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- PDB-3w8h: Crystal structure of CCM3 in complex with the C-terminal regulato... -

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Basic information

Entry
Database: PDB / ID: 3w8h
TitleCrystal structure of CCM3 in complex with the C-terminal regulatory domain of STK25
Components
  • Programmed cell death protein 10
  • Serine/threonine-protein kinase 25
KeywordsPROTEIN BINDING/TRANSFERASE / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


intrinsic apoptotic signaling pathway in response to hydrogen peroxide / Golgi localization / regulation of Golgi organization / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / FAR/SIN/STRIPAK complex / endothelium development / positive regulation of stress-activated MAPK cascade / establishment of Golgi localization / positive regulation of intracellular protein transport ...intrinsic apoptotic signaling pathway in response to hydrogen peroxide / Golgi localization / regulation of Golgi organization / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / FAR/SIN/STRIPAK complex / endothelium development / positive regulation of stress-activated MAPK cascade / establishment of Golgi localization / positive regulation of intracellular protein transport / negative regulation of cell migration involved in sprouting angiogenesis / wound healing, spreading of cells / positive regulation of axonogenesis / establishment or maintenance of cell polarity / positive regulation of Notch signaling pathway / regulation of angiogenesis / axonogenesis / cellular response to leukemia inhibitory factor / 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 / angiogenesis / response to oxidative stress / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / protein phosphorylation / Golgi membrane / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / signal transduction / protein homodimerization activity / extracellular exosome / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine kinase 25, catalytic domain / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1950 / 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 ...Serine/threonine kinase 25, catalytic domain / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1950 / 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
Serine/threonine-protein kinase 25 / Programmed cell death protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.426 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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_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: Programmed cell death protein 10
B: Serine/threonine-protein kinase 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1779
Polymers33,5042
Non-polymers6727
Water2,090116
1
A: Programmed cell death protein 10
B: Serine/threonine-protein kinase 25
hetero molecules

A: Programmed cell death protein 10
B: Serine/threonine-protein kinase 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,35318
Polymers67,0094
Non-polymers1,34514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area11250 Å2
ΔGint-298 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.560, 68.560, 229.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-501-

SO4

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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 25 / Ste20-like kinase / Sterile 20/oxidant stress-response kinase 1 / SOK-1 / Ste20/oxidant stress ...Ste20-like kinase / Sterile 20/oxidant stress-response kinase 1 / SOK-1 / Ste20/oxidant stress response kinase 1


Mass: 8607.665 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 355-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOK1, STK25, YSK1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O00506, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris, 25% PEG3350, 0.2M ammonium sulfate, pH 5.5, 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: Jul 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.426→59.34 Å / Num. all: 12964 / Num. obs: 12822 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 26.73 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 21.4
Reflection shellResolution: 2.43→2.56 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 7.7 / Num. unique all: 1747 / Rsym value: 0.323 / % possible all: 95.8

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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: 2.426→41.238 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 622 4.89 %RANDOM
Rwork0.2092 ---
all0.2118 12903 --
obs0.2118 12731 98.66 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.785 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5317 Å2-0 Å2-0 Å2
2--1.5317 Å20 Å2
3----3.0634 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.426→41.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 35 116 2206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032113
X-RAY DIFFRACTIONf_angle_d0.6842844
X-RAY DIFFRACTIONf_dihedral_angle_d15.018801
X-RAY DIFFRACTIONf_chiral_restr0.052323
X-RAY DIFFRACTIONf_plane_restr0.003359
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4261-2.67020.33141510.2384283696
2.6702-3.05640.27461520.2123296299
3.0564-3.85040.23921520.18963058100
3.8504-41.24360.24921670.21153253100

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