[English] 日本語
Yorodumi
- PDB-7p73: The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p73
TitleThe PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1
Components
  • Protein Tax-1
  • Synaptojanin-2-binding protein,Annexin A2
KeywordsPEPTIDE BINDING PROTEIN / PDZ / complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / negative regulation of sprouting angiogenesis / AnxA2-p11 complex / membrane raft assembly / symbiont-mediated activation of host NF-kappaB cascade / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / phospholipase A2 inhibitor activity / positive regulation of low-density lipoprotein particle clearance ...symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / negative regulation of sprouting angiogenesis / AnxA2-p11 complex / membrane raft assembly / symbiont-mediated activation of host NF-kappaB cascade / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / phospholipase A2 inhibitor activity / positive regulation of low-density lipoprotein particle clearance / positive regulation of vesicle fusion / myelin sheath adaxonal region / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / regulation of Notch signaling pathway / cadherin binding involved in cell-cell adhesion / cornified envelope / Schmidt-Lanterman incisure / vesicle budding from membrane / plasma membrane protein complex / calcium-dependent phospholipid binding / osteoclast development / 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 / negative regulation of endothelial cell proliferation / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / regulation of endocytosis / positive regulation of receptor recycling / basement membrane / positive regulation of exocytosis / Smooth Muscle Contraction / regulation of neurogenesis / protein targeting / cytoskeletal protein binding / fibrinolysis / Rho protein signal transduction / phosphatidylinositol-4,5-bisphosphate binding / lipid droplet / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lung development / 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 / serine-type endopeptidase inhibitor activity / mRNA transcription by RNA polymerase II / sarcolemma / negative regulation of ERK1 and ERK2 cascade / SH3 domain binding / RNA polymerase II transcription regulator complex / nuclear matrix / calcium-dependent protein binding / azurophil granule lumen / late endosome membrane / melanosome / : / protease binding / midbody / angiogenesis / basolateral plasma membrane / vesicle / host cell cytoplasm / mitochondrial outer membrane / early endosome / endosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / positive regulation of DNA-templated transcription / host cell nucleus / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / DNA binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
HTLV Tax / HTLV Tax / Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat ...HTLV Tax / HTLV Tax / 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
Protein Tax-1 / Annexin A2 / Synaptojanin-2-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human T-cell leukemia virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGogl, G. / Cousido-Siah, A. / Trave, G.
CitationJournal: Nat Commun / Year: 2022
Title: Quantitative fragmentomics allow affinity mapping of interactomes.
Authors: Gogl, G. / Zambo, B. / Kostmann, C. / Cousido-Siah, A. / Morlet, B. / Durbesson, F. / Negroni, L. / Eberling, P. / Jane, P. / Nomine, Y. / Zeke, A. / Ostergaard, S. / Monsellier, E. / Vincentelli, R. / Trave, G.
History
DepositionJul 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Synaptojanin-2-binding protein,Annexin A2
B: Protein Tax-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,89113
Polymers49,2422
Non-polymers64911
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-67 kcal/mol
Surface area21120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.450, 63.990, 146.950
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: 47646.832 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 Protein Tax-1 / Protein X-LOR / Protein PX / Trans-activating transcriptional regulatory protein of HTLV-1


Mass: 1595.643 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: N-terminal biotin-ttds label
Source: (synth.) Human T-cell leukemia virus 1 (strain Japan ATK-1 subtype A)
References: UniProt: P03409
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / 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.: 421 / 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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 120mM Monosaccharides, 100mM Buffer System 3 pH 8.5, 50 % Precipitant Mix 2 (F10 Morpheus)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→47 Å / Num. obs: 48765 / % possible obs: 98.3 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rrim(I) all: 0.142 / Net I/σ(I): 15.18
Reflection shellResolution: 1.85→1.9 Å / Mean I/σ(I) obs: 1.75 / Num. unique obs: 3522 / CC1/2: 0.593 / Rrim(I) all: 2.29

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N7D, 2JIK

5n7d

2jik


Resolution: 1.85→46.682 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1918 2435 5 %
Rwork0.1679 46273 -
obs0.1691 48708 98.35 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.96 Å2 / Biso mean: 38.4789 Å2 / Biso min: 17.2 Å2
Refinement stepCycle: final / Resolution: 1.85→46.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 31 421 3847
Biso mean--44.99 45.1 -
Num. residues----426
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.88770.31471410.2788266897
1.8877-1.92870.31211370.2643263497
1.9287-1.97360.26551400.241264798
1.9736-2.02290.23711410.2124268598
2.0229-2.07760.24611410.1951267297
2.0776-2.13880.2361410.1858268398
2.1388-2.20780.21561410.1686267198
2.2078-2.28670.21841410.1733268398
2.2867-2.37830.20281430.1714271298
2.3783-2.48650.20671420.1671269399
2.4865-2.61760.20611440.1672273499
2.6176-2.78160.20351430.1697272198
2.7816-2.99630.17561450.1652274799
2.9963-3.29770.17221430.1636275599
3.2977-3.77480.17391470.155279899
3.7748-4.75510.14891480.1336281099
4.7551-46.6820.18431570.1698296099
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)
14.2459-1.04164.37443.3667-1.42855.1267-0.0691-0.1538-0.24780.19560.1076-0.2240.2409-0.1738-0.02650.44820.02510.12120.33730.00010.2674-2.600630.90571.5225
21.16260.36650.25741.00160.41290.70480.02570.00110.01830.0192-0.05440.12680.0071-0.06350.03780.1690.0036-0.00050.17070.02410.184511.49528.302535.3321
33.32982.6031-0.23173.4063-3.38449.4565-0.11630.1938-0.9004-1.5636-0.04110.17320.9466-0.07320.17580.937-0.0067-0.06090.4589-0.06140.473-4.941723.4338-7.0646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 102 )A3 - 102
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 422 )A103 - 422
3X-RAY DIFFRACTION3chain 'B' and (resid 348 through 353 )B348 - 353

+
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://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