[English] 日本語
Yorodumi
- PDB-1mhi: THREE-DIMENSIONAL SOLUTION STRUCTURE OF AN INSULIN DIMER. A STUDY... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mhi
TitleTHREE-DIMENSIONAL SOLUTION STRUCTURE OF AN INSULIN DIMER. A STUDY OF THE B9(ASP) MUTANT OF HUMAN INSULIN USING NUCLEAR MAGNETIC RESONANCE DISTANCE GEOMETRY AND RESTRAINED MOLECULAR DYNAMICS
Components(INSULIN) x 2
KeywordsHORMONE
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / 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 ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / 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 reactive oxygen species biosynthetic process / COPI-mediated anterograde transport / regulation of cellular amino acid metabolic process / regulation of protein localization to plasma membrane / Regulation of insulin secretion / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Signal attenuation / negative regulation of protein secretion / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of insulin receptor signaling pathway / neuron projection maintenance / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / negative regulation of acute inflammatory response / positive regulation of cell differentiation / regulation of transmembrane transporter activity / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / regulation of synaptic plasticity / positive regulation of brown fat cell differentiation / cognition / regulation of protein localization / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / acute-phase response / activation of protein kinase B activity / positive regulation of glucose import / vasodilation / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor binding / positive regulation of protein localization to nucleus / insulin receptor signaling pathway / glucose metabolic process / Golgi lumen / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / endoplasmic reticulum to Golgi vesicle-mediated transport / wound healing / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell migration / positive regulation of protein kinase B signaling / Golgi membrane / Amyloid fiber formation / G protein-coupled receptor signaling pathway / amyloid fibril formation / endoplasmic reticulum lumen / regulation of transcription, DNA-templated / positive regulation of gene expression / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin / insulin-like growth factor / relaxin family. / Insulin/IGF/Relaxin family / Insulin-like / Insulin, conserved site / Insulin-like superfamily / Insulin family signature.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsJorgensen, A.M.M. / Kristensen, S.M. / Led, J.J. / Balschmidt, P.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Three-dimensional solution structure of an insulin dimer. A study of the B9(Asp) mutant of human insulin using nuclear magnetic resonance, distance geometry and restrained molecular dynamics.
Authors: Jorgensen, A.M. / Kristensen, S.M. / Led, J.J. / Balschmidt, P.
#1: Journal: Magn.Reson.Chem. / Year: 1995
Title: A Carbon-13 NMR Study of the B9(Asp) Mutant of Human Insulin
Authors: Kristensen, S.M. / Led, J.J.
#2: Journal: Biochemistry / Year: 1994
Title: Structural Details of Asp(B9) Human Insulin at Low Ph from 2D NMR Titration Studies
Authors: Sorensen, M.D. / Led, J.J.
#3: Journal: J.Am.Chem.Soc. / Year: 1994
Title: A New Linear Prediction Model Method for the Determination of Slow Amide Proton Exchange Rates from a Series of One-Dimensional 1H NMR Spectra
Authors: Moss, R. / Gesmar, H. / Led, J.J.
#4: Journal: J.Am.Chem.Soc. / Year: 1993
Title: Slow Amide Proton Exchange Rates from the Line Widths in a Single Two-Dimensional 1H NMR Spectrum
Authors: Olsen, H.B. / Gesmar, H. / Led, J.J.
#5: Journal: J.Mol.Biol. / Year: 1991
Title: Proton Nuclear Magnetic Resonance Study of the B9(Asp) Mutant of Human Insulin. Sequential Assignment and Secondary Structure
Authors: Kristensen, S.M. / Jorgensen, A.M.M. / Led, J.J. / Balschmidt, P. / Hansen, F.B.
History
DepositionNov 30, 1994Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INSULIN
B: INSULIN


Theoretical massNumber of molelcules
Total (without water)5,8462
Polymers5,8462
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: THR B 27 - PRO B 28 MODEL 1 OMEGA = 41.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: THR B 27 - PRO B 28 MODEL 3 OMEGA = 214.06 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: THR B 27 - PRO B 28 MODEL 4 OMEGA = 213.37 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: THR B 27 - PRO B 28 MODEL 8 OMEGA = 216.24 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: THR B 27 - PRO B 28 MODEL 10 OMEGA = 241.03 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: THR B 27 - PRO B 28 MODEL 11 OMEGA = 217.65 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: THR B 27 - PRO B 28 MODEL 13 OMEGA = 233.42 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: CIS PROLINE - PRO B 28 MODEL 15
9: THR B 27 - PRO B 28 MODEL 19 OMEGA = 240.85 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: THR B 27 - PRO B 28 MODEL 20 OMEGA = 91.63 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

-
Components

#1: Protein/peptide INSULIN /


Mass: 2383.698 Da / Num. of mol.: 1 / Mutation: S(B 9)D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P01308
#2: Protein/peptide INSULIN /


Mass: 3461.963 Da / Num. of mol.: 1 / Mutation: S(B 9)D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P01308

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

NMR software
NameVersionDeveloperClassification
DISGEOHAVEL,WUTHRICHrefinement
X-PLOR2.1BRUNGERrefinement
NMR ensembleConformers submitted total number: 20

+
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