[English] 日本語
Yorodumi
- PDB-1b2a: PH AFFECTS GLU B13 SWITCHING AND SULFATE BINDING IN CUBIC INSULIN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b2a
TitlePH AFFECTS GLU B13 SWITCHING AND SULFATE BINDING IN CUBIC INSULIN CRYSTALS (PH 6.00 COORDINATES)
Components
  • PROTEIN (INSULIN A CHAIN)
  • PROTEIN (INSULIN B CHAIN)
KeywordsHORMONE/GROWTH FACTOR / HORMONE / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


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 / glycoprotein biosynthetic process / response to L-arginine ...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 / glycoprotein biosynthetic process / response to L-arginine / positive regulation of lipoprotein lipase activity / lactate biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / lipid biosynthetic process / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / positive regulation of DNA replication / positive regulation of protein secretion / hormone activity / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / positive regulation of cell migration / extracellular space / 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.7 Å
AuthorsDiao, J.S. / Caspar, D.L.D.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallographic titration of cubic insulin crystals: pH affects GluB13 switching and sulfate binding.
Authors: Diao, J.
#1: Journal: Biophys.J. / Year: 1992
Title: Conformational Changes in Cubic Insulin Crystals in the Ph Range 7-11
Authors: Gursky, O. / Badger, J. / Li, Y. / Caspar, D.L.
#2: Journal: Biophys.J. / Year: 1992
Title: Monovalent Cation Binding in Cubic Insulin Crystals
Authors: Gursky, O. / Li, Y. / Badger, J. / Caspar, D.L.
#3: Journal: Biophys.J. / Year: 1992
Title: Flexibility in Crystalline Insulins
Authors: Badger, J.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Structure of the Pig Insulin Dimer in the Cubic Crystal
Authors: Badger, J. / Harris, M.R. / Reynolds, C.D. / Evans, A.C. / Dodson, E.J. / Dodson, G.G. / North, A.C.T.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Water Structure in Cubic Insulin Crystals
Authors: Badger, J. / Caspar, D.L.
#6: Journal: J.Mol.Biol. / Year: 1978
Title: Zinc-Free Cubic Pig Insulin: Crystallization and Structure Determination
Authors: Dodson, E.J. / Dodson, G.G. / Lewitova, A. / Sabesan, M.
History
DepositionNov 26, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (INSULIN A CHAIN)
B: PROTEIN (INSULIN B CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8843
Polymers5,7882
Non-polymers961
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-26 kcal/mol
Surface area3450 Å2
MethodPISA
2
A: PROTEIN (INSULIN A CHAIN)
B: PROTEIN (INSULIN B CHAIN)
hetero molecules

A: PROTEIN (INSULIN A CHAIN)
B: PROTEIN (INSULIN B CHAIN)
hetero molecules

A: PROTEIN (INSULIN A CHAIN)
B: PROTEIN (INSULIN B CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6519
Polymers17,3636
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6760 Å2
ΔGint-112 kcal/mol
Surface area8650 Å2
MethodPISA
3
A: PROTEIN (INSULIN A CHAIN)
B: PROTEIN (INSULIN B CHAIN)
hetero molecules

A: PROTEIN (INSULIN A CHAIN)
B: PROTEIN (INSULIN B CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7676
Polymers11,5754
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_565x,-y+1,-z+1/21
Buried area4660 Å2
ΔGint-57 kcal/mol
Surface area5620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.748, 78.748, 78.748
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-87-

HOH

21B-88-

HOH

-
Components

#1: Protein/peptide PROTEIN (INSULIN A CHAIN)


Mass: 2383.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P01315
#2: Protein/peptide PROTEIN (INSULIN B CHAIN)


Mass: 3403.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P01315
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.52 Å3/Da / Density % sol: 65 %
Crystal growpH: 6 / Details: pH 6.00
Components of the solutionsName: SODIUM SULFATE SOLUTION AT PH 6.00
Crystal grow
*PLUS
pH: 9.2 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.05 Msodium phosphate11
20.001 Msodium EDTA11pH11
318 mg/mlprotein11
40.15 Msodium phosphate12
50.001 Msodium EDTA12pH9.2

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceWavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→55 Å / Num. obs: 8958 / % possible obs: 98.4 % / Redundancy: 3.78 % / Biso Wilson estimate: 20.47 Å2 / Rsym value: 0.124
Reflection
*PLUS
% possible obs: 98.43 % / Rmerge(I) obs: 0.124

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843refinement
RefinementMethod to determine structure: OTHER / Resolution: 1.7→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.23 887 9.81 %RANDOM
Rwork0.1879 ---
obs-8808 97.4 %-
Displacement parametersBiso mean: 22.83 Å2
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms408 0 5 66 479
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.12
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.16
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.09
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3224 46 7.6 %
Rwork0.3186 524 -
obs--94.22 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3SO4.PARSO4.TOP
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.16
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.09

+
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