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- PDB-3w8i: Crystal structure of CCM3 in complex with the C-terminal regulato... -

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Basic information

Entry
Database: PDB / ID: 3w8i
TitleCrystal structure of CCM3 in complex with the C-terminal regulatory domain of MST4
Components
  • Programmed cell death protein 10
  • Serine/threonine-protein kinase MST4
KeywordsPROTEIN BINDING/TRANSFERASE / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


intrinsic apoptotic signaling pathway in response to hydrogen peroxide / microvillus assembly / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / endothelium development / Golgi reassembly / FAR/SIN/STRIPAK complex / positive regulation of stress-activated MAPK cascade / positive regulation of intracellular protein transport / establishment of Golgi localization / negative regulation of cell migration involved in sprouting angiogenesis ...intrinsic apoptotic signaling pathway in response to hydrogen peroxide / microvillus assembly / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / endothelium development / Golgi reassembly / FAR/SIN/STRIPAK complex / positive regulation of stress-activated MAPK cascade / positive regulation of intracellular protein transport / establishment of Golgi localization / negative regulation of cell migration involved in sprouting angiogenesis / vesicle membrane / wound healing, spreading of cells / Golgi-associated vesicle / Apoptotic cleavage of cellular proteins / positive regulation of Notch signaling pathway / positive regulation of MAP kinase activity / positive regulation of protein serine/threonine kinase activity / positive regulation of peptidyl-serine phosphorylation / regulation of angiogenesis / negative regulation of cell migration / cellular response to starvation / cellular response to leukemia inhibitory factor / cell periphery / protein autophosphorylation / cellular response to oxidative stress / angiogenesis / regulation of apoptotic process / protein phosphorylation / protein kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / protein stabilization / positive regulation of cell migration / apical plasma membrane / Golgi membrane / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / positive regulation of gene expression / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / magnesium ion binding / Golgi apparatus / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / membrane / 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) - #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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXu, X. / Wang, D.C. / Ding, J.
CitationJournal: Structure / Year: 2013
Title: Structural Basis for the Unique Heterodimeric Assembly between Cerebral Cavernous Malformation 3 and Germinal Center Kinase III.
Authors: Xu, X. / Wang, X. / Zhang, Y. / Wang, D.C. / Ding, J.
History
DepositionMar 13, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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


Theoretical massNumber of molelcules
Total (without water)33,1022
Polymers33,1022
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-32 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.100, 69.100, 117.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: 24896.619 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 8-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCM3, PDCD10, TFAR15 / Plasmid: pET22b / 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: 8205.410 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 346-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MASK, MST4, SOK1, STK25, YSK1 / Plasmid: pET32a / 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


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M Bis-Tris, 25% PEG3350, 0.3M ammonium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→48.85 Å / Num. all: 11764 / Num. obs: 11764 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 37.57 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 27.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 7.4 / Num. unique all: 1666 / Rsym value: 0.353 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AJM

3ajm


Resolution: 2.4→45.12 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 556 4.75 %RANDOM
Rwork0.2223 ---
all0.2247 11717 --
obs0.2247 11715 99.98 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.618 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2036 Å2-0 Å2-0 Å2
2--0.2036 Å20 Å2
3----0.4071 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 0 112 2119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032033
X-RAY DIFFRACTIONf_angle_d0.7472732
X-RAY DIFFRACTIONf_dihedral_angle_d15.895790
X-RAY DIFFRACTIONf_chiral_restr0.055320
X-RAY DIFFRACTIONf_plane_restr0.003348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4-2.64150.35651260.25722718
2.6415-3.02370.32321450.2482738
3.0237-3.80920.26451380.21212767
3.8092-45.12770.22251470.20832936

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