[English] 日本語
Yorodumi
- PDB-1t1q: NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ABA, P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t1q
TitleNMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ABA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES
Components
  • Insulin
  • insulin
KeywordsHORMONE/GROWTH FACTOR / Aba-B12-DKP-insulin / protein unfolding / insulin receptor / receptor binding / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / positive regulation of cellular protein metabolic process / negative regulation of acute inflammatory response / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / COPI-mediated anterograde transport / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / regulation of protein localization to plasma membrane / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / Regulation of insulin secretion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Signal attenuation / positive regulation of nitric oxide mediated signal transduction / negative regulation of protein secretion / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / positive regulation of insulin receptor signaling pathway / transport vesicle / neuron projection maintenance / endosome lumen / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of cell differentiation / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of brown fat cell differentiation / regulation of synaptic plasticity / regulation of transmembrane transporter activity / positive regulation of long-term synaptic potentiation / cognition / regulation of protein localization / activation of protein kinase B activity / positive regulation of cytokine production / positive regulation of glucose import / acute-phase response / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor signaling pathway / insulin receptor binding / positive regulation of protein localization to nucleus / vasodilation / Golgi lumen / glucose metabolic process / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / wound healing / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of MAPK cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of protein kinase B signaling / positive regulation of NF-kappaB transcription factor activity / G protein-coupled receptor signaling pathway / positive regulation of cell migration / Amyloid fiber formation / Golgi membrane / regulation of transcription, DNA-templated / endoplasmic reticulum lumen / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsHuang, K. / Xu, B. / Hu, S.Q. / Chu, Y.C. / Hua, Q.X. / Whittaker, J. / Nakagawa, S.H. / De Meyts, P. / Katsoyannis, P.G. / Weiss, M.A.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: How Insulin Binds: the B-Chain alpha-Helix Contacts the L1 beta-Helix of the Insulin Receptor.
Authors: Huang, K. / Xu, B. / Hu, S.Q. / Chu, Y.C. / Hua, Q.X. / Qu, Y. / Li, B. / Wang, S. / Wang, R.Y. / Nakagawa, S.H. / Theede, A.M. / Whittaker, J. / De Meyts, P. / Katsoyannis, P.G. / Weiss, M.A.
#1: Journal: Biochemistry / Year: 2000
Title: MUTATIONAL ANALYSIS OF INVARIANT VALINE B12 IN INSULIN: IMPLICATION FOR RECEPTOR BINDING
Authors: Nakagawa, S.H. / Tager, H.S. / Steiner, D.F.
#2: Journal: J.Biol.Chem. / Year: 1997
Title: ALANINE SCANNING MUTAGENESIS OF INSULIN
Authors: Kristen, C. / Kjeldsen, T. / Wiberg, F.C. / Schaffer, L. / Hach, M. / Havelund, S. / Bass, J. / Steiner, D.F. / Andersen, A.S.
#3: Journal: BIOCHEM.MOL.BIOL.INT. / Year: 1996
Title: STUDIES ON RECEPTOR BINDING SITE OF INSULIN: THE HYDROPHOBIC B12VALCAN BE SUBSTITUTED BY HYDROPHILIC THR
Authors: Wang, Q.Q. / Feng, Y.M. / Zhang, Y.S.
#4: Journal: Biochemistry / Year: 1993
Title: STERIC REQUIRMENTS AT POSITION B12 FOR HIGH BIOLOGICAL ACTIVITY IN INSULIN
Authors: Hu, S.Q. / Burke, G.T. / Schwartz, G.P. / Ferderigos, N. / Ross, J.B. / Katsoyannis, P.G.
#5: Journal: INT.J.PEPT.PROTEIN RES. / Year: 1981
Title: [12-ASPARAGINE-B] HUMAN INSULIN. AN ANALOGUE WITH MODIFICATION IN THEHYDROPHOBIC CORE OF INSULIN
Authors: Schwartz, G.P. / Burke, P.G. / Katsoyannis, P.G.
History
DepositionApr 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2012Group: Database references
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: insulin
B: Insulin


Theoretical massNumber of molelcules
Total (without water)5,7812
Polymers5,7812
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)15 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide insulin /


Mass: 2383.698 Da / Num. of mol.: 1 / Fragment: INSULIN A CHAIN
Mutation: HIS-B10-ASP, VAL-B12-ABA, PRO-B28-LYS, LYS-B29-PRO
Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS(HUMAN)
References: UniProt: P01308
#2: Protein/peptide Insulin /


Mass: 3396.868 Da / Num. of mol.: 1 / Fragment: INSULIN B CHAIN / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS(HUMAN)
References: UniProt: P01308

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1,2,311,2,32D NOESY
1,2,321,2,32D TOCSY
1,2,331,2,3DQF-COSY
NMR detailsText: This structure was determined by using standard 2D homonuclear techniques

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM ABA-B12-DKP-insulin, 90% H2O, 10% D2O90% H2O/10% D2O
21.2 mM ABA-B12-DKP-insulin,100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (Pa)Temperature (K)
17.0 ambient 298 K
27.6 ambient 305 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameVersionDeveloperClassification
DGIIINSIGHTII 2000Molecular Simulations INC.structure solution
X-PLOR3.85Brungerrefinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: the structures are based on a total of 590 restraints: 527 are NOE-derived distance constraints, 39 are dihedral angle restraints, 24 are hydrogen bond restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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