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- PDB-3l8j: Crystal structure of CCM3, a cerebral cavernous malformation prot... -

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Basic information

Entry
Database: PDB / ID: 3l8j
TitleCrystal structure of CCM3, a cerebral cavernous malformation protein critical for vascular integrity
ComponentsProgrammed cell death protein 10
KeywordsPROTEIN BINDING / cerebral cavernous malformation / FAT domain / dimerization
Function / homology
Function and homology information


FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / 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 / negative regulation of cell migration involved in sprouting angiogenesis ...FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / 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 / negative regulation of cell migration involved in sprouting angiogenesis / wound healing, spreading of cells / stress-activated protein kinase signaling cascade / positive regulation of Notch signaling pathway / regulation of angiogenesis / 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 / angiogenesis / protein stabilization / positive regulation of cell migration / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / protein homodimerization activity / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Nucleotidyltransferases domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle ...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 / Nucleotidyltransferases domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Programmed cell death protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsLi, X. / Zhang, R. / Zhang, H. / He, Y. / Ji, W. / Min, W. / Boggon, T.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of CCM3, a cerebral cavernous malformation protein critical for vascular integrity.
Authors: Li, X. / Zhang, R. / Zhang, H. / He, Y. / Ji, W. / Min, W. / Boggon, T.J.
History
DepositionDec 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed cell death protein 10


Theoretical massNumber of molelcules
Total (without water)23,3771
Polymers23,3771
Non-polymers00
Water0
1
A: Programmed cell death protein 10

A: Programmed cell death protein 10


Theoretical massNumber of molelcules
Total (without water)46,7542
Polymers46,7542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area3700 Å2
ΔGint-39 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.445, 77.445, 108.629
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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


Mass: 23376.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD10, CCM3, TFAR15 / Plasmid: modified pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9BUL8
Sequence detailsRESIDUES -3, -2 AND -1 ARE BUILT INTO POOR DENSITY, RESIDUE ASSIGNMENT IS UNCLEAR. THE COMPLETE ...RESIDUES -3, -2 AND -1 ARE BUILT INTO POOR DENSITY, RESIDUE ASSIGNMENT IS UNCLEAR. THE COMPLETE CRYSTALLIZED SEQUENCE IS: GHMRMTMEEMKNEAETTSMVSMPLYAVMYPVFNELERVNLSAAQTLRAAFIKAEKENPGLTQDIIMKILEKKSVEVNFTESL LRMAADDVEEYMIERPEPEFQDLNEKARALKQILSKIPDEINDRVRFLQTIKDIASAIKELLDTVNNVFKKYQYQNRRALEH QKKEFVKYSKSFSDTLKTYFKDGKAINVFVSANRLIHQTNLILQTFKTVA

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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: 3.48 Å3/Da / Density % sol: 64.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.5, 20% glycerol, 13.5% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9551 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 14, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9551 Å / Relative weight: 1
ReflectionResolution: 3.05→25 Å / Num. all: 6769 / Num. obs: 6699 / Observed criterion σ(I): 2 / Redundancy: 13.7 % / Biso Wilson estimate: 109 Å2 / Rsym value: 0.084 / Net I/σ(I): 19.3
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 634 / Rsym value: 0.491

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE P212121 MODEL, PDB entry 3L8I

3l8i


Resolution: 3.05→25 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.934 / SU B: 70.715 / SU ML: 0.532 / Cross valid method: THROUGHOUT / ESU R Free: 0.472 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residues -3, -2 and -1 are built into poor density, residue assignment is unclear.
RfactorNum. reflection% reflectionSelection details
Rfree0.2926 316 4.9 %RANDOM
Rwork0.27827 ---
obs0.27895 6170 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 146.451 Å2
Baniso -1Baniso -2Baniso -3
1-5.61 Å20 Å20 Å2
2--5.61 Å20 Å2
3----11.23 Å2
Refinement stepCycle: LAST / Resolution: 3.05→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 0 0 1630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221654
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8811.9722224
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8995198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88324.93779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17815329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0581510
X-RAY DIFFRACTIONr_chiral_restr0.0540.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211207
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1061.51002
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.19921630
X-RAY DIFFRACTIONr_scbond_it0.2283652
X-RAY DIFFRACTIONr_scangle_it0.44.5594
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 30 -
Rwork0.349 420 -
obs--95.34 %
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)
110.22473.13136.26611.07030.674614.91141.13380.2457-0.29710.20810.0414-0.34272.23971.8038-1.17530.38990.3363-0.20130.4479-0.27850.203554.264527.38419.2442
212.87974.8837-2.86618.3192-4.90427.0042-0.2006-0.3794-0.6435-0.41621.06931.22070.128-0.8815-0.86870.34780.1576-0.10180.55350.46630.589220.858719.968614.6578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 69
2X-RAY DIFFRACTION2A70 - 210

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