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- PDB-4tvq: CCM3 in complex with CCM2 LD-like motif -

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Basic information

Entry
Database: PDB / ID: 4tvq
TitleCCM3 in complex with CCM2 LD-like motif
Components
  • Cerebral cavernous malformations 2 proteinCavernous hemangioma
  • Cerebral cavernous malformations 3 proteinCavernous hemangioma
KeywordsPROTEIN BINDING / FAT-HOMOLOGY DOMAIN
Function / homology
Function and homology information


endothelial cell development / FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / venous blood vessel morphogenesis / blood vessel endothelial cell differentiation / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / positive regulation of stress-activated MAPK cascade / pericardium development ...endothelial cell development / FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / venous blood vessel morphogenesis / blood vessel endothelial cell differentiation / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / positive regulation of stress-activated MAPK cascade / pericardium development / endothelium development / endothelial tube morphogenesis / establishment of Golgi localization / positive regulation of intracellular protein transport / cell-cell junction organization / 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 / inner ear development / vasculogenesis / regulation of angiogenesis / stress-activated MAPK cascade / cellular response to leukemia inhibitory factor / integrin-mediated signaling pathway / multicellular organism growth / positive regulation of MAP kinase activity / positive regulation of protein serine/threonine kinase activity / positive regulation of peptidyl-serine phosphorylation / heart development / angiogenesis / in utero embryonic development / 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 / protein-containing complex / mitochondrion / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cerebral cavernous malformations 2 / Cerebral cavernous malformations 2, harmonin-homology domain / Cerebral cavernous malformation protein, harmonin-homology / 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 ...Cerebral cavernous malformations 2 / Cerebral cavernous malformations 2, harmonin-homology domain / Cerebral cavernous malformation protein, harmonin-homology / 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 / Phosphotyrosine interaction domain (PID) profile. / PTB/PI domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / PH-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cerebral cavernous malformations 2 protein / Programmed cell death protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLi, X. / Zhang, R. / Fisher, O.S. / Boggon, T.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS085078 United States
American Heart Association11POST7630017 United States
CitationJournal: J.Cell Biol. / Year: 2015
Title: CCM2-CCM3 interaction stabilizes their protein expression and permits endothelial network formation.
Authors: Draheim, K.M. / Li, X. / Zhang, R. / Fisher, O.S. / Villari, G. / Boggon, T.J. / Calderwood, D.A.
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Data collection / Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Cerebral cavernous malformations 3 protein
B: Cerebral cavernous malformations 3 protein
C: Cerebral cavernous malformations 3 protein
D: Cerebral cavernous malformations 3 protein
E: Cerebral cavernous malformations 2 protein


Theoretical massNumber of molelcules
Total (without water)101,4535
Polymers101,4535
Non-polymers00
Water0
1
A: Cerebral cavernous malformations 3 protein
B: Cerebral cavernous malformations 3 protein


Theoretical massNumber of molelcules
Total (without water)49,8622
Polymers49,8622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-38 kcal/mol
Surface area18280 Å2
MethodPISA
2
C: Cerebral cavernous malformations 3 protein
D: Cerebral cavernous malformations 3 protein
E: Cerebral cavernous malformations 2 protein


Theoretical massNumber of molelcules
Total (without water)51,5913
Polymers51,5913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-54 kcal/mol
Surface area21640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.855, 113.552, 120.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24930.779 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD10, CCM3, TFAR15 / Plasmid: PET32 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA BL21 / References: UniProt: Q9BUL8
#2: Protein/peptide Cerebral cavernous malformations 2 protein / Cavernous hemangioma / Malcavernin


Mass: 1729.864 Da / Num. of mol.: 1 / Fragment: INTERDOMAIN LINKER LD-LIKE MOTIF RESIDUES 224-239 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BSQ5

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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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15-20% PEG3350, 0.1-0.2M POTASSIUM FLUORIDE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR + SAGITTALLY-FOCUSING SECOND CRYSTAL + MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 130452 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 78.96 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 16
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 1.654 / Rsym value: 0.937 / % possible all: 97.5

