[English] 日本語
Yorodumi
- PDB-1zei: CROSS-LINKED B28 ASP INSULIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zei
TitleCROSS-LINKED B28 ASP INSULIN
ComponentsINSULIN
KeywordsHORMONE / METABOLIC ROLE / CHEMICAL ACTIVITY / INSULIN MUTANT / CROSS-LINK / GLUCOSE METABOLISM / DIABETES
Function / homology
Function and homology information


positive regulation of lipoprotein lipase activity / Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / response to L-arginine ...positive regulation of lipoprotein lipase activity / Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / response to L-arginine / glycoprotein biosynthetic process / lactate biosynthetic process / positive regulation of glucose metabolic process / positive regulation of fatty acid biosynthetic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / 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 / lipid biosynthetic process / positive regulation of respiratory burst / negative regulation of acute inflammatory response / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / positive regulation of insulin receptor signaling pathway / negative regulation of respiratory burst involved in inflammatory response / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of mitotic nuclear division / positive regulation of glycolytic process / positive regulation of DNA replication / positive regulation of cytokine production / acute-phase response / positive regulation of D-glucose import across plasma membrane / positive regulation of protein secretion / insulin receptor binding / wound healing / hormone activity / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / vasodilation / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / protease binding / 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 / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / identical protein binding
Similarity search - Function
Insulin-like, subunit E / Insulin-like / 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 ...Insulin-like, subunit E / Insulin-like / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWhittingham, J.L. / Edwards, E.J. / Antson, A.A. / Clarkson, J.M. / Dodson, G.G.
Citation
Journal: Biochemistry / Year: 1998
Title: Interactions of phenol and m-cresol in the insulin hexamer, and their effect on the association properties of B28 pro --> Asp insulin analogues.
Authors: Whittingham, J.L. / Edwards, D.J. / Antson, A.A. / Clarkson, J.M. / Dodson, G.G.
#1: Journal: Structure / Year: 1995
Title: Role of C-Terminal B-Chain Residues in Insulin Assembly: The Structure of Hexameric Lysb28Prob29-Human Insulin
Authors: Ciszak, E. / Beals, J.M. / Frank, B.H. / Baker, J.C. / Carter, N.D. / Smith, G.D.
#2: Journal: Biopolymers / Year: 1992
Title: The Structure of a Rhombohedral R6 Insulin Hexamer that Binds Phenol
Authors: Smith, G.D. / Dodson, G.G.
History
DepositionJul 14, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INSULIN
B: INSULIN
C: INSULIN
D: INSULIN
E: INSULIN
F: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,99418
Polymers35,9276
Non-polymers1,06712
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-132 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.952, 64.772, 48.914
Angle α, β, γ (deg.)90.00, 109.81, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
INSULIN / B28ASP-X-MCR


Mass: 5987.840 Da / Num. of mol.: 6 / Mutation: P28D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01315
#2: Chemical
ChemComp-CRS / M-CRESOL


Mass: 108.138 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H8O
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.4 / Details: pH 6.4
Crystal grow
*PLUS
Temperature: 50 ℃ / Method: batch method / PH range low: 6.4 / PH range high: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13.5 mg/mlinsulin11
20.02 M110.5mlHCl
30.15 Mzinc acetate110.050ml
40.2 Mtrisodium citrate110.360ml
52.5 %m-cresol in ethanol110.200ml
61160mgNaCl

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.88
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.9→19.9 Å / Num. obs: 21942 / % possible obs: 87.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.054
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.216 / % possible all: 49.6
Reflection
*PLUS
Num. measured all: 79085
Reflection shell
*PLUS
Lowest resolution: 2 Å / % possible obs: 77 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE MONOCLINIC PHENOL INSULIN DIMER

Resolution: 1.9→20 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 -5 %5
Rwork0.176 ---
obs-21942 87.8 %-
Displacement parametersBiso mean: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 68 229 2799
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0410.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.3932
X-RAY DIFFRACTIONp_mcangle_it3.463
X-RAY DIFFRACTIONp_scbond_it3.2522
X-RAY DIFFRACTIONp_scangle_it4.9443
X-RAY DIFFRACTIONp_plane_restr0.0280.03
X-RAY DIFFRACTIONp_chiral_restr0.1160.1
X-RAY DIFFRACTIONp_singtor_nbd0.1710.3
X-RAY DIFFRACTIONp_multtor_nbd0.2720.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1690.3
X-RAY DIFFRACTIONp_planar_tor4.97
X-RAY DIFFRACTIONp_staggered_tor17.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor16.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1762
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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