[English] 日本語
Yorodumi
- PDB-2lkn: Solution structure of the PPIase domain of human aryl-hydrocarbon... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lkn
TitleSolution structure of the PPIase domain of human aryl-hydrocarbon receptor-interacting protein (AIP)
ComponentsAH receptor-interacting protein
KeywordsPROTEIN BINDING / FKBP-TYPE DOMAIN / IMMUNOPHILIN HOMOLOG
Function / homology
Function and homology information


GAF domain binding / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / regulation of protein kinase A signaling / protein targeting to mitochondrion / protein maturation by protein folding / aryl hydrocarbon receptor binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / xenobiotic metabolic process / peptidyl-prolyl cis-trans isomerase activity ...GAF domain binding / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / regulation of protein kinase A signaling / protein targeting to mitochondrion / protein maturation by protein folding / aryl hydrocarbon receptor binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / xenobiotic metabolic process / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / transcription coactivator activity / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
AIP/AIPL1 / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat ...AIP/AIPL1 / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
AH receptor-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsLinnert, M. / Lin, Y. / Manns, A. / Haupt, K. / Paschke, A. / Fischer, G. / Weiwad, M. / Luecke, C.
CitationJournal: Biochemistry / Year: 2013
Title: The FKBP-Type Domain of the Human Aryl Hydrocarbon Receptor-Interacting Protein Reveals an Unusual Hsp90 Interaction.
Authors: Linnert, M. / Lin, Y.J. / Manns, A. / Haupt, K. / Paschke, A.K. / Fischer, G. / Weiwad, M. / Luecke, C.
History
DepositionOct 17, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AH receptor-interacting protein


Theoretical massNumber of molelcules
Total (without water)18,6751
Polymers18,6751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

-
Components

#1: Protein AH receptor-interacting protein / / AIP / Aryl-hydrocarbon receptor-interacting protein / HBV X-associated protein 2 / XAP-2 / ...AIP / Aryl-hydrocarbon receptor-interacting protein / HBV X-associated protein 2 / XAP-2 / Immunophilin homolog ARA9 / FKBP37.7


Mass: 18675.402 Da / Num. of mol.: 1 / Fragment: PPIase FKBP-type domain containing residues 1-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIP, XAP2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00170

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1322D 1H-15N HSQC
1422D 1H-15N TROSY
1532D 1H-13C HSQC
1623D 1H-15N TOCSY
1723D 1H-15N NOESY
1833D 1H-13C NOESY aliphatic
1933D HNCA
11033D HN(CA)CB
11133D HNCO
11233D CC(CO)NH
11333D H(CC)(CO)NH
11433D (H)CCH-TOCSY
11533D CCH-TOCSY
11633D HN(CA)CO

-
Sample preparation

Details
Solution-IDContentsSolvent system
12 mM AIP, 10 mM sodium phosphate, 5 mM DTT, 0.05 mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
22 mM [U-15N] AIP, 10 mM sodium phosphate, 5 mM DTT, 0.05 mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
32 mM [U-13C; U-15N] AIP, 10 mM sodium phosphate, 5 mM DTT, 0.05 mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMAIP-11
10 mMsodium phosphate-21
5 mMDTT-31
0.05 mMsodium azide-41
2 mMAIP-5[U-15N]2
10 mMsodium phosphate-62
5 mMDTT-72
0.05 mMsodium azide-82
2 mMAIP-9[U-13C; U-15N]3
10 mMsodium phosphate-103
5 mMDTT-113
0.05 mMsodium azide-123
Sample conditionsIonic strength: 10 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AvanceBrukerAVANCE8002

-
Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
FelixAccelrys Software Inc.data analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
DYANAGuntert, Braun and Wuthrichstructure solution
DiscoverAccelrys Software Inc.refinement
DYANAGuntert, Braun and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / 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