[English] 日本語
Yorodumi
- PDB-9lvc: Temperature induces a shift from the dihexamer to the hexamer for... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lvc
TitleTemperature induces a shift from the dihexamer to the hexamer form of insulin
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin structure / hexamer form / temperature jump
Function / homology
Function and homology information


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 / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...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 / regulation of protein secretion / Insulin processing / 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 / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / 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 mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / 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: 2.3 Å
AuthorsAyan, E. / Kepceoglu, A.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Protein Sci. / Year: 2025
Title: Temperature induces a shift from insulin dihexamer to hexamer in collective dynamics.
Authors: Ayan, E.
History
DepositionFeb 12, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
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
Water97354
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_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area21110 Å2
ΔGint-560 kcal/mol
Surface area14140 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_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area18550 Å2
ΔGint-578 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.064, 79.064, 79.496
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

61F-103-

CL

71H-102-

ZN

81H-103-

CL

91B-208-

HOH

101F-208-

HOH

111F-210-

HOH

121H-204-

HOH

-
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, 70 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.: 54 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium acetate trihydrate, 0.1M tris hydrochloride pH 9

-
Data collection

DiffractionMean temperature: 100 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: Sep 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.3→19.77 Å / Num. obs: 8131 / % possible obs: 98.77 % / Redundancy: 4.1 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 30.01
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 8131 / CC1/2: 0.99

