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- PDB-7r2t: SYNJ2BP complex with a phosphorylated Vangl2 peptide at the P-1 p... -

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Basic information

Entry
Database: PDB / ID: 7r2t
TitleSYNJ2BP complex with a phosphorylated Vangl2 peptide at the P-1 position.
Components
  • Synaptojanin-2-binding protein,Annexin
  • Vangle2 peptide binding motif with the P-1 phosphrylated
KeywordsMEMBRANE PROTEIN / PDZ domain / Peptide Binding Motif / phosphorylation
Function / homology
Function and homology information


phospholipase inhibitor activity / negative regulation of sprouting angiogenesis / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / regulation of Notch signaling pathway / calcium-dependent phospholipid binding / vesicle membrane / negative regulation of endothelial cell migration / phosphatidylserine binding / negative regulation of endothelial cell proliferation / regulation of endocytosis ...phospholipase inhibitor activity / negative regulation of sprouting angiogenesis / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / regulation of Notch signaling pathway / calcium-dependent phospholipid binding / vesicle membrane / negative regulation of endothelial cell migration / phosphatidylserine binding / negative regulation of endothelial cell proliferation / regulation of endocytosis / basement membrane / Rho protein signal transduction / protein targeting / cytoskeletal protein binding / negative regulation of angiogenesis / negative regulation of ERK1 and ERK2 cascade / mitochondrial outer membrane / calcium ion binding / mitochondrion / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / : / Annexin V; domain 1 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Annexin / Synaptojanin-2-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCarrasco, K. / Cousido Siah, A. / Gogl, G. / Betzi, S. / McEwen, A. / Kostmann, C. / Trave, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2024
Title: PDZome-wide and structural characterization of the PDZ-binding motif of VANGL2.
Authors: Montserrat-Gomez, M. / Gogl, G. / Carrasco, K. / Betzi, S. / Durbesson, F. / Cousido-Siah, A. / Kostmann, C. / Essig, D.J. / Stromgaard, K. / Ostergaard, S. / Morelli, X. / Trave, G. / ...Authors: Montserrat-Gomez, M. / Gogl, G. / Carrasco, K. / Betzi, S. / Durbesson, F. / Cousido-Siah, A. / Kostmann, C. / Essig, D.J. / Stromgaard, K. / Ostergaard, S. / Morelli, X. / Trave, G. / Vincentelli, R. / Bailly, E. / Borg, J.P.
History
DepositionFeb 5, 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
Revision 1.2Sep 4, 2024Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptojanin-2-binding protein,Annexin
B: Vangle2 peptide binding motif with the P-1 phosphrylated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2919
Polymers48,9062
Non-polymers3857
Water41423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.100, 61.380, 145.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 47774.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNJ2BP, OMP25, ANXA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P57105, UniProt: A0A4W2GEM6
#2: Protein/peptide Vangle2 peptide binding motif with the P-1 phosphrylated


Mass: 1131.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
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: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→46.888 Å / Num. obs: 19104 / % possible obs: 98.8 % / Redundancy: 12.945 % / Biso Wilson estimate: 62.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.086 / Χ2: 0.886 / Net I/σ(I): 20.45 / Num. measured all: 247294 / Scaling rejects: 2
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
2.5-2.5712.1421.3221.7616198138313340.6061.3896.5
2.57-2.6412.4511.0422.4117195138213810.7621.08799.9
2.64-2.7114.1480.8563.1918138131112820.8340.88897.8
2.71-2.813.9650.6424.2517861130412790.8990.66698.1
2.8-2.8913.9230.475.7417432125212520.9430.488100
2.89-2.9914.0720.3737.4116774121211920.9660.38798.3
2.99-3.113.7430.289.6515873117211550.980.2998.5
3.1-3.2313.6740.20712.9515561115011380.9880.21499
3.23-3.3713.3530.15916.5314395108010780.9940.16699.8
3.37-3.5413.2660.12521.3213677104510310.9950.1398.7
3.54-3.7312.7890.092271267410009910.9980.09699.1
3.73-3.9511.3560.07232.41105279359270.9980.07599.1
3.95-4.2311.7480.05940.08105269028960.9980.06299.3
4.23-4.5612.3010.05145.81101618328260.9990.05499.3
4.56-512.1410.0514694707837800.9990.05399.6
5-5.5911.1260.05241.4677667036980.9990.05499.3
5.59-6.4613.2570.0546.7882596256230.9990.05399.7
6.46-7.9112.7340.03951.73695354954610.04199.5
7.91-11.1812.0970.02961.16525043643410.03199.5
11.18-46.8889.9770.02755.78260427426110.02995.3

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Processing

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

2jik


Resolution: 2.5→46.888 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 955 5.01 %
Rwork0.2167 18109 -
obs0.2178 19064 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.5 Å2 / Biso mean: 78.2494 Å2 / Biso min: 35.01 Å2
Refinement stepCycle: final / Resolution: 2.5→46.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 17 23 3324
Biso mean--82.82 63.69 -
Num. residues----421
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.63180.36521320.322251698
2.6318-2.79670.35411320.2814251298
2.7967-3.01260.3021350.264255999
3.0126-3.31560.28571350.241256099
3.3156-3.79520.23191360.2174258599
3.7952-4.78090.20531390.196263199
4.7809-46.80.21591460.19432746100
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)
14.6464-4.4099-3.68934.31233.32823.1091-0.9019-0.4717-1.21550.92430.23190.58420.5835-0.43111.09271.3206-0.13240.21610.9057-0.08650.89230.907924.91727.7946
20.4651.44581.52613.33423.42373.7373-0.14230.30730.0817-0.716-0.0140.2493-0.75360.4031-0.09490.8466-0.08070.0780.9394-0.0360.5945-0.703829.6303-2.7322
31.5049-0.36540.27142.2252-1.59942.80150.11620.0548-0.0582-0.3608-0.2697-0.45280.38840.79230.0370.46360.1015-0.00040.5275-0.06020.5676-12.11886.4199-34.589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 202 through 206 )B202 - 206
2X-RAY DIFFRACTION2chain 'A' and (resid 7 through 117 )A7 - 117
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 422 )A118 - 422

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