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- PDB-8ael: SYNJ2BP complex with a synthetic Vangl2 peptide (3mer). -

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Basic information

Entry
Database: PDB / ID: 8ael
TitleSYNJ2BP complex with a synthetic Vangl2 peptide (3mer).
Components
  • GLY-GLY-GLY-THR-SER-VAL
  • Synaptojanin-2-binding protein,Annexin A2
KeywordsMEMBRANE PROTEIN / PDZ domain / Peptide Binding Motif
Function / homology
Function and homology information


negative regulation of sprouting angiogenesis / : / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process ...negative regulation of sprouting angiogenesis / : / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / regulation of Notch signaling pathway / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / cornified envelope / vesicle budding from membrane / osteoclast development / plasma membrane protein complex / calcium-dependent phospholipid binding / negative regulation of receptor internalization / Dissolution of Fibrin Clot / S100 protein binding / collagen fibril organization / vesicle membrane / : / negative regulation of endothelial cell migration / epithelial cell apoptotic process / phosphatidylserine binding / positive regulation of receptor recycling / negative regulation of endothelial cell proliferation / positive regulation of exocytosis / regulation of endocytosis / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / Rho protein signal transduction / protein targeting / cytoskeletal protein binding / fibrinolysis / lipid droplet / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of angiogenesis / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / response to activity / adherens junction / lung development / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / negative regulation of ERK1 and ERK2 cascade / sarcolemma / RNA polymerase II transcription regulator complex / nuclear matrix / calcium-dependent protein binding / azurophil granule lumen / late endosome membrane / melanosome / midbody / protease binding / : / basolateral plasma membrane / angiogenesis / vesicle / mitochondrial outer membrane / early endosome / endosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / plasma membrane / cytosol / 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 / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Annexin A2 / Synaptojanin-2-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionJul 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: pdbx_database_related

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptojanin-2-binding protein,Annexin A2
B: GLY-GLY-GLY-THR-SER-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,23710
Polymers47,7082
Non-polymers5298
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-35 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.670, 75.060, 108.920
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 A2 / Mitochondrial outer membrane protein 25 / Annexin II / Annexin-2 / Calpactin I heavy chain / ...Mitochondrial outer membrane protein 25 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / Lipocortin II / Placental anticoagulant protein IV / PAP-IV / Protein I / p36


Mass: 47231.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNJ2BP, OMP25, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: P57105, UniProt: P07355
#2: Protein/peptide GLY-GLY-GLY-THR-SER-VAL


Mass: 476.483 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.88 %
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-1 / 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: 2.2→37.53 Å / Num. obs: 24694 / % possible obs: 96.6 % / Redundancy: 13.802 % / Biso Wilson estimate: 35.97 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.298 / Rrim(I) all: 0.309 / Χ2: 0.803 / Net I/σ(I): 6 / Num. measured all: 340828
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
2.2-2.2614.2251.1870.9926089185118340.7221.23199.1
2.26-2.3214.2661.0951.1725279181817720.7641.13697.5
2.32-2.3913.9660.9731.5224091176217250.8011.0197.9
2.39-2.4613.8570.8611.8923488170416950.8470.89399.5
2.46-2.5413.8160.7792.2622589166516350.8510.80998.2
2.54-2.6313.6070.7422.4221241159915610.8480.77197.6
2.63-2.7313.3950.6393.0420227156515100.8780.66596.5
2.73-2.8413.1140.5463.8518674151314240.9010.56894.1
2.84-2.9712.7190.4374.8315594142512260.9260.45686
2.97-3.1113.8280.3846.1515446139411170.9580.39980.1
3.11-3.2814.4170.3387.3918684131012960.9730.3598.9
3.28-3.4814.4470.289.1117958125412430.9830.2999.1
3.48-3.7214.2760.22910.6416788118711760.9890.23899.1
3.72-4.0214.1780.18712.7715567110810980.9920.19499.1
4.02-4.413.9920.16613.8814188101910140.9930.17299.5
4.4-4.9213.8380.16213.98126769209160.9930.16899.6
4.92-5.6813.6950.1812.03114358418350.9920.18799.3
5.68-6.9613.2730.18812.0294777177140.9910.19599.6
6.96-9.8413.0460.11616.0873325655620.9970.12199.5
9.84-37.5311.7450.08318.0940053543410.9980.08696.3

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Processing

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

2jik


Resolution: 2.2→37.53 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 1231 5 %
Rwork0.2214 23398 -
obs0.2235 24629 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.85 Å2 / Biso mean: 45.1786 Å2 / Biso min: 21.37 Å2
Refinement stepCycle: final / Resolution: 2.2→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 28 224 3536
Biso mean--54.62 44.8 -
Num. residues----423
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2880.36461370.3116259098
2.288-2.39220.34711350.3028259198
2.3922-2.51830.39121380.2991261099
2.5183-2.6760.32631380.2781261698
2.676-2.88250.31021320.2577251294
2.8825-3.17250.22691180.2269225184
3.1725-3.63120.22851420.2094267799
3.6312-4.57370.21331430.172272699
4.5737-37.530.26571480.2004282599
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)
14.656-2.4288-5.85760.68462.63085.9574-0.1333-0.0764-0.39860.0029-0.0363-0.038-0.0450.30770.14350.4702-0.0615-0.03190.51310.06360.42670.0299-2.955218.7156
21.3195-0.9743-0.38131.98110.63520.8619-0.1215-0.1911-0.08820.22350.1496-0.00180.09640.0071-0.02170.24870.002-0.02450.3009-0.00270.27226.96541.94037.5222
32.4005-2.4572-1.61856.47910.00135.4929-0.19810.67850.53460.1037-0.1324-1.57360.04170.92260.32520.58660.29560.05570.95560.23480.84553.2901-4.760430.8409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 117 )A6 - 117
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 422 )A118 - 422
3X-RAY DIFFRACTION3chain 'B' and (resid 34 through 39 )B34 - 39

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