[English] 日本語
Yorodumi
- PDB-9lvx: di-hexamer form of insulin detemir at ambient temperature -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lvx
Titledi-hexamer form of insulin detemir at ambient temperature
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin structure / dihexamer insulin / ambient temperature
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 / Signaling by Insulin receptor / negative regulation of feeding behavior / 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 / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / positive regulation of protein autophosphorylation / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / Signal attenuation / fatty acid homeostasis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of insulin receptor signaling pathway / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / COPI-mediated anterograde transport / transport vesicle / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / Insulin receptor recycling / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of nitric-oxide synthase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / regulation of transmembrane transporter activity / positive regulation of glycolytic process / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / endosome lumen / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / positive regulation of cell differentiation / Regulation of insulin secretion / insulin receptor binding / wound healing / negative regulation of protein catabolic process / hormone activity / regulation of synaptic plasticity / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / cognition / glucose metabolic process / vasodilation / insulin receptor signaling pathway / glucose homeostasis / cell-cell signaling / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / positive regulation of cell growth / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / 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 / positive regulation of gene expression / regulation of DNA-templated transcription / 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
PHENOL / MYRISTIC ACID / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAyan, E. / Bahar, I.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government Turkey
CitationJournal: To Be Published
Title: di-hexamer form of insulin detemir at ambient temperature
Authors: Ayan, E. / Bahar, I.
History
DepositionFeb 13, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
E: Insulin A chain
F: Insulin B chain
G: Insulin A chain
H: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,56024
Polymers22,8668
Non-polymers1,69316
Water2,756153
1
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules

A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules

A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,83936
Polymers34,29912
Non-polymers2,54024
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 area24440 Å2
ΔGint-932 kcal/mol
Surface area10180 Å2
MethodPISA
2
E: Insulin A chain
F: Insulin B chain
G: Insulin A chain
H: Insulin B chain
hetero molecules

E: Insulin A chain
F: Insulin B chain
G: Insulin A chain
H: Insulin B chain
hetero molecules

E: Insulin A chain
F: Insulin B chain
G: Insulin A chain
H: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,83936
Polymers34,29912
Non-polymers2,54024
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 area26730 Å2
ΔGint-839 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.898, 80.898, 80.414
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-102-

ZN

21B-103-

CL

31D-102-

ZN

41D-103-

CL

51F-102-

ZN

61H-102-

ZN

71H-103-

CL

-
Components

-
Protein/peptide , 2 types, 8 molecules ACEGBDFH

#1: Protein/peptide
Insulin A chain / Small chain


Mass: 2383.698 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide
Insulin B chain


Mass: 3332.849 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308

-
Non-polymers , 5 types, 169 molecules

#3: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium acetate trihydrate, 0.1M tris hydrochloride pH 9

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5 Å
DetectorType: RIGAKU HyPix-Arc 150 / Detector: PIXEL / Date: Aug 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.7→19.32 Å / Num. obs: 5361 / % possible obs: 97.3 % / Redundancy: 12.9 % / CC1/2: 0.884 / Net I/σ(I): 5.81
Reflection shellResolution: 2.7→2.797 Å / Num. unique obs: 479 / CC1/2: 0.737

