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- PDB-7r2m: SYNJ2BP complex with a synthetic Vangl2 peptide (9mer). -

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Basic information

Entry
Database: PDB / ID: 7r2m
TitleSYNJ2BP complex with a synthetic Vangl2 peptide (9mer).
Components
  • Synaptojanin-2-binding protein,Annexin
  • Vangl2 peptide
KeywordsMEMBRANE PROTEIN / PDZ domain / Peptide Binding Motif
Function / homology
Function and homology information


phospholipase inhibitor activity / negative regulation of sprouting angiogenesis / regulation of Notch signaling pathway / embryo development / receptor localization to synapse / calcium-dependent phospholipid binding / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of endothelial cell migration / receptor clustering / negative regulation of endothelial cell proliferation ...phospholipase inhibitor activity / negative regulation of sprouting angiogenesis / regulation of Notch signaling pathway / embryo development / receptor localization to synapse / calcium-dependent phospholipid binding / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of endothelial cell migration / receptor clustering / negative regulation of endothelial cell proliferation / Rho protein signal transduction / regulation of endocytosis / basement membrane / protein targeting / cytoskeletal protein binding / negative regulation of angiogenesis / postsynaptic density membrane / neuromuscular junction / negative regulation of ERK1 and ERK2 cascade / cell-cell adhesion / chemical synaptic transmission / basolateral plasma membrane / mitochondrial outer membrane / neuron projection / calcium ion binding / mitochondrion / extracellular region / membrane
Similarity search - Function
Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / PDZ domain ...Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Annexin / Synaptojanin-2-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCarrasco, K. / Cousido Siah, A. / Gogl, G. / Betzi, S. / McEwen, A. / Kostmann, C. / Trave, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: SYNJ2BP PDZ domain in complex with a synthetic Vangl2 peptide.
Authors: Carrasco, K. / Cousido Siah, A. / Gogl, G. / Betzi, S. / McEwen, A. / Kostmann, C. / Trave, G.
History
DepositionFeb 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Synaptojanin-2-binding protein,Annexin
A: Synaptojanin-2-binding protein,Annexin
B: Vangl2 peptide
E: Vangl2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,60718
Polymers100,5234
Non-polymers1,08414
Water1,44180
1
D: Synaptojanin-2-binding protein,Annexin
E: Vangl2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,00110
Polymers50,2622
Non-polymers7398
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-44 kcal/mol
Surface area21370 Å2
2
A: Synaptojanin-2-binding protein,Annexin
B: Vangl2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6068
Polymers50,2622
Non-polymers3456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-36 kcal/mol
Surface area20900 Å2
Unit cell
Length a, b, c (Å)60.270, 60.710, 143.150
Angle α, β, γ (deg.)90.000, 92.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules DABE

#1: Protein Synaptojanin-2-binding protein,Annexin / Mitochondrial outer membrane protein 25


Mass: 47774.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNJ2BP, OMP25, ANXA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P57105, UniProt: A0A4W2GEM6
#2: Protein/peptide Vangl2 peptide


Mass: 2486.738 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 94 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Ammonium sulfate, 0.1 M Sodium formate, 0.1 M HEPES 7.0, 25 % v/v PEG Smear Broad

