[English] 日本語
Yorodumi
- PDB-4iyd: Insulin glargine crystal structure 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iyd
TitleInsulin glargine crystal structure 1
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / regulation of amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of protein autophosphorylation / transport vesicle / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / activation of protein kinase B activity / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / endosome lumen / Regulation of insulin secretion / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / positive regulation of neuron projection development / cognition / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / regulation of protein localization / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å
AuthorsBarba de la Rosa, A.P. / Lara-Gonzalez, S. / Montero-Moran, G.M. / Escobedo-Moratilla, A.
CitationJournal: to be published
Title: Physicochemical and structural analysis of a biosimilar insulin glargine formulation and its reference
Authors: Barba de la Rosa, A.P. / Lara-Gonzalez, S. / Montero-Moran, G.M. / Escobedo-Moratilla, A. / Perez-Urizar, J.T.
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Insulin A chain
B: Insulin B chain


Theoretical massNumber of molelcules
Total (without water)5,6592
Polymers5,6592
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-14 kcal/mol
Surface area3280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.325, 77.325, 77.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

-
Components

#1: Protein/peptide Insulin A chain


Mass: 2326.647 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3332.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P01308
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris, 30% PEG-400 v/v, 0.2 M sodium citrate dihydrate, pH 8.0, vapor diffusion, sitting drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.502 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 1.66→31.57 Å / Num. obs: 9252 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.29 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.067 / Χ2: 0.95 / Net I/σ(I): 11.1 / Scaling rejects: 301
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.66-1.724.190.454239019300.53100
1.72-1.794.220.3532.737858970.6100
1.79-1.874.250.2723.738669090.67100
1.87-1.974.280.234.939779280.83100
1.97-2.094.340.1756.739939190.85100
2.09-2.254.350.1358.739349040.8499.9
2.25-2.484.410.11110.641279360.8100
2.48-2.844.40.09213.640419170.85100
2.84-3.584.370.07121.841619391.3199.8
3.58-31.574.050.06135.441669732.2699.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
d*TREK9.9.8.6 W9RSSIdata reduction
PHASER2.5.3phasing
PHENIXdev_1184refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1trz

1trz


Resolution: 1.66→31.568 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.15 / Isotropic thermal model: ISOTROPIC / σ(F): 1.4 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 915 9.89 %RANDOM
Rwork0.1969 ---
all0.1995 9250 --
obs-9250 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.8 Å2 / Biso mean: 36.1302 Å2 / Biso min: 22.01 Å2
Refinement stepCycle: LAST / Resolution: 1.66→31.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms379 0 0 11 390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016389
X-RAY DIFFRACTIONf_angle_d1.37523
X-RAY DIFFRACTIONf_chiral_restr0.09459
X-RAY DIFFRACTIONf_plane_restr0.00967
X-RAY DIFFRACTIONf_dihedral_angle_d13.41130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
1.66-1.74820.29681300.247117613061176
1.7482-1.85780.2621290.2298118713161187
1.8578-2.00120.25991280.2216117213001172
2.0012-2.20250.2241350.1985117113061171
2.2025-2.52110.20171310.1965118313141183
2.5211-3.17590.25871300.2002120513351205
3.1759-31.57340.2051320.1868124113731241
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2448-0.12120.30290.205-0.13570.3483-0.0795-0.3195-0.37670.2590.2008-0.13670.21790.3293-0.00040.32620.0458-0.01740.4054-0.01530.4122-4.8684-19.23473.1234
20.11340.016-0.1410.2471-0.08040.1813-0.45740.1801-0.7974-0.11360.1597-0.49130.72890.7001-0.00650.33030.04760.04530.29560.00320.3159-9.6492-23.9749-3.8626
30.0640.04510.04890.153-0.02170.0495-0.21650.63490.8687-0.3770.3224-0.3763-0.41720.3277-0.00080.3511-0.0143-0.01510.5290.01440.3497-6.0517-11.840.2859
40.2808-0.00060.00490.0691-0.10490.15-0.1672-0.37910.44530.15430.1924-0.3228-0.5795-0.07610.00010.25340.04590.02240.3015-0.02190.2789-14.9229-13.6973-0.3997
50.74010.01260.44130.1370.08140.67340.20510.26-0.42080.02910.0882-0.11720.4287-0.09230.01410.289-0.00140.01750.3013-0.03020.2277-16.1235-20.5556-7.935
60.0595-0.0007-0.0290.044-0.00130.0466-0.10890.2124-0.80210.62190.4558-1.04580.17630.2502-0.00340.39440.0699-0.01840.42870.05010.3446-15.3215-22.93775.9176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:14)A1 - 14
2X-RAY DIFFRACTION2(CHAIN A AND RESID 15:21)A15 - 21
3X-RAY DIFFRACTION3(CHAIN B AND RESID 1:7)B1 - 7
4X-RAY DIFFRACTION4(CHAIN B AND RESID 8:16)B8 - 16
5X-RAY DIFFRACTION5(CHAIN B AND RESID 17:24)B17 - 24
6X-RAY DIFFRACTION6(CHAIN B AND RESID 25:29)B25 - 29

+
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