[English] 日本語
Yorodumi
- PDB-7pc8: The PDZ domain of SNTG1 complexed with the phosphomimetic mutant ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pc8
TitleThe PDZ domain of SNTG1 complexed with the phosphomimetic mutant PDZ-binding motif of RSK1
Components
  • Gamma-1-syntrophin,Annexin A2
  • Ribosomal protein S6 kinase alpha-1
KeywordsPEPTIDE BINDING PROTEIN / PDZ / complex / crystallization chaperone
Function / homology
Function and homology information


syntrophin complex / regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / dystrophin-associated glycoprotein complex / ribosomal protein S6 kinase activity / phospholipase A2 inhibitor activity ...syntrophin complex / regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / dystrophin-associated glycoprotein complex / ribosomal protein S6 kinase activity / phospholipase A2 inhibitor activity / positive regulation of low-density lipoprotein particle clearance / positive regulation of vesicle fusion / hepatocyte proliferation / CREB phosphorylation / positive regulation of hepatic stellate cell activation / 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 / cell communication / cadherin binding involved in cell-cell adhesion / cornified envelope / Schmidt-Lanterman incisure / vesicle budding from membrane / TORC1 signaling / plasma membrane protein complex / Gastrin-CREB signalling pathway via PKC and MAPK / calcium-dependent phospholipid binding / osteoclast development / negative regulation of receptor internalization / RSK activation / Dissolution of Fibrin Clot / S100 protein binding / collagen fibril organization / negative regulation of TOR signaling / vesicle membrane / epithelial cell apoptotic process / phosphatidylserine binding / ERK/MAPK targets / positive regulation of receptor recycling / Recycling pathway of L1 / basement membrane / positive regulation of exocytosis / Smooth Muscle Contraction / regulation of neurogenesis / cytoskeletal protein binding / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / lipid droplet / protein serine/threonine/tyrosine kinase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lung development / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / response to activity / adherens junction / positive regulation of cell differentiation / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / RNA polymerase II transcription regulator complex / ruffle membrane / nuclear matrix / calcium-dependent protein binding / azurophil granule lumen / late endosome membrane / melanosome / : / actin binding / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / protease binding / midbody / angiogenesis / basolateral plasma membrane / chemical synaptic transmission / vesicle / cytoskeleton / early endosome / protein phosphorylation / non-specific serine/threonine protein kinase / endosome / lysosomal membrane / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / synapse / Neutrophil degranulation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / structural molecule activity / magnesium ion binding / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / RNA binding / extracellular exosome
Similarity search - Function
: / Syntrophin / Syntrophin C-terminal PH domain / Annexin A2 / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin ...: / Syntrophin / Syntrophin C-terminal PH domain / Annexin A2 / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Protein kinase, C-terminal / Protein kinase C terminal domain / PDZ domain / Pdz3 Domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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 / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Annexin A2 / Ribosomal protein S6 kinase alpha-1 / Gamma-1-syntrophin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionAug 3, 2021Deposition 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
B: Gamma-1-syntrophin,Annexin A2
C: Ribosomal protein S6 kinase alpha-1
D: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,88519
Polymers95,9724
Non-polymers91315
Water3,981221
1
A: Gamma-1-syntrophin,Annexin A2
C: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,46310
Polymers47,9862
Non-polymers4778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-46 kcal/mol
Surface area20740 Å2
MethodPISA
2
B: Gamma-1-syntrophin,Annexin A2
D: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4229
Polymers47,9862
Non-polymers4377
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-41 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.580, 59.820, 125.210
Angle α, β, γ (deg.)90.000, 117.840, 90.000
Int Tables number5
Space group name H-MC121

-
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 Ribosomal protein S6 kinase alpha-1 / S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / p90RSK1 / p90S6K / MAP kinase- ...S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / p90RSK1 / p90S6K / MAP kinase-activated protein kinase 1a / MAPK-activated protein kinase 1a / MAPKAP kinase 1a / MAPKAPK-1a / Ribosomal S6 kinase 1 / RSK-1


Mass: 1215.465 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: N-terminal biotin-ttds (trioxatridecan-succinamic acid) label
Source: (synth.) Homo sapiens (human)
References: UniProt: Q15418, non-specific serine/threonine protein kinase
#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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growTemperature: 293 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: Jun 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.334 Å / Num. obs: 51681 / % possible obs: 99.5 % / Redundancy: 6.83 % / CC1/2: 0.995 / Rrim(I) all: 0.198 / Net I/σ(I): 9.56
Reflection shellResolution: 2.5→2.56 Å / Mean I/σ(I) obs: 1.26 / Num. unique obs: 3761 / CC1/2: 0.532 / Rrim(I) all: 1.66

-
Processing

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

5n7d

2pdz


Resolution: 2.5→48.334 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 2584 5 %
Rwork0.2023 49085 -
obs0.2037 51669 99.68 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.84 Å2 / Biso mean: 61.7162 Å2 / Biso min: 29.78 Å2
Refinement stepCycle: final / Resolution: 2.5→48.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6638 0 45 221 6904
Biso mean--63.02 52.36 -
Num. residues----836
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.5480.41071420.32552698100
2.548-2.60.35251400.3404266399
2.6-2.65660.34531420.29942700100
2.6566-2.71840.29871430.269272499
2.7184-2.78630.29551410.25832675100
2.7863-2.86170.31541430.2516270999
2.8617-2.94590.31241420.24712708100
2.9459-3.04090.31471420.2487268799
3.0409-3.14960.24631440.22982749100
3.1496-3.27570.23361420.21372694100
3.2757-3.42470.28091430.20372714100
3.4247-3.60520.21671440.20612743100
3.6052-3.8310.20271440.18212718100
3.831-4.12670.23021450.1662759100
4.1267-4.54170.16551440.16042740100
4.5417-5.19820.20021450.16872753100
5.1982-6.54660.22691470.20732792100
6.5466-48.3340.16731510.1672859100
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)
18.34750.7909-1.33827.71832.79826.90280.69920.5084-1.6157-0.4324-0.68850.2230.8617-0.0947-0.02790.69720.1499-0.29380.4924-0.07780.843111.515930.330714.7046
20.5538-0.08950.060.96281.33282.9880.00730.00670.08480.0111-0.17340.068-0.072-0.23350.16630.3374-0.0336-0.05410.32840.02840.331818.4298-1.656938.6974
35.99893.7674.83672.35323.05133.88990.12970.8409-0.1915-0.27580.02160.02920.02830.3156-0.16650.6256-0.0399-0.11880.88050.24660.669411.812-14.4899-14.1916
43.2736-1.06810.05641.45960.22170.60550.19240.55030.2992-0.2944-0.1324-0.1769-0.03990.0117-0.06390.3720.01290.04870.4220.10580.356141.27394.0015-10.4242
54.98882.5670.76411.9381.92343.9127-0.24130.2998-0.6116-0.234-0.66592.0696-0.2677-0.13410.90431.58320.2796-0.43070.7785-0.17441.514111.343618.143712.082
67.1013-0.49359.04910.0342-0.628720.6045-0.263-0.57130.34880.1589-0.00630.4558-0.257-0.76181.03120.0966-0.19792.01370.17061.188317.1144-22.0985-20.3877
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 'B' and (resid 54 through 157 )B54 - 157
4X-RAY DIFFRACTION4chain 'B' and (resid 158 through 462 )B158 - 462
5X-RAY DIFFRACTION5chain 'C' and (resid 182 through 189 )C182 - 189
6X-RAY DIFFRACTION6chain 'D' and (resid 184 through 189 )D184 - 189

+
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