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.4→47.656 Å / Num. obs: 39408 / % possible obs: 96.5 % / Redundancy: 7.277 % / Biso Wilson estimate: 50.54 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.14 / Χ2: 0.849 / Net I/σ(I): 10.15 / Num. measured all: 286773 / Scaling rejects: 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.467.4481.2911.2221807299229280.5731.38797.9
2.46-2.537.3811.0851.521190294228710.6521.16797.6
2.53-2.67.3880.9781.7220791283028140.6931.05299.4
2.6-2.687.3810.8192.1319832274626870.7540.88197.9
2.68-2.777.2750.6582.6619177269426360.8280.70997.8
2.77-2.877.2560.5133.4918647260325700.8870.55298.7
2.87-2.987.2330.414.4117324245923950.9180.44297.4
2.98-3.17.1080.3225.6116455239923150.9430.34896.5
3.1-3.246.9960.2427.115454232622090.9720.26295
3.24-3.396.8610.1829.2514051223020480.9830.19791.8
3.39-3.587.0320.14511.8711314211416090.9880.15776.1
3.58-3.797.4120.11115.7413935198518800.9940.11994.7
3.79-4.067.5630.08719.9314204188518780.9960.09499.6
4.06-4.387.5250.0724.213064174317360.9970.07699.6
4.38-4.87.4690.06524.8512018161616090.9970.0799.6
4.8-5.377.3670.06923.710800146914660.9970.07599.8
5.37-6.27.2610.07521.539417130112970.9970.08199.7
6.2-7.597.1750.06325.068000111911150.9970.06899.6
7.59-10.737.110.03935.9260868648560.9980.04399.1
10.73-47.6566.5580.03637.0532075034890.9990.03997.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JIK

2jik


Resolution: 2.4→47.656 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 1969 5 %
Rwork0.2152 37416 -
obs0.2163 39385 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.78 Å2 / Biso mean: 67.5008 Å2 / Biso min: 26.44 Å2
Refinement stepCycle: final / Resolution: 2.4→47.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6701 0 47 80 6828
Biso mean--72.47 58.6 -
Num. residues----846
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.460.33961410.3266268298
2.46-2.52650.35331430.2949270698
2.5265-2.60090.28111430.2899271799
2.6009-2.68480.31341400.2888266898
2.6848-2.78080.2961430.2821270198
2.7808-2.89210.28841410.2628269298
2.8921-3.02370.2571420.2565269998
3.0237-3.18310.27051410.237267496
3.1831-3.38240.27961330.2208252192
3.3824-3.64350.2321140.2265217779
3.6435-4.010.19861460.1977277599
4.01-4.58990.20641450.1753275499
4.5899-5.78110.23681470.19572792100
5.7811-47.6560.20041500.1797285899
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)
11.3171-1.67612.07062.4126-2.56273.23260.1027-0.0409-0.17810.0840.1408-0.0036-0.2237-0.481-0.22430.70830.04340.15980.9460.06310.6047.77919.8976-103.654
21.8760.43230.58811.95021.08891.91560.0427-0.00420.01530.0201-0.24560.46950.0911-0.37870.15990.3342-0.02560.00030.30630.00220.471715.5801-5.4651-72.8471
33.352-2.21-2.92842.12872.00792.5606-0.2035-0.77530.2920.32080.3088-0.0212-0.04510.6558-0.17450.59560.0705-0.11540.7579-0.02010.389532.2643-39.9439-32.8047
42.45450.7006-0.72012.1588-1.23732.42650.0591-0.07920.03420.1746-0.1479-0.3205-0.2090.54180.05260.4338-0.0608-0.00050.4557-0.07620.422718.0709-15.9538-2.0298
55.8586-0.2390.81868.28781.91047.24240.0656-0.19350.69550.2906-0.13060.3126-0.5961-0.35560.07880.87380.00690.02880.857-0.03140.452335.6853-35.1035-42.6186
65.6589-3.37551.72635.92062.02172.9098-0.05960.6402-0.4288-1.62450.11-0.11190.6962-0.107-0.13361.0736-0.07490.09810.95510.16350.5266.606715.4834-113.3411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 6 through 117 )D6 - 117
2X-RAY DIFFRACTION2chain 'D' and (resid 118 through 422 )D118 - 422
3X-RAY DIFFRACTION3chain 'A' and (resid 6 through 117 )A6 - 117
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 422 )A118 - 422
5X-RAY DIFFRACTION5chain 'B' and (resid 201 through 206 )B201 - 206
6X-RAY DIFFRACTION6chain 'E' and (resid 202 through 206 )E202 - 206

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