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- PDB-3rqg: Cerebral cavernous malformation 3 (CCM3) in complex with paxillin LD4 -

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Basic information

Entry
Database: PDB / ID: 3rqg
TitleCerebral cavernous malformation 3 (CCM3) in complex with paxillin LD4
Components
  • Paxillin LD4 peptide
  • Programmed cell death protein 10
KeywordsPROTEIN BINDING / Protein-peptide complex / FAT domain / Dimerization / Cerebral Cavernous Malformation
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
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: 2.5 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 LD4 peptide


Theoretical massNumber of molelcules
Total (without water)101,1605
Polymers101,1605
Non-polymers00
Water27015
1
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 LD4 peptide


Theoretical massNumber of molelcules
Total (without water)101,1605
Polymers101,1605
Non-polymers00
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-76 kcal/mol
Surface area45920 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10950 Å2
ΔGint-105 kcal/mol
Surface area43120 Å2
MethodPISA
3
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 LD4 peptide


Theoretical massNumber of molelcules
Total (without water)101,1605
Polymers101,1605
Non-polymers00
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation1_655x+1,y,z1
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-104 kcal/mol
Surface area42510 Å2
MethodPISA
4
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 LD4 peptide


Theoretical massNumber of molelcules
Total (without water)101,1605
Polymers101,1605
Non-polymers00
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation1_655x+1,y,z1
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-75 kcal/mol
Surface area45970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.941, 116.159, 124.635
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 LD4 peptide


Mass: 1436.609 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 / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.25 Å3/Da / Density % sol: 45.38 %
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: 2.5→50 Å / Num. all: 272233 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 70.2 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 18.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 2.436 / Rsym value: 0.984 / % 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: 2.5→44.28 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 26.803 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29106 1617 5 %RANDOM
Rwork0.24101 ---
all0.244 32327 --
obs0.24359 32327 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.602 Å2
Baniso -1Baniso -2Baniso -3
1--2.77 Å20 Å20 Å2
2--1.13 Å20 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6740 0 0 15 6755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226840
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9851.9739198
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3785820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36725.045333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.224151369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6591542
X-RAY DIFFRACTIONr_chiral_restr0.0690.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215016
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_it0.3651.54136
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.68826723
X-RAY DIFFRACTIONr_scbond_it0.91732704
X-RAY DIFFRACTIONr_scangle_it1.5034.52475
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 95 -
Rwork0.291 2232 -
obs-2327 99.79 %
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)
19.0117-0.77341.06144.6785-0.29156.5064-0.0207-0.43010.82350.0623-0.0413-0.07-0.23450.48070.0620.0246-0.02030.01070.19790.00540.1785-10.599-4.481738.1236
28.803-1.7540.14693.0743-0.5336.103-0.0513-0.72371.21750.25740.1456-0.2409-0.37760.2178-0.09430.0903-0.07440.00030.2022-0.01220.4172-23.0416-0.488639.636
35.6638-0.51770.2133.0736-0.81612.69630.16570.49260.5165-0.2798-0.0831-0.1933-0.0819-0.1166-0.08270.0898-0.0050.04520.15950.03790.16082.5065-6.628327.9704
47.28582.05240.45974.67921.40215.6607-0.08820.68390.3689-0.35480.0145-0.0084-0.1692-0.04260.07370.06510.00060.02950.21410.04640.217517.7764-3.325326.9058
520.64-6.69089.48569.764-0.449216.49960.17920.8474-1.50041.9092-0.68310.72591.6164-0.03180.50391.61970.20190.2921.9197-0.08481.240121.1817-1.829768.2067
61.6675-0.88880.48481.1032-0.74770.5346-0.0226-0.18210.4699-0.08750.1172-0.04190.087-0.1318-0.09460.3482-0.08610.03770.4671-0.13630.60894.1812-8.147835.8262
73.28782.0872-1.77462.9625-2.75298.5634-0.17250.8129-0.1609-0.33330.34150.0370.09860.0915-0.1690.10780.00730.05970.4111-0.04560.0992-29.1855-5.419311.1251
84.10790.7874-1.74027.2524-4.1128.12250.0993-0.7796-0.40281.29830.18850.64880.1599-0.4618-0.28790.5402-0.07840.13310.27850.21090.3296-12.2617-29.515353.2766
95.2927-1.0153-0.73243.29891.43368.9342-0.0516-0.90661.09760.27790.44650.0294-1.1947-0.0453-0.39490.2410.04370.07910.3602-0.14590.360824.83085.925654.7653
104.01430.1014-1.319911.50133.58869.22530.09630.3978-0.4595-1.35590.0771-0.76010.88990.48-0.17340.51560.1430.02320.1043-0.02870.3555.9848-33.864825.5638
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 DIFFRACTION4D8 - 69
5X-RAY DIFFRACTION5E262 - 273
6X-RAY DIFFRACTION6A213 - 214
7X-RAY DIFFRACTION6C213 - 217
8X-RAY DIFFRACTION6B213 - 214
9X-RAY DIFFRACTION6E9
10X-RAY DIFFRACTION6D213 - 217
11X-RAY DIFFRACTION7A70 - 212
12X-RAY DIFFRACTION8B70 - 210
13X-RAY DIFFRACTION9C70 - 210
14X-RAY DIFFRACTION10D70 - 210

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