[English] 日本語
Yorodumi
- PDB-5udp: High resolution x-ray crystal structure of synthetic insulin lispro -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5udp
TitleHigh resolution x-ray crystal structure of synthetic insulin lispro
Components(Insulin Lispro ...) x 2
KeywordsHORMONE / insulin lispro / chemical protein synthesis / Fmoc chemistry
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / IRS activation / negative regulation of NAD(P)H oxidase activity / Insulin processing / Insulin receptor recycling / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / IRS activation / negative regulation of NAD(P)H oxidase activity / Insulin processing / Insulin receptor recycling / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / alpha-beta T cell activation / negative regulation of gluconeogenesis / negative regulation of acute inflammatory response / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of dendritic spine maintenance / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of glycogen biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of protein secretion / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of lipid biosynthetic process / Signal attenuation / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / positive regulation of insulin receptor signaling pathway / Regulation of insulin secretion / endoplasmic reticulum-Golgi intermediate compartment membrane / transport vesicle / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of protein metabolic process / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of brown fat cell differentiation / positive regulation of mitotic nuclear division / positive regulation of long-term synaptic potentiation / regulation of transmembrane transporter activity / positive regulation of cell differentiation / regulation of synaptic plasticity / activation of protein kinase B activity / cognition / positive regulation of cytokine production / positive regulation of protein secretion / acute-phase response / positive regulation of glucose import / negative regulation of proteolysis / positive regulation of nitric-oxide synthase activity / hormone activity / insulin receptor binding / vasodilation / insulin receptor signaling pathway / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / wound healing / Golgi lumen / regulation of protein localization / glucose metabolic process / glucose homeostasis / cell-cell signaling / positive regulation of phosphatidylinositol 3-kinase signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / positive regulation of NF-kappaB transcription factor activity / positive regulation of protein kinase B signaling / positive regulation of MAPK cascade / protease binding / G protein-coupled receptor signaling pathway / positive regulation of cell migration / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / endoplasmic reticulum lumen / 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/IGF/Relaxin family / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin family signature. / Insulin, conserved site / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.348 Å
AuthorsMandal, K. / Dhayalan, B. / Kent, S.B.H.
CitationJournal: Chemistry / Year: 2017
Title: Scope and Limitations of Fmoc Chemistry SPPS-Based Approaches to the Total Synthesis of Insulin Lispro via Ester Insulin.
Authors: Dhayalan, B. / Mandal, K. / Rege, N. / Weiss, M.A. / Eitel, S.H. / Meier, T. / Schoenleber, R.O. / Kent, S.B.
History
DepositionDec 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Insulin Lispro A chain
B: Insulin Lispro B chain
C: Insulin Lispro A chain
D: Insulin Lispro B chain
E: Insulin Lispro A chain
F: Insulin Lispro B chain
G: Insulin Lispro A chain
H: Insulin Lispro B chain
I: Insulin Lispro A chain
J: Insulin Lispro B chain
K: Insulin Lispro A chain
L: Insulin Lispro B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,69523
Polymers34,90612
Non-polymers78911
Water3,639202
1
A: Insulin Lispro A chain
D: Insulin Lispro B chain
F: Insulin Lispro B chain
G: Insulin Lispro A chain
I: Insulin Lispro A chain
L: Insulin Lispro B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,83611
Polymers17,4536
Non-polymers3835
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-61 kcal/mol
Surface area13450 Å2
MethodPISA
2
B: Insulin Lispro B chain
C: Insulin Lispro A chain
E: Insulin Lispro A chain
H: Insulin Lispro B chain
J: Insulin Lispro B chain
K: Insulin Lispro A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,85912
Polymers17,4536
Non-polymers4066
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-70 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.644, 61.470, 59.148
Angle α, β, γ (deg.)90.000, 110.600, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Insulin Lispro ... , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
Insulin Lispro A chain


Mass: 2383.698 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Chemical Synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide
Insulin Lispro B chain


Mass: 3433.953 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Chemical Synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308

-
Non-polymers , 5 types, 213 molecules

#3: Chemical
ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O
#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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.3 M TRIS, 0.5 M sodium sulfate, 0.6 mM Zinc acetate, 0.06% phenol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.348→50 Å / Num. obs: 67860 / % possible obs: 98.3 % / Redundancy: 6.2 % / Biso Wilson estimate: 21.93 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2% possible all
1.348-1.373.50.77731160.77290
1.37-1.44.10.7060.7195.1
1.4-1.434.60.6260.75597.9
1.43-1.4550.5950.80998.8
1.45-1.496.20.5160.86699.5
1.49-1.526.50.3940.92799.6
1.52-1.566.60.3280.94299.3
1.56-1.66.70.2730.95299.3
1.6-1.656.50.2330.96498.5
1.65-1.760.1870.97198.3
1.7-1.766.80.1650.98299.4
1.76-1.8370.1370.98899.5
1.83-1.926.80.1240.98899.2
1.92-2.026.70.0990.99298.9
2.02-2.146.20.0790.99397.6
2.14-2.3170.0650.99799.7
2.31-2.5470.0540.99899.7
2.54-2.916.80.0470.99898.8
2.91-3.666.70.050.99798.2
3.666.60.0730.99398.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXdev_2283refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZS2
Resolution: 1.348→25.718 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.36
RfactorNum. reflection% reflection
Rfree0.1943 1969 2.9 %
Rwork0.1604 --
obs0.1613 67807 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.66 Å2 / Biso mean: 37.8803 Å2 / Biso min: 17.95 Å2
Refinement stepCycle: final / Resolution: 1.348→25.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 47 202 2540
Biso mean--25.6 46.7 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052609
X-RAY DIFFRACTIONf_angle_d0.7653555
X-RAY DIFFRACTIONf_chiral_restr0.069375
X-RAY DIFFRACTIONf_plane_restr0.003466
X-RAY DIFFRACTIONf_dihedral_angle_d22.949952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3476-1.38130.35431210.31444350447190
1.3813-1.41870.30371410.24844601474297
1.4187-1.46040.21591430.20844689483299
1.4604-1.50750.21551510.168247484899100
1.5075-1.56140.17471300.14264734486499
1.5614-1.62390.18161430.14474710485399
1.6239-1.69780.17321450.13484710485598
1.6978-1.78730.15611360.137947494885100
1.7873-1.89920.18421510.14284746489799
1.8992-2.04580.19451380.15414724486299
2.0458-2.25160.16841420.1534723486599
2.2516-2.57710.17121450.15847964941100
2.5771-3.24590.21641430.1724715485898
3.2459-25.72240.19851400.1584843498399

+
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