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Processing

Software
NameVersionClassification
Coot0.8-pre-4968model building
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
PHASERccp4-6.4.0phasing
HKL-20002000.0.98.705adata reduction
HKL-20002000.0.98.705adata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L8I
Resolution: 2.8→49.49 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1076 5.09 %Random selection
Rwork0.239 ---
obs0.241 21136 98.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5969 0 0 0 5969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026050
X-RAY DIFFRACTIONf_angle_d0.5838124
X-RAY DIFFRACTIONf_dihedral_angle_d10.9272336
X-RAY DIFFRACTIONf_chiral_restr0.041945
X-RAY DIFFRACTIONf_plane_restr0.0031026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.92920.30151270.25562352X-RAY DIFFRACTION95
2.9292-3.08360.32871420.26632441X-RAY DIFFRACTION98
3.0836-3.27680.3121330.24442437X-RAY DIFFRACTION98
3.2768-3.52970.29531310.24452489X-RAY DIFFRACTION99
3.5297-3.88480.28181270.23192530X-RAY DIFFRACTION100
3.8848-4.44670.24641210.22262556X-RAY DIFFRACTION100
4.4467-5.60110.28771520.23512560X-RAY DIFFRACTION100
5.6011-49.49520.25871430.24652695X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.15570.2455-0.35194.0061-1.46532.54420.03570.11740.86390.51110.2770.4385-0.0179-0.1683-0.3130.33040.01420.09220.4495-0.00640.58548.0787-4.9489-35.9601
22.2165-0.21580.16881.695-0.0142.54840.3748-0.93-0.36750.2987-0.1807-0.0472-0.6261-0.1518-0.14620.5363-0.14690.05090.64280.1070.318525.6286-10.5976-15.9201
33.35640.6656-0.43664.4947-0.66353.45570.1650.41310.4901-0.42520.27370.4493-0.3523-0.4042-0.17890.28540.0990.09490.43850.05490.497220.1542-1.0011-37.1491
40.8376-0.1013-1.0743.19473.27383.8551-0.07770.032-0.4007-0.51340.6005-0.5811-0.23690.5455-0.15770.6243-0.08670.02280.3782-0.18320.703710.4132-30.5244-47.8668
53.3093-1.0008-0.65072.91720.88851.94690.2249-0.11340.7330.3476-0.0775-0.57090.03280.33630.00310.2635-0.0774-0.00850.3909-0.03740.4591-4.4248-7.0251-25.5012
60.88460.9046-0.18453.4564-1.84733.8986-0.0730.2013-0.1664-0.11870.22090.3831-0.5630.22450.00680.3893-0.03250.03290.4022-0.05630.0974-26.01375.8678-52.0921
72.4756-1.27361.22243.40671.87852.80320.05910.05460.00580.4028-0.2542-0.07510.18360.13390.22230.2895-0.10090.01430.34760.02110.3195-18.4006-4.9048-24.9562
83.7852-0.3434-1.92445.20821.57465.23560.0251-0.181-0.0890.36240.2953-0.1960.833-0.0527-0.1510.3685-0.0216-0.16570.1642-0.03640.512-8.6128-33.6724-24.4606
95.1286-0.44812.12732.57180.26440.96920.42770.047-0.5513-0.75980.032-0.1879-1.0382-0.58420.1760.66340.09250.20110.6592-0.0270.4068-21.93611.5475-65.275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 69 )
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 207 )
3X-RAY DIFFRACTION3chain 'B' and (resid 12 through 69 )
4X-RAY DIFFRACTION4chain 'B' and (resid 70 through 209 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 69 )
6X-RAY DIFFRACTION6chain 'C' and (resid 70 through 210 )
7X-RAY DIFFRACTION7chain 'D' and (resid 15 through 69 )
8X-RAY DIFFRACTION8chain 'D' and (resid 70 through 210 )
9X-RAY DIFFRACTION9chain 'E' and (resid 224 through 239 )

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