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RCSB PDB
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 2VJZ|pdb_00002vjz

Crystal structure form ultalente insulin microcrystals


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.239 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model:experimental
View more details

wwPDB Validation  3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of Ultralente-A Microcrystalline Insulin Suspension.

Wagner, A.Diez, J.Schulze-Briese, C.Schluckebier, G.

(2009) Proteins 74: 1018

  • PubMed18767151 Search on PubMed
  • DOI: https://doi.org/10.1002/prot.22213
  • Primary Citation of Related Structures:  
    2VJZ,2VK0

  • PubMed Abstract: 

    Ultralente insulin has been one of the commercially most important insulin preparations in diabetes treatment over the last 50 years. It is a suspension of insulin microcrystals which dissolve slowly following subcutaneous injection. Because of the small crystal size of about 25 x 25 x 5 microm(3) the atomic structure has been elusive until now. Here we present the crystal structures from Ultralente and their precursor microcrystals from the industrial manufacturing process. During this process insulin undergoes a conformational change within the microcrystals. Both structures show canonical folding of the insulin molecules but exhibit a number of new features when compared with other insulin structures. Surprisingly, we found that the Ultralente crystals bind the conservation agent methylparaben, which slows down dissolution of the crystals and thus contributes to the long duration of action.


  • Organizational Affiliation
    • Swiss Light Source, Paul Scherrer Institute, CH-5323 Villigen PSI, Switzerland. armin.wagner@diamond.ac.uk
Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (ZN)


Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 
Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A3B3C3D3 


Find Similar Assemblies

Biological assembly 1 assigned by authors and generated by PQS (software)

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Macromolecule Content 

  • Total Structure Weight: 11.91 kDa 
  • Atom Count: 906 
  • Modeled Residue Count: 99 
  • Deposited Residue Count: 102 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INSULIN A CHAIN21Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
PHAROS:  P01308
GTEx:  ENSG00000254647 
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
INSULIN B CHAIN30Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
PHAROS:  P01308
GTEx:  ENSG00000254647 
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth B],
H [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth B],
G [auth B],
I [auth D],
J [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.239 (Depositor), 0.230 (DCC) 
  • R-Value Work: 0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.82α = 90
b = 79.82β = 90
c = 36.71γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2020-11-18
    Changes: Derived calculations, Other
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.


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