[English] 日本語
Yorodumi
- PDB-2k18: Solution structure of bb' domains of human protein disulfide isomerase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k18
TitleSolution structure of bb' domains of human protein disulfide isomerase
ComponentsProtein disulfide-isomerase
KeywordsISOMERASE / PDI / endoplasmic reticulum / disulfide bonds / protein folding / Chaperone / Membrane / Redox-active center
Function / homology
Function and homology information


regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline ...regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / endoplasmic reticulum chaperone complex / Chylomicron assembly / protein folding in endoplasmic reticulum / Collagen biosynthesis and modifying enzymes / Interleukin-23 signaling / interleukin-12-mediated signaling pathway / cellular response to interleukin-7 / Interleukin-12 signaling / Insulin processing / protein disulfide isomerase activity / Detoxification of Reactive Oxygen Species / positive regulation of cell adhesion / protein-disulfide reductase activity / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of substrate adhesion-dependent cell spreading / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / Hedgehog ligand biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / integrin binding / protein folding / lamellipodium / actin binding / cellular response to hypoxia / positive regulation of viral entry into host cell / cytoskeleton / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / cytosol
Similarity search - Function
Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein disulfide-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDenisov, A.Y. / Maattanen, P. / Dabrowski, C. / Kozlov, G. / Thomas, D.Y. / Gehring, K.
CitationJournal: Febs J. / Year: 2009
Title: Solution structure of the bb' domains of human protein disulfide isomerase.
Authors: Denisov, A.Y. / Maattanen, P. / Dabrowski, C. / Kozlov, G. / Thomas, D.Y. / Gehring, K.
History
DepositionFeb 22, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein disulfide-isomerase


Theoretical massNumber of molelcules
Total (without water)25,5651
Polymers25,5651
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)10 / 200structures with the lowest energy and the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein Protein disulfide-isomerase / / PDI / Prolyl 4- hydroxylase subunit beta / Cellular thyroid hormone-binding protein / p55


Mass: 25564.928 Da / Num. of mol.: 1 / Fragment: residues 135-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P4HB, ERBA2L, PDI, PDIA1, PO4DB / Plasmid: pGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07237, protein disulfide-isomerase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D 1H-15N NOESY
1423D 1H-13C NOESY
153IPAP-HSQC
NMR detailsText: Structure was determined using multi-dimentional NMR spectroscopy

-
Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-99% 13C; U-99% 15N] hPDI-bb, 25 mM sodium phosphate, 70 mM sodium chloride, 0.5 mM EDTA, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
22 mM hPDI-bb, 25 mM sodium phosphate, 70 mM sodium chloride, 0.5 mM EDTA, 5 mM DTT, 100% D2O100% D2O
30.5 mM [U-99% 15N] hPDI-bb, 25 mM sodium phosphate, 70 mM sodium chloride, 0.5 mM EDTA, 5 mM DTT, 12 mg/mL Pf1 phages, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMhPDI-bb[U-99% 13C; U-99% 15N]1
25 mMsodium phosphate1
70 mMsodium chloride1
0.5 mMEDTA1
5 mMDTT1
2 mMhPDI-bb2
25 mMsodium phosphate2
70 mMsodium chloride2
0.5 mMEDTA2
5 mMDTT2
0.5 mMhPDI-bb[U-99% 15N]3
25 mMsodium phosphate3
70 mMsodium chloride3
0.5 mMEDTA3
5 mMDTT3
12 mg/mLPf1 phages3
Sample conditionsIonic strength: 0.1 / pH: 7.0 / Pressure: 1 atm / Temperature: 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Unity InovaVarianUnity Inova8001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASY1.3.13Bartels et al.data analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA1.1Linge, O'Donoghue and Nilgesdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: structure was refined by using standard protocol in CNS with restraints from NOE distances, backbone torsions, hydrogen bonds and residual dipolar couplings
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy and the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10

+
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