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.32 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 36.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3223 527 10.07 %
Rwork0.2728 --
obs0.2778 5233 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 96 153 1841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021723
X-RAY DIFFRACTIONf_angle_d0.3962299
X-RAY DIFFRACTIONf_dihedral_angle_d16.053627
X-RAY DIFFRACTIONf_chiral_restr0.032242
X-RAY DIFFRACTIONf_plane_restr0.002290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80.3506500.3372431X-RAY DIFFRACTION93
2.8-2.910.3445520.327460X-RAY DIFFRACTION96
2.91-3.040.3503530.3042476X-RAY DIFFRACTION97
3.04-3.20.339560.2966464X-RAY DIFFRACTION97
3.2-3.40.304540.2858486X-RAY DIFFRACTION99
3.4-3.660.3635490.2853471X-RAY DIFFRACTION98
3.66-4.020.4263530.2693476X-RAY DIFFRACTION98
4.03-4.60.2732520.2318485X-RAY DIFFRACTION100
4.6-5.750.2719570.236479X-RAY DIFFRACTION99
5.77-100.285510.2663478X-RAY DIFFRACTION97
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)
14.1768-2.3062-0.56481.40840.71921.30450.17780.25170.281-0.1946-0.1619-0.1581-0.11170.0181-0.21250.3640.27730.29110.29950.21530.6506-12.69399.4242-37.0718
20.33240.51130.2811.8356-0.58512.186-0.01090.24880.0269-0.7429-0.1811-0.12030.4397-0.1363-0.04680.4280.16380.09960.50120.07530.4585-6.136412.2734-37.1769
33.44811.0910.30892.3305-1.82292.99720.2515-0.16340.5595-0.22430.520.3847-0.4106-0.3763-0.18790.37490.01280.16680.20350.02180.5687-12.468916.3244-28.3139
43.4907-0.5258-0.28853.9467-0.77072.0558-0.14480.28620.37830.1404-0.1430.16120.0461-0.4304-0.16070.25950.00040.10260.19220.10960.3466-8.24775.8202-28.1985
53.01920.3421-0.72931.5641-0.85082.66770.05950.41930.077-0.31080.15440.09090.0609-0.30960.57210.3829-0.11780.11020.45730.08350.0977-16.90455.4763-29.3504
62.59261.14362.0232.2685-1.43364.6501-0.0032-0.40920.32110.23070.0950.4243-0.0241-0.6835-0.23050.2096-0.0445-0.05030.33250.01580.3896-13.8475-3.3317-10.7462
70.2498-0.48241.14211.7343-2.94725.87660.02830.13660.0914-0.3775-0.11550.10990.86460.2574-0.15280.3713-0.12680.10760.44870.02150.1925-19.1858-6.3531-19.9522
84.4056-0.4645-1.22733.17-0.49172.05070.3501-0.49610.30860.12910.19440.1468-0.08560.25080.57070.5628-0.0560.02550.17060.04080.1539-9.65840.1903-19.9252
94.1622-1.56041.00526.68460.76363.5603-0.0245-0.35680.0176-0.00330.12060.1695-0.2721-0.39840.19720.36870.3789-0.03920.51580.23390.1972-16.84455.5496-18.8158
100.52540.3765-0.22910.8588-0.21850.29040.05850.00860.09540.1018-0.05590.2165-0.0966-0.1699-0.03430.06450.02120.18320.228-0.0070.5698-10.083710.14932.8991
113.37392.0252-0.20471.225-0.15651.4780.047-0.07060.21250.12360.56940.4635-0.2419-0.0205-0.03540.33520.11270.13640.2756-0.03090.5244-13.33315.395911.9296
122.78451.02460.65931.8326-0.55175.0507-0.34970.3030.15030.1591-0.13650.3091-0.5677-0.4133-0.92160.06560.03740.2840.2807-0.077-0.0672-8.5665.164211.9251
132.1515-0.22640.45770.0975-0.22970.55160.21580.4313-0.187-0.1401-0.06790.07780.0455-0.00850.61790.32330.3470.1470.3273-0.167-0.0276-17.26474.549410.7921
143.7010.3350.35813.3317-0.63892.41550.1806-0.2540.61580.78230.5090.389-0.2212-0.3094-0.13090.38360.03260.08170.44750.12430.1701-13.5271-4.446129.2733
150.34210.9714-0.05973.4758-1.31881.7930.00450.07290.1271-0.2863-0.25490.3668-0.1308-0.5369-0.40860.34090.0266-0.00830.18860.01270.3938-18.657-7.722420.1662
163.72560.68050.99744.42280.69043.4610.2454-0.13820.30940.38210.09790.0188-0.13490.1423-0.10130.19730.0573-0.00210.24440.09390.1348-9.6612-0.307420.3021
178.68-0.37090.86758.5528-0.42432.87030.0367-0.65670.24680.92520.17670.376-0.4123-0.4358-0.11140.23460.05830.18920.39260.23190.3953-17.05384.505621.4188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 6 )
2X-RAY DIFFRACTION2chain 'A' and (resid 7 through 12 )
3X-RAY DIFFRACTION3chain 'A' and (resid 13 through 21 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 22 )
5X-RAY DIFFRACTION5chain 'B' and (resid 23 through 29 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 12 )
7X-RAY DIFFRACTION7chain 'C' and (resid 13 through 21 )
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 22 )
9X-RAY DIFFRACTION9chain 'D' and (resid 23 through 29 )
10X-RAY DIFFRACTION10chain 'E' and (resid 1 through 12 )
11X-RAY DIFFRACTION11chain 'E' and (resid 13 through 21 )
12X-RAY DIFFRACTION12chain 'F' and (resid 1 through 22 )
13X-RAY DIFFRACTION13chain 'F' and (resid 23 through 29 )
14X-RAY DIFFRACTION14chain 'G' and (resid 1 through 12 )
15X-RAY DIFFRACTION15chain 'G' and (resid 13 through 21 )
16X-RAY DIFFRACTION16chain 'H' and (resid 1 through 22 )
17X-RAY DIFFRACTION17chain 'H' and (resid 23 through 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