d0.010.023524
X-RAY DIFFRACTIONr_angle_refined_deg1.5922.0024720
X-RAY DIFFRACTIONr_angle_other_deg1.59638163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.845414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18825.401187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09215759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7991528
X-RAY DIFFRACTIONr_chiral_restr0.0880.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213830
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02726
X-RAY DIFFRACTIONr_mcbond_it2.2522.6031608
X-RAY DIFFRACTIONr_mcbond_other2.2512.6021607
X-RAY DIFFRACTIONr_mcangle_it3.2563.8662002
X-RAY DIFFRACTIONr_mcangle_other3.2553.8682003
X-RAY DIFFRACTIONr_scbond_it3.8263.0951919
X-RAY DIFFRACTIONr_scbond_other3.8253.0951919
X-RAY DIFFRACTIONr_scangle_other6.0054.4472707
X-RAY DIFFRACTIONr_long_range_B_refined8.77621.6954286
X-RAY DIFFRACTIONr_long_range_B_other8.77521.7034287
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A22440.16
12B22440.16
21A27240.12
22C27240.12
31A24470.15
32D24470.15
41A27530.1
42E27530.1
51A23450.15
52F23450.15
61A25340.16
62G25340.16
71A27490.11
72H27490.11
81B23290.13
82C23290.13
91B23400.11
92D23400.11
101B22940.13
102E22940.13
111B24590.1
112F24590.1
121B23640.12
122G23640.12
131B23030.13
132H23030.13
141C24800.13
142D24800.13
151C27330.08
152E27330.08
161C23530.13
162F23530.13
171C25360.15
172G25360.15
181C27760.1
182H27760.1
191D24820.12
192E24820.12
201D24690.1
202F24690.1
211D24790.14
212G24790.14
221D24740.14
222H24740.14
231E23590.12
232F23590.12
241E25360.16
242G25360.16
251E27540.08
252H27540.08
261F24460.12
262G24460.12
271F23350.13
272H23350.13
281G25480.16
282H25480.16
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 122 -
Rwork0.315 2401 -
obs--97.45 %
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)
10.78190.44881.13173.5192-1.84955.1556-0.0397-0.03580.0602-0.07630.25660.11480.0158-0.383-0.21690.02550.04140.01850.19830.0230.12843.23841.99457.564
22.83-1.94694.52461.4607-3.703814.20650.1116-0.1607-0.1435-0.10760.17230.020.933-0.3768-0.28390.25620.0462-0.03910.1396-0.0120.121852.61327.29586.358
313.34444.01859.52931.26273.383712.175-0.4940.1455-1.0748-0.0620.0554-0.19960.4451-0.38410.43860.97240.26220.08231.03560.0010.452364.58625.04896.898
41.1557-1.45792.86852.1593-4.790511.8031-0.0673-0.03230.14240.1628-0.0745-0.1161-0.39490.12090.14180.1166-0.02670.00160.1846-0.01110.133551.46741.17977.165
52.0076-0.2068-3.78820.3985-0.23178.75590.1251-0.1462-0.1219-0.1323-0.03890.08170.1410.2492-0.08620.16670.0296-0.07760.1651-0.00240.133667.37257.49357.345
614.728-0.3238-10.61724.52434.427111.5730.0362-0.3009-0.0325-0.4911-0.53570.6424-0.5277-0.26380.49950.122-0.0380.00540.360.09020.602551.36153.84684.979
73.20420.385-6.23080.1565-0.735914.9431-0.1593-0.2651-0.4547-0.0817-0.1548-0.0280.89030.55990.31410.18480.101-0.0940.17240.02240.23470.46149.97759.01
80.2281-0.5134-0.01022.1421-2.593311.02170.0122-0.01740.0336-0.18780.0213-0.0180.3555-0.0439-0.03360.1611-0.0012-0.00930.1120.00380.080447.75334.5650.306
90.0604-0.18210.74043.5435-5.215817.1565-0.07460.00990.021-0.14360.0366-0.0897-0.22550.65180.0380.1732-0.0097-0.0020.1669-0.00540.107554.43436.01241.044
1028.197714.47945.07187.70814.775418.4667-0.0143-1.3156-0.26790.1027-0.7593-0.01710.4158-0.86220.77361.1337-0.2990.19060.2047-0.00030.226532.74914.90860.937
112.49351.6994-5.22311.9182-2.408212.7538-0.0131-0.1158-0.05320.28020.0379-0.16940.40960.4672-0.02480.23860.0558-0.06220.15140.02230.115851.33322.84536.712
122.0423-3.1964-2.4397.16361.74126.86890.25120.0425-0.1827-0.5135-0.17450.1155-0.38130.2464-0.07670.1035-0.0467-0.00510.0975-0.02260.16953.88228.42716.003
131.6191.3599-3.49932.0856-2.18910.44770.2003-0.00910.13340.346-0.04470.13660.1564-0.1741-0.15570.244-0.1070.01870.15390.00610.096539.56325.62843.891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 457
2X-RAY DIFFRACTION2A458 - 480
3X-RAY DIFFRACTION3B434 - 439
4X-RAY DIFFRACTION4B440 - 480
5X-RAY DIFFRACTION5C-1 - 480
6X-RAY DIFFRACTION6D432 - 446
7X-RAY DIFFRACTION7D447 - 480
8X-RAY DIFFRACTION8E-1 - 480
9X-RAY DIFFRACTION9F434 - 480
10X-RAY DIFFRACTION10G-1 - 445
11X-RAY DIFFRACTION11G446 - 480
12X-RAY DIFFRACTION12H-1 - 446
13X-RAY DIFFRACTION13H447 - 480

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  • 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

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