[English] 日本語
Yorodumi
- PDB-7qqn: The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qqn
TitleThe PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of TRPV3
Components
  • Gamma-1-syntrophin,Annexin A2
  • Transient receptor potential cation channel subfamily V member 3
KeywordsPEPTIDE BINDING PROTEIN / PDZ / linear motif / crystallization chaperone
Function / homology
Function and homology information


syntrophin complex / 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 / negative regulation of hair cycle ...syntrophin complex / 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 / negative regulation of hair cycle / 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 / cell communication / 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 / TRP channels / osteoclast development / positive regulation of low-density lipoprotein receptor activity / epithelial cell apoptotic process / response to temperature stimulus / positive regulation of receptor recycling / phosphatidylserine binding / positive regulation of calcium ion import / positive regulation of exocytosis / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / phosphatidylinositol-4,5-bisphosphate binding / fibrinolysis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytoskeletal protein binding / lipid droplet / cell-matrix adhesion / response to activity / calcium ion transmembrane transport / adherens junction / lung development / sarcolemma / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / calcium channel activity / ruffle membrane / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / late endosome membrane / actin binding / midbody / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / receptor complex / cytoskeleton / early endosome / endosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / structural molecule activity / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Syntrophin / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Syntrophin / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat / 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 / Ankyrin repeats (3 copies) / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Annexin A2 / Transient receptor potential cation channel subfamily V member 3 / Gamma-1-syntrophin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsCousido-Siah, A. / Trave, G. / Gogl, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: A scalable strategy to solve structures of PDZ domains and their complexes.
Authors: Cousido-Siah, A. / Carneiro, L. / Kostmann, C. / Ecsedi, P. / Nyitray, L. / Trave, G. / Gogl, G.
History
DepositionJan 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: Gamma-1-syntrophin,Annexin A2
C: Gamma-1-syntrophin,Annexin A2
B: Transient receptor potential cation channel subfamily V member 3
D: Transient receptor potential cation channel subfamily V member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,32414
Polymers95,8714
Non-polymers45310
Water3,855214
1
A: Gamma-1-syntrophin,Annexin A2
B: Transient receptor potential cation channel subfamily V member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0966
Polymers47,9362
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-41 kcal/mol
Surface area21050 Å2
MethodPISA
2
C: Gamma-1-syntrophin,Annexin A2
D: Transient receptor potential cation channel subfamily V member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2288
Polymers47,9362
Non-polymers2926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-50 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.830, 132.440, 63.660
Angle α, β, γ (deg.)90.000, 100.770, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Gamma-1-syntrophin,Annexin A2 / G1SYN / Syntrophin-4 / SYN4 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy ...G1SYN / Syntrophin-4 / SYN4 / 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: 46770.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNTG1, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NSN8, UniProt: P07355
#2: Protein/peptide Transient receptor potential cation channel subfamily V member 3 / TrpV3 / Vanilloid receptor-like 3 / VRL-3


Mass: 1165.202 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: N-terminal biotin-ado-ado linker (amino-dodecanoic acid)
Source: (synth.) Homo sapiens (human) / References: UniProt: Q8NET8
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Lithium sulfate 0.05 M Magnesium chloride hexahydrate 0.1 M HEPES 7.8 20 % v/v PEG Smear High

-
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: Oct 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→45.467 Å / Num. obs: 35752 / % possible obs: 99.8 % / Redundancy: 6.66 % / CC1/2: 0.996 / Rrim(I) all: 0.222 / Net I/σ(I): 8.22
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 6.66 % / Mean I/σ(I) obs: 1.18 / Num. unique obs: 2621 / CC1/2: 0.529 / Rrim(I) all: 2.042 / % possible all: 99.6

-
Processing

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

5n7d


Resolution: 2.45→45.467 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 1788 5.01 %
Rwork0.2199 33917 -
obs0.2221 35705 99.86 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.44 Å2 / Biso mean: 63.1659 Å2 / Biso min: 22.5 Å2
Refinement stepCycle: final / Resolution: 2.45→45.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6641 0 15 214 6870
Biso mean--66.38 47.23 -
Num. residues----838
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.45-2.51630.39511360.33152590
2.5163-2.59030.3761380.32332617
2.5903-2.67390.34981350.30592567
2.6739-2.76950.36951380.3152617
2.7695-2.88030.38391370.2842600
2.8803-3.01140.32161380.27032608
3.0114-3.17010.33391370.26742608
3.1701-3.36870.29881380.25582613
3.3687-3.62870.28141360.22552582
3.6287-3.99370.23051390.19662638
3.9937-4.57110.2111370.16692611
4.5711-5.75730.20751380.18672614
5.7573-45.4670.19411410.16352652
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)
18.13030.5901-2.80714.3774-1.42433.8134-0.013-0.37370.25590.60550.0069-1.0121-0.38310.31070.03260.93160.1067-0.24610.6811-0.17890.748732.614-0.636-47.8701
21.15260.1743-0.22422.0841-1.06491.7809-0.09920.2059-0.0872-0.23930.12590.22480.1015-0.2126-0.04010.465-0.004-0.04710.3595-0.02740.252638.891710.9302-11.3289
31.01920.14791.12511.68610.3185.79510.08470.112-0.0448-0.0079-0.10970.18670.5714-0.12480.06740.9579-0.0759-0.05030.440.03340.428310.936355.0036-59.2321
40.67980.25160.26921.72510.59541.57740.07370.04010.02930.0279-0.0273-0.14710.01770.0606-0.06710.60560.0042-0.08470.3315-0.01850.287312.710733.7013-36.8821
56.97022.9921-1.7054.5096-4.20744.1632-0.1421-0.17031.66760.42150.4715-0.2624-1.7319-0.4892-0.33381.23370.2221-0.0720.7337-0.03121.603441.4348-4.9473-51.6438
65.16662.8761-4.744.591-5.44656.9852-0.7014-0.221-0.687-0.4808-0.11630.32340.91420.09660.75091.86990.051-0.21070.45720.01660.62968.171242.4147-67.0463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 138 )A50 - 138
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 462 )A139 - 462
3X-RAY DIFFRACTION3chain 'C' and (resid 49 through 170 )C49 - 170
4X-RAY DIFFRACTION4chain 'C' and (resid 171 through 462 )C171 - 462
5X-RAY DIFFRACTION5chain 'B' and (resid 786 through 790 )B786 - 790
6X-RAY DIFFRACTION6chain 'D' and (resid 785 through 790 )D785 - 790

+
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