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- PDB-3rqf: Cerebral cavernous malformation 3 (CCM3) in complex with paxillin LD2 -

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Basic information

Entry
Database: PDB / ID: 3rqf
TitleCerebral cavernous malformation 3 (CCM3) in complex with paxillin LD2
Components
  • Paxillin LD2 peptide
  • Programmed cell death protein 10
KeywordsPROTEIN BINDING / Protein-peptide complex / FAT domain / Dimerization / Cerebral Cavernous Malformation
Function / homology
Function and homology information


intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / endothelium development / FAR/SIN/STRIPAK complex / positive regulation of intracellular protein transport / positive regulation of stress-activated MAPK cascade / establishment of Golgi localization / negative regulation of cell migration involved in sprouting angiogenesis / wound healing, spreading of cells ...intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / endothelium development / FAR/SIN/STRIPAK complex / positive regulation of intracellular protein transport / positive regulation of stress-activated MAPK cascade / establishment of Golgi localization / negative regulation of cell migration involved in sprouting angiogenesis / wound healing, spreading of cells / positive regulation of Notch signaling pathway / positive regulation of peptidyl-serine phosphorylation / regulation of angiogenesis / positive regulation of protein serine/threonine kinase activity / positive regulation of MAP kinase activity / cellular response to leukemia inhibitory factor / angiogenesis / protein stabilization / intracellular signal transduction / 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
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 / Nucleotidyltransferases domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) ...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 / 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)
Homo Sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, X. / Zhang, R. / Boggon, T.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular Recognition of Leucine-Aspartate Repeat (LD) Motifs by the Focal Adhesion Targeting Homology Domain of Cerebral Cavernous Malformation 3 (CCM3).
Authors: Li, X. / Ji, W. / Zhang, R. / Folta-Stogniew, E. / Min, W. / Boggon, T.J.
History
DepositionApr 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref_seq_dif.details

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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: Programmed cell death protein 10
C: Programmed cell death protein 10
D: Programmed cell death protein 10
E: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)101,2665
Polymers101,2665
Non-polymers00
Water724
1
B: Programmed cell death protein 10

A: Programmed cell death protein 10
C: Programmed cell death protein 10
D: Programmed cell death protein 10
E: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)101,2665
Polymers101,2665
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_655x+1,y,z1
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-67 kcal/mol
Surface area44510 Å2
MethodPISA
2
C: Programmed cell death protein 10
D: Programmed cell death protein 10

A: Programmed cell death protein 10
B: Programmed cell death protein 10
E: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)101,2665
Polymers101,2665
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
identity operation1_555x,y,z1
Buried area11700 Å2
ΔGint-97 kcal/mol
Surface area41000 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11120 Å2
ΔGint-102 kcal/mol
Surface area41580 Å2
MethodPISA
4
D: Programmed cell death protein 10

A: Programmed cell death protein 10
B: Programmed cell death protein 10
C: Programmed cell death protein 10
E: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)101,2665
Polymers101,2665
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-69 kcal/mol
Surface area44390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.862, 115.469, 124.379
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
Programmed cell death protein 10


Mass: 24930.779 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD10 / Plasmid: Modified pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9BUL8
#2: Protein/peptide Paxillin LD2 peptide


Mass: 1542.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo Sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1-0.2 M potassium fluoride,15-20% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.078 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 1, 2010 / Details: mirrors
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 207195 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 78.5 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 18.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.263 / Rsym value: 0.82 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L8I

3l8i


Resolution: 2.7→42.52 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.897 / SU B: 36.684 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1292 5.1 %RANDOM
Rwork0.2373 ---
all0.24 25361 --
obs0.2399 25361 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.315 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å20 Å2
2--1.76 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6470 0 0 4 6474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226560
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8971.9748813
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8355785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65225.079315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.243151318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4491539
X-RAY DIFFRACTIONr_chiral_restr0.0620.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214777
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_it0.2331.53975
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.44126452
X-RAY DIFFRACTIONr_scbond_it0.54532585
X-RAY DIFFRACTIONr_scangle_it0.9134.52361
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.705→2.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 81 -
Rwork0.322 1683 -
obs-1764 96.45 %
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)
112.50280.8141-0.91715.1987-0.83698.4468-0.1084-0.43051.1290.00750.2874-0.1322-0.08890.5457-0.1790.0058-0.01120.00680.2262-0.06250.1895-10.6476-4.694638.0908
29.4168-1.94321.30213.2348-0.3729.4645-0.0025-0.20131.29980.24380.09880.0074-0.44430.1818-0.09630.0613-0.05270.02590.1242-0.00010.3681-23.1407-0.579139.36
38.2213-1.60181.06345.3329-0.70982.77190.11210.58440.7628-0.3143-0.1254-0.4456-0.1356-0.14760.01330.11550.00710.11670.23350.01950.182.4288-6.661627.9169
49.79612.45921.26833.83492.047.6794-0.34060.79470.9875-0.20820.0760.2869-0.0784-0.09530.26470.04110.01180.02030.23190.09370.264117.4085-3.67526.7784
53.36382.3228-2.74823.8438-4.529611.457-0.01060.580.1-0.11750.34730.27820.04870.0561-0.33670.08680.07120.03320.3635-0.02030.0824-29.2407-5.524310.9361
64.51460.9897-2.91039.0636-5.659210.14710.0507-0.5236-0.46141.2940.16390.6036-0.1824-0.1713-0.21460.3904-0.01570.09090.11690.1390.2417-12.2988-29.65952.3435
76.3043-1.6516-0.07585.49253.015210.579-0.3471-1.17350.98540.2690.4502-0.1123-0.7565-0.4853-0.10310.13650.10460.01950.5553-0.17860.266324.59143.889154.8192
83.8620.6915-2.905414.22545.887212.1014-0.27610.1408-0.3574-1.13540.3992-1.02520.76150.4368-0.12310.39830.09310.07220.0782-0.03680.32977.0305-33.735926.2365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 69
2X-RAY DIFFRACTION2B10 - 69
3X-RAY DIFFRACTION3C-1 - 69
4X-RAY DIFFRACTION4D9 - 69
5X-RAY DIFFRACTION5A70 - 212
6X-RAY DIFFRACTION6B70 - 210
7X-RAY DIFFRACTION7C70 - 209
8X-RAY DIFFRACTION8D70 - 209

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