[English] 日本語
Yorodumi
- PDB-7rm8: Solution NMR structure of PDLIM7 PDZ bound to SNX17 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rm8
TitleSolution NMR structure of PDLIM7 PDZ bound to SNX17 peptide
ComponentsIsoform 4 of PDZ and LIM domain protein 7,Sorting nexin-17 fusion
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


muscle structure development / cardiac septum development / muscle alpha-actinin binding / coronary vasculature development / endocytic recycling / aorta development / endosomal transport / low-density lipoprotein particle receptor binding / filamentous actin / cholesterol catabolic process ...muscle structure development / cardiac septum development / muscle alpha-actinin binding / coronary vasculature development / endocytic recycling / aorta development / endosomal transport / low-density lipoprotein particle receptor binding / filamentous actin / cholesterol catabolic process / regulation of endocytosis / RET signaling / stress fiber / ruffle / phosphatidylinositol binding / ossification / receptor-mediated endocytosis / kidney development / adherens junction / intracellular protein transport / Z disc / actin cytoskeleton / actin binding / heart development / cytoplasmic vesicle / actin cytoskeleton organization / early endosome / cell differentiation / endosome membrane / endosome / signaling receptor binding / intracellular membrane-bounded organelle / focal adhesion / Golgi apparatus / signal transduction / protein-containing complex / nucleoplasm / membrane / metal ion binding / cytosol
Similarity search - Function
Sorting nexin-17 / SNX17, atypical FERM-like domain / Sorting nexin-17/31, FERM domain / : / : / Sorting Nexin 17 FERM C-terminal domain / Sortin nexin 17/31, FERM domain, F2 lobe / Sortin nexin 17/27/31, FERM domain, F1 lobe / SNX17/27/31 / Ras-associating (RA) domain profile. ...Sorting nexin-17 / SNX17, atypical FERM-like domain / Sorting nexin-17/31, FERM domain / : / : / Sorting Nexin 17 FERM C-terminal domain / Sortin nexin 17/31, FERM domain, F2 lobe / Sortin nexin 17/27/31, FERM domain, F1 lobe / SNX17/27/31 / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ 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
Sorting nexin-17 / PDZ and LIM domain protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHealy, M.D. / Collins, B.M. / Mobli, M.
Funding support Australia, United Kingdom, 8items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1156732 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1136021 Australia
Australian Research Council (ARC)DP190101177 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1162597 Australia
Medical Research Council (MRC, United Kingdom)MR/P018807/1 United Kingdom
Wellcome Trust104568/Z/14/Z United Kingdom
Wellcome Trust220260/Z/20/Z United Kingdom
Royal SocietyRSRP/R1/211004 United Kingdom
CitationJournal: Structure / Year: 2022
Title: Proteomic identification and structural basis for the interaction between sorting nexin SNX17 and PDLIM family proteins.
Authors: Healy, M.D. / Sacharz, J. / McNally, K.E. / McConville, C. / Tillu, V.A. / Hall, R.J. / Chilton, M. / Cullen, P.J. / Mobli, M. / Ghai, R. / Stroud, D.A. / Collins, B.M.
History
DepositionJul 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform 4 of PDZ and LIM domain protein 7,Sorting nexin-17 fusion


Theoretical massNumber of molelcules
Total (without water)11,3181
Polymers11,3181
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

-
Components

#1: Protein Isoform 4 of PDZ and LIM domain protein 7,Sorting nexin-17 fusion / LIM mineralization protein / LMP / Protein enigma


Mass: 11317.567 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDLIM7, ENIGMA, SNX17, KIAA0064 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NR12, UniProt: Q15036

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D HBHA(CO)NH
171isotropic13D H(CCO)NH
181isotropic13D H(CCO)NH

-
Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] PDLIM7_SNX17_Fusion, 95% H2O/5% D2O
Details: Protein was gel filtered in a buffer containing 75 mM NaCl, 20 mM Bis-Tris (pH 5.8), 4 mM DTT.
Label: PDLIM7_SNX17_Fusion / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPDLIM7_SNX17_Fusion[U-13C; U-15N]1
75 mMNaClnatural abundance1
20 mMBis-Trisnatural abundance1
4 mMDTTnatural abundance1
Sample conditionsDetails: Protein was gel filtered in a buffer containing 75 mM NaCl, 20 mM Bis-Tris (pH 5.8), 4 mM DTT.
Ionic strength: 75 mM NaCl mM / Label: Condition 1 / pH: 5.8 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis3CCPNrefinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis3CCPNchemical shift assignment
CcpNmr Analysis3CCPNpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

+
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