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.77 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 30.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2868 809 9.95 %
Rwork0.2321 --
obs0.2375 8131 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 96 54 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.381
X-RAY DIFFRACTIONf_dihedral_angle_d14.517630
X-RAY DIFFRACTIONf_chiral_restr0.033244
X-RAY DIFFRACTIONf_plane_restr0.002290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.2653820.2573731X-RAY DIFFRACTION99
2.38-2.480.349840.2601715X-RAY DIFFRACTION98
2.48-2.590.3193770.2505729X-RAY DIFFRACTION99
2.59-2.730.2653820.2573737X-RAY DIFFRACTION99
2.73-2.90.3198800.2624729X-RAY DIFFRACTION99
2.9-3.120.2874830.2464745X-RAY DIFFRACTION99
3.12-3.430.2837810.2331724X-RAY DIFFRACTION100
3.43-3.920.2766830.2224741X-RAY DIFFRACTION100
3.93-4.930.2713770.1917734X-RAY DIFFRACTION98
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)
16.2406-2.2584-1.44291.9999-4.78686.2196-0.0454-1.0401-0.08491.0972-0.0224-0.5457-0.31240.45210.28210.15940.02770.00810.31950.1580.333413.79938.077434.2361
27.85960.14841.97916.41825.62825.93650.6006-0.10420.0492-0.1773-0.3146-0.2256-0.03950.24560.06760.08110.0120.00660.1476-0.05390.164613.150445.413834.2208
32.0384-0.62010.85764.0565-0.03643.4379-0.04780.5830.3545-0.27120.1833-0.6096-0.47680.627-0.18220.1127-0.04790.05290.2785-0.06230.219219.51341.60225.3811
43.7371.4467-1.6932.6004-0.52221.782-0.0683-0.07810.3010.23830.0917-0.2446-0.0353-0.1055-0.13170.08110.0505-0.01880.149-0.02620.16516.482540.992327.131
55.4426-0.5612-0.45081.26351.37391.4977-0.1685-0.7328-0.352-0.31530.0356-0.51270.45140.53070.22630.04140.15340.23710.28070.0140.071414.533235.231422.6005
61.9226-1.5196-0.30951.44130.98672.3399-0.18070.2953-0.4784-0.5546-0.1774-0.0108-0.19070.26750.24460.4746-0.09410.11770.2878-0.04240.28685.580631.28547.7139
71.0630.27250.36360.2235-0.45342.08770.2110.008-0.0553-0.2653-0.1033-0.02790.3688-0.42220.97310.4808-0.0253-0.00870.1507-0.02080.1243-1.304132.44388.0512
88.04652.46222.45243.54720.68222.79480.41220.2706-0.44570.22770.1041-0.4290.19440.1175-0.04880.2578-0.02160.04620.1462-0.0190.17482.020925.836916.931
92.55470.33660.43814.7959-2.71784.68060.12430.21530.1469-0.0278-0.3265-0.12220.03860.82770.04230.082-0.06260.02320.17170.00980.18964.167938.68315.1279
104.6691.13050.38628.0226-1.62263.8192-0.070.7069-0.5426-1.01690.3855-0.41750.39490.0004-0.19860.27370.1338-0.07070.4556-0.03920.168110.072231.223219.2427
116.3364-0.9781.78952.9752-0.5458.49740.1587-0.9642-0.35770.4204-0.1327-0.4492-0.02180.3137-0.48690.32240.058-0.02080.2895-0.00460.325914.392839.7426-5.6538
120.4707-0.3638-0.5510.28050.42310.6460.2309-0.12710.3543-0.44560.595-0.6712-0.56691.18652.18560.2161-0.06120.06980.4532-0.43280.252113.315147.0997-5.6761
131.61221.38440.99314.05421.27574.1045-0.31250.27380.2347-0.6902-0.06230.1894-0.55230.4162-0.15710.1537-0.0140.03330.2842-0.01030.283319.970843.5926-14.5228
145.05590.5132-2.04932.2438-0.13033.0084-0.449-0.2299-0.19650.1420.23270.13930.57030.0664-0.160.23290.03750.01430.1422-0.0060.19826.93541.7168-12.7849
155.05820.11340.31672.37021.8971.8331-0.1141-0.3549-0.07320.220.2734-0.04930.65740.30180.15920.16280.04790.03070.3763-0.07390.082415.406436.6184-17.1525
161.8522-0.85650.75783.4546-0.05151.1739-0.2002-0.1230.0388-0.4792-0.04950.2982-0.13960.09340.00440.146-0.05620.0220.25290.02060.17047.833732.1093-32.0719
173.84041.00710.21843.05730.69811.1943-0.1544-0.25760.03460.47120.4782-0.11420.46120.16550.33760.2250.0436-0.05370.07250.02180.15920.855232.5338-32.0693
185.0316-0.31180.20740.47260.65254.0614-0.15190.293-0.2168-0.0056-0.1724-0.3899-0.2861-0.3381-0.27530.17220.02360.02690.1339-0.00970.30354.252226.36-22.8353
190.9752-0.22390.68592.3631-1.92842.0094-0.06070.0040.2111-0.0763-0.2396-0.2788-0.10110.1829-0.01010.1469-0.0228-0.00930.1315-0.0210.16844.921339.3024-24.7247
206.15920.8182-0.4956.7925-1.96236.5711-0.16180.3431-0.1126-0.5033-0.5366-0.27160.1238-0.3124-0.04620.21580.01-0.08240.2555-0.02560.272611.452532.2288-20.3563
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 19 )
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 29 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 6 )
7X-RAY DIFFRACTION7chain 'C' and (resid 7 through 12 )
8X-RAY DIFFRACTION8chain 'C' and (resid 13 through 21 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 19 )
10X-RAY DIFFRACTION10chain 'D' and (resid 20 through 29 )
11X-RAY DIFFRACTION11chain 'E' and (resid 1 through 6 )
12X-RAY DIFFRACTION12chain 'E' and (resid 7 through 12 )
13X-RAY DIFFRACTION13chain 'E' and (resid 13 through 21 )
14X-RAY DIFFRACTION14chain 'F' and (resid 1 through 19 )
15X-RAY DIFFRACTION15chain 'F' and (resid 20 through 29 )
16X-RAY DIFFRACTION16chain 'G' and (resid 1 through 6 )
17X-RAY DIFFRACTION17chain 'G' and (resid 7 through 12 )
18X-RAY DIFFRACTION18chain 'G' and (resid 13 through 21 )
19X-RAY DIFFRACTION19chain 'H' and (resid 1 through 19 )
20X-RAY DIFFRACTION20chain 'H' and (resid 20 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