[English] 日本語
Yorodumi
- PDB-3mth: X-RAY CRYSTALLOGRAPHIC STUDIES ON HEXAMERIC INSULINS IN THE PRESE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mth
TitleX-RAY CRYSTALLOGRAPHIC STUDIES ON HEXAMERIC INSULINS IN THE PRESENCE OF HELIX-STABILIZING AGENTS, THIOCYANATE, METHYLPARABEN AND PHENOL
Components(METHYLPARABEN ...) x 2
KeywordsHORMONE
Function / homology
Function and homology information


Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine ...Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine / positive regulation of lipoprotein lipase activity / lactate biosynthetic process / lipoprotein biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / COPI-mediated anterograde transport / lipid biosynthetic process / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / negative regulation of lipid catabolic process / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / positive regulation of DNA replication / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / wound healing / insulin receptor binding / negative regulation of protein catabolic process / hormone activity / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
4-HYDROXY-BENZOIC ACID METHYL ESTER / Insulin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsWhittingham, J.L. / Dodson, E.J. / Moody, P.C.E. / Dodson, G.G.
Citation
Journal: Biochemistry / Year: 1995
Title: X-ray crystallographic studies on hexameric insulins in the presence of helix-stabilizing agents, thiocyanate, methylparaben, and phenol.
Authors: Whittingham, J.L. / Chaudhuri, S. / Dodson, E.J. / Moody, P.C. / Dodson, G.G.
#1: Journal: Biopolymers / Year: 1992
Title: The Structure of a Rhombohedral R6 Insulin Hexamer that Binds Phenol
Authors: Smith, G.D. / Dodson, G.G.
#2: Journal: Nature / Year: 1989
Title: Phenol Stabilizes More Helix in a New Symmetrical Zinc Insulin Hexamer
Authors: Derewenda, U. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D. / Smith, G.D. / Sparks, C. / Swenson, D.
History
DepositionSep 13, 1995-
SupersessionJan 29, 1996ID: 2MTH
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9299
Polymers11,5754
Non-polymers3545
Water1,35175
1
A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0415
Polymers5,7882
Non-polymers2533
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-11 kcal/mol
Surface area3910 Å2
MethodPISA
2
C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8884
Polymers5,7882
Non-polymers1012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-14 kcal/mol
Surface area3700 Å2
MethodPISA
3
A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules

A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules

A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,78727
Polymers34,72612
Non-polymers1,06215
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area19870 Å2
ΔGint-315 kcal/mol
Surface area11830 Å2
MethodPISA
4
A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
hetero molecules

C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9299
Polymers11,5754
Non-polymers3545
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area4060 Å2
ΔGint-33 kcal/mol
Surface area6360 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-34 kcal/mol
Surface area5940 Å2
MethodPISA
6
C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules

C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules

C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,66512
Polymers17,3636
Non-polymers3036
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6080 Å2
ΔGint-123 kcal/mol
Surface area10540 Å2
MethodPISA
7
A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
hetero molecules

A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
hetero molecules

A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,12215
Polymers17,3636
Non-polymers7599
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5080 Å2
ΔGint-145 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.380, 80.380, 37.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-31-

ZN

21B-32-

CL

31D-31-

ZN

41D-32-

CL

-
Components

-
METHYLPARABEN ... , 2 types, 4 molecules ACBD

#1: Protein/peptide METHYLPARABEN INSULIN


Mass: 2383.698 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315
#2: Protein/peptide METHYLPARABEN INSULIN


Mass: 3403.927 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315

-
Non-polymers , 4 types, 80 molecules

#3: Chemical ChemComp-MPB / 4-HYDROXY-BENZOIC ACID METHYL ESTER / Methylparaben


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal grow
*PLUS
pH: 8 / Method: batch method
Components of the solutions
*PLUS
Conc.: 0.02 M / Common name: hydrochrolic acid

-
Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 5.95 Å / Num. obs: 6095 / % possible obs: 86.3 % / Num. measured all: 6620 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 28.1 % / Mean I/σ(I) obs: 4.32

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.1843 6095
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms789 0 15 75 879
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.2163
X-RAY DIFFRACTIONp_mcangle_it3.8013.5
X-RAY DIFFRACTIONp_scbond_it2.4763
X-RAY DIFFRACTIONp_scangle_it3.9453.5
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.0780.1
X-RAY DIFFRACTIONp_singtor_nbd0.1640.3
X-RAY DIFFRACTIONp_multtor_nbd0.2560.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1780.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.20820
X-RAY DIFFRACTIONp_staggered_tor22.54520
X-RAY DIFFRACTIONp_orthonormal_tor15.11420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
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