[English] 日本語
Yorodumi
- PDB-8pi6: Crystal structure of the monomeric zinc free human insulin A22K, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pi6
TitleCrystal structure of the monomeric zinc free human insulin A22K, B3E, B26E, B29R, desB30 precursor with a Ser-Glu-Asp-Trp-Trp-Arg C-peptide and a Glu-Glu-Gly-Glu-Pro-Arg N-terminal extension
ComponentsInsulin B chain,Insulin A chain
KeywordsHORMONE / insulin / precursor / dimer
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 / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsJohansson, E. / Schluckebier, G.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Not funded Denmark
CitationJournal: Trends Biotechnol / Year: 2024
Title: Molecular engineering of insulin for recombinant expression in yeast.
Authors: Kjeldsen, T. / Andersen, A.S. / Hubalek, F. / Johansson, E. / Kreiner, F.F. / Schluckebier, G. / Kurtzhals, P.
History
DepositionJun 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Insulin B chain,Insulin A chain
B: Insulin B chain,Insulin A chain
C: Insulin B chain,Insulin A chain
D: Insulin B chain,Insulin A chain
E: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)36,9815
Polymers36,9815
Non-polymers00
Water28816
1
A: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)7,3961
Polymers7,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)7,3961
Polymers7,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)7,3961
Polymers7,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)7,3961
Polymers7,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)7,3961
Polymers7,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.240, 60.020, 90.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein
Insulin B chain,Insulin A chain


Mass: 7396.271 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 8 mg/ml protein in water precipitant: 0.1 M sodium citrate, pH 5.6, 1.o M ammonium phosphate monobasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.075 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.075 Å / Relative weight: 1
ReflectionResolution: 2.14→45.88 Å / Num. obs: 14677 / % possible obs: 84.68 % / Redundancy: 109.8 % / Biso Wilson estimate: 41.94 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.01512 / Rrim(I) all: 0.1727 / Net I/σ(I): 33.01
Reflection shellResolution: 2.14→2.219 Å / Redundancy: 16.1 % / Rmerge(I) obs: 2.496 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 726 / CC1/2: 0.0712 / CC star: 0.365 / Rpim(I) all: 0.5138 / Rrim(I) all: 2.562 / % possible all: 44.84

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
HKL2Mapphasing
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→45.88 Å / SU ML: 0.2676 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 34.4413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2878 1390 9.94 %
Rwork0.2378 12594 -
obs0.243 13984 84.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.09 Å2
Refinement stepCycle: LAST / Resolution: 2.14→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 0 16 2302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182357
X-RAY DIFFRACTIONf_angle_d0.52013193
X-RAY DIFFRACTIONf_chiral_restr0.0323327
X-RAY DIFFRACTIONf_plane_restr0.0025414
X-RAY DIFFRACTIONf_dihedral_angle_d3.7551311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.220.3867700.4513656X-RAY DIFFRACTION44.87
2.22-2.310.39251010.3594908X-RAY DIFFRACTION62.55
2.31-2.410.3741270.32451141X-RAY DIFFRACTION77.98
2.41-2.540.31751380.28111231X-RAY DIFFRACTION84.45
2.54-2.70.32341470.2811311X-RAY DIFFRACTION89.67
2.7-2.910.3821440.30271367X-RAY DIFFRACTION92.3
2.91-3.20.30441570.26581419X-RAY DIFFRACTION95.75
3.2-3.660.30111630.23991470X-RAY DIFFRACTION98.08
3.66-4.610.27361650.19671497X-RAY DIFFRACTION98.93
4.61-45.880.2361780.19941594X-RAY DIFFRACTION99.66
Refinement TLS params.Method: refined / Origin x: 60.4524471165 Å / Origin y: 65.770051835 Å / Origin z: 82.5634760152 Å
111213212223313233
T0.22385873665 Å2-0.0181292366532 Å2-0.0312291707996 Å2-0.32357026202 Å2-0.0156804799795 Å2--0.129379031979 Å2
L0.588678353765 °2-0.224359917688 °2-0.331966836156 °2-0.82213179722 °2-0.330423659663 °2--0.996888283131 °2
S-0.00940211826019 Å °-0.0269265768922 Å °-0.0421415122721 Å °0.0629819483566 Å °-0.0274519272117 Å °0.0257553097211 Å °0.223313349123 Å °-0.0659990416274 Å °0.0237832339152 Å °
Refinement TLS groupSelection details: all

+
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