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- PDB-4geh: Crystal structure of MST4 dimerization domain complex with PDCD10 -

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Basic information

Entry
Database: PDB / ID: 4geh
TitleCrystal structure of MST4 dimerization domain complex with PDCD10
Components
  • Programmed cell death protein 10
  • Serine/threonine-protein kinase MST4
KeywordsPROTEIN BINDING/TRANSFERASE / alpha helix-rich protein / serine/threonine-protein kinase / protein binding / cell proliferation / cell growth / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / microvillus assembly / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / positive regulation of stress-activated MAPK cascade / endothelium development / establishment of Golgi localization / positive regulation of intracellular protein transport ...FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / microvillus assembly / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / positive regulation of stress-activated MAPK cascade / endothelium development / establishment of Golgi localization / positive regulation of intracellular protein transport / vesicle membrane / negative regulation of cell migration involved in sprouting angiogenesis / wound healing, spreading of cells / Golgi-associated vesicle / positive regulation of Notch signaling pathway / Apoptotic cleavage of cellular proteins / regulation of angiogenesis / cellular response to starvation / negative regulation of cell migration / cellular response to leukemia inhibitory factor / cell periphery / positive regulation of MAP kinase activity / positive regulation of protein serine/threonine kinase activity / positive regulation of peptidyl-serine phosphorylation / cellular response to oxidative stress / regulation of apoptotic process / angiogenesis / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / apical plasma membrane / Golgi membrane / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / protein homodimerization activity / extracellular exosome / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1950 / MST4, kinase domain / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #70 / Programmed cell death protein 10 / Programmed cell death protein 10, C-terminal / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1950 / MST4, kinase domain / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #70 / Programmed cell death protein 10 / Programmed cell death protein 10, C-terminal / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Programmed cell death protein 10 / Serine/threonine-protein kinase 26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsZhang, M. / Shi, Z.B. / Zhou, Z.C.
CitationJournal: Structure / Year: 2013
Title: Structural mechanism of CCM3 heterodimerization with GCKIII kinases
Authors: Zhang, M. / Dong, L. / Shi, Z. / Jiao, S. / Zhang, Z. / Zhang, W. / Liu, G. / Chen, C. / Feng, M. / Hao, Q. / Wang, W. / Yin, M. / Zhao, Y. / Zhang, L. / Zhou, Z.
History
DepositionAug 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed cell death protein 10
B: Serine/threonine-protein kinase MST4
C: Programmed cell death protein 10
D: Serine/threonine-protein kinase MST4


Theoretical massNumber of molelcules
Total (without water)67,9304
Polymers67,9304
Non-polymers00
Water3,135174
1
A: Programmed cell death protein 10
B: Serine/threonine-protein kinase MST4


Theoretical massNumber of molelcules
Total (without water)33,9652
Polymers33,9652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-35 kcal/mol
Surface area13390 Å2
MethodPISA
2
C: Programmed cell death protein 10
D: Serine/threonine-protein kinase MST4


Theoretical massNumber of molelcules
Total (without water)33,9652
Polymers33,9652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-35 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.243, 84.018, 109.679
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
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRALAALAAA15 - 21210 - 207
21THRTHRALAALACC15 - 21210 - 207
12ASPASPLYSLYSBB345 - 40923 - 87
22ASPASPLYSLYSDD345 - 40923 - 87

NCS ensembles :
ID
1
2

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Components

#1: Protein Programmed cell death protein 10 / / Cerebral cavernous malformations 3 protein / TF-1 cell apoptosis-related protein 15


Mass: 23953.596 Da / Num. of mol.: 2 / Fragment: UNP residues 9-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD10, CCM3, TFAR15 / Plasmid: HT-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BUL8
#2: Protein Serine/threonine-protein kinase MST4 / Mammalian STE20-like protein kinase 4 / MST-4 / Mst3 and SOK1-related kinase / STE20-like kinase ...Mammalian STE20-like protein kinase 4 / MST-4 / Mst3 and SOK1-related kinase / STE20-like kinase MST4 / Serine/threonine-protein kinase MASK


Mass: 10011.504 Da / Num. of mol.: 2 / Fragment: Dimerization domain, UNP residues 325-413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MST4, MASK / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9P289, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2% v/v Tacsimate pH 6.0, 0.1M BIS-TRIS pH 6.5, 18% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K
PH range: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97930, 0.97907
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 15, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.979071
ReflectionResolution: 1.95→50 Å / Num. all: 52340 / Num. obs: 52288 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.114
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2568 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AutoSolphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→45.97 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.164 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 2619 5.1 %RANDOM
Rwork0.22002 ---
all0.2217 48799 --
obs0.2217 48740 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.103 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å20 Å20 Å2
2---2.13 Å20 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4213 0 0 174 4387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194282
X-RAY DIFFRACTIONr_bond_other_d0.0040.024244
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9745769
X-RAY DIFFRACTIONr_angle_other_deg1.01839782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5115529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77425.838197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90115840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3431519
X-RAY DIFFRACTIONr_chiral_restr0.0710.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024780
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02911
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A117060.12
12C117060.12
21B31540.16
22D31540.16
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 187 -
Rwork0.315 3557 -
obs--99.87 %

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