[English] 日本語
Yorodumi
- PDB-7p70: The PDZ-domain of SNTB1 complexed with the PDZ-binding motif of H... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p70
TitleThe PDZ-domain of SNTB1 complexed with the PDZ-binding motif of HPV35-E6
Components
  • Beta-1-syntrophin,Annexin A2
  • Protein E6
KeywordsPEPTIDE BINDING PROTEIN / PDZ / complex
Function / homology
Function and homology information


: / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / dystrophin-associated glycoprotein complex / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion ...: / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / dystrophin-associated glycoprotein complex / 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 / 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 / collagen fibril organization / S100 protein binding / Dissolution of Fibrin Clot / virion binding / osteoclast development / positive regulation of low-density lipoprotein receptor activity / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / positive regulation of exocytosis / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytoskeletal protein binding / lipid droplet / cell-matrix adhesion / response to activity / muscle contraction / PDZ domain binding / adherens junction / lung development / sarcolemma / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / calcium channel activity / : / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / late endosome membrane / actin binding / midbody / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / host cell cytoplasm / cytoskeleton / calmodulin binding / early endosome / endosome / lysosomal membrane / focal adhesion / DNA-templated transcription / synapse / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / calcium ion binding / Neutrophil degranulation / regulation of DNA-templated transcription / structural molecule activity / cell surface / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Syntrophin, split Pleckstrin homology (PH) domain / PH domain / Syntrophin / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin ...Syntrophin, split Pleckstrin homology (PH) domain / PH domain / Syntrophin / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / PDZ domain / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Annexin A2 / Protein E6 / Beta-1-syntrophin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus 35
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
C: Protein E6
A: Beta-1-syntrophin,Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6219
Polymers48,2362
Non-polymers3857
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-49 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.800, 60.580, 140.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide Protein E6


Mass: 1536.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: N-terminal biotin-ttds label / Source: (synth.) Human papillomavirus 35 / References: UniProt: P27228
#2: Protein Beta-1-syntrophin,Annexin A2 / 59 kDa dystrophin-associated protein A1 basic component 1 / DAPA1B / BSYN2 / Syntrophin-2 / Tax ...59 kDa dystrophin-associated protein A1 basic component 1 / DAPA1B / BSYN2 / Syntrophin-2 / Tax interaction protein 43 / TIP-43 / 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: 46699.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNTB1, SNT2B1, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: Q13884, UniProt: P07355
#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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% polyethylene glycol 3350, 200 mM sodium malonate buffered at pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46 Å / Num. obs: 32358 / % possible obs: 99.5 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rrim(I) all: 0.153 / Net I/σ(I): 12.57
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 1.36 / Num. unique obs: 2327 / CC1/2: 0.503 / Rrim(I) all: 2.13

-
Processing

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

5n7d

2vrf


Resolution: 2→45.897 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 1613 4.99 %
Rwork0.1826 30686 -
obs0.184 32299 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.63 Å2 / Biso mean: 46.0567 Å2 / Biso min: 17.57 Å2
Refinement stepCycle: final / Resolution: 2→45.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 17 253 3553
Biso mean--45.07 48.32 -
Num. residues----414
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0001-2.05890.33291300.2848248399
2.0589-2.12540.28761330.2502251299
2.1254-2.20130.2581320.2224251999
2.2013-2.28950.23351320.2171251299
2.2895-2.39360.25061320.20012534100
2.3936-2.51980.20671330.19182523100
2.5198-2.67770.24351330.19772523100
2.6777-2.88440.22721360.19592583100
2.8844-3.17460.23741340.18712543100
3.1746-3.63380.21661370.17512590100
3.6338-4.57760.15871370.14782623100
4.5776-45.8970.17941440.16892741100

+
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