[English] 日本語
Yorodumi
- PDB-8ael: SYNJ2BP complex with a synthetic Vangl2 peptide (3mer). -

+
Open data


ID or keywords:

Loading...

-
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


positive regulation of low-density lipoprotein particle receptor binding / negative regulation of sprouting angiogenesis / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / 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 low-density lipoprotein particle receptor binding / negative regulation of sprouting angiogenesis / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / 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 / regulation of Notch signaling pathway / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / embryo development / receptor localization to synapse / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / plasma membrane protein complex / calcium-dependent phospholipid binding / negative regulation of receptor internalization / establishment or maintenance of epithelial cell apical/basal polarity / collagen fibril organization / Dissolution of Fibrin Clot / S100 protein binding / virion binding / positive regulation of low-density lipoprotein receptor activity / negative regulation of endothelial cell migration / osteoclast development / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / receptor clustering / positive regulation of exocytosis / negative regulation of endothelial cell proliferation / Rho protein signal transduction / regulation of endocytosis / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / protein targeting / fibrinolysis / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / negative regulation of angiogenesis / cell-matrix adhesion / response to activity / adherens junction / postsynaptic density membrane / lung development / calcium channel activity / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / neuromuscular junction / negative regulation of ERK1 and ERK2 cascade / sarcolemma / nuclear matrix / cell-cell adhesion / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / late endosome membrane / midbody / chemical synaptic transmission / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / mitochondrial outer membrane / early endosome / endosome / neuron projection / lysosomal membrane / calcium ion binding / Neutrophil degranulation / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more