[English] 日本語
Yorodumi
- PDB-1cph: CONFORMATIONAL CHANGES IN CUBIC INSULIN CRYSTALS IN THE PH RANGE 7-11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cph
TitleCONFORMATIONAL CHANGES IN CUBIC INSULIN CRYSTALS IN THE PH RANGE 7-11
Components(INSULIN (PH 10)) x 2
KeywordsHORMONE
Function / homology
Function and homology information


estradiol secretion / negative regulation of lactation / positive regulation of blood circulation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / response to butyrate ...estradiol secretion / negative regulation of lactation / positive regulation of blood circulation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / response to butyrate / feeding behavior / response to growth hormone / response to food / positive regulation of Rho protein signal transduction / positive regulation of peptide hormone secretion / protein secretion / response to glucose / negative regulation of lipid catabolic process / response to nutrient levels / positive regulation of protein secretion / insulin receptor binding / hormone activity / positive regulation of insulin secretion / glucose metabolic process / glucose homeostasis / response to heat / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
1,2-DICHLOROETHANE / Insulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsGursky, O. / Badger, J. / Li, Y. / Caspar, D.L.D.
Citation
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.
#1: Journal: Biophys.J. / Year: 1992
Title: Monovalent Cation Binding in Cubic Insulin Crystals
Authors: Gursky, O. / Li, Y. / Badger, J. / Caspar, D.L.D.
#2: Journal: Biophys.J. / Year: 1992
Title: Flexibility in Crystalline Insulins
Authors: Badger, J.
#3: 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.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Water Structure in Cubic Insulin Crystals
Authors: Badger, J. / Caspar, D.L.D.
#5: 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
DepositionOct 30, 1992Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Remark 700SHEET THERE IS A SHEET COMPRISING TWO ANTIPARALLEL STRANDS PHE B 24 - TYR B 26 FROM TWO DIMER- ...SHEET THERE IS A SHEET COMPRISING TWO ANTIPARALLEL STRANDS PHE B 24 - TYR B 26 FROM TWO DIMER-FORMING INSULIN MOLECULES.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INSULIN (PH 10)
B: INSULIN (PH 10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8664
Polymers5,7442
Non-polymers1222
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-27 kcal/mol
Surface area3510 Å2
MethodPISA
2
A: INSULIN (PH 10)
B: INSULIN (PH 10)
hetero molecules

A: INSULIN (PH 10)
B: INSULIN (PH 10)
hetero molecules

A: INSULIN (PH 10)
B: INSULIN (PH 10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,59712
Polymers17,2316
Non-polymers3666
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6860 Å2
ΔGint-95 kcal/mol
Surface area8930 Å2
MethodPISA
3
A: INSULIN (PH 10)
B: INSULIN (PH 10)
hetero molecules

A: INSULIN (PH 10)
B: INSULIN (PH 10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7318
Polymers11,4874
Non-polymers2444
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_565x,-y+1,-z+1/21
Buried area4940 Å2
ΔGint-71 kcal/mol
Surface area5580 Å2
MethodPISA
4
A: INSULIN (PH 10)
hetero molecules

A: INSULIN (PH 10)
hetero molecules

B: INSULIN (PH 10)
hetero molecules

B: INSULIN (PH 10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7318
Polymers11,4874
Non-polymers2444
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556-x+1/2,y,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation20_556-z+1/2,x,-y+11
Buried area3310 Å2
ΔGint-65 kcal/mol
Surface area7210 Å2
MethodPISA
5
A: INSULIN (PH 10)
B: INSULIN (PH 10)
hetero molecules

A: INSULIN (PH 10)
B: INSULIN (PH 10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7318
Polymers11,4874
Non-polymers2444
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556-x+1/2,y,-z+11
Buried area4490 Å2
ΔGint-68 kcal/mol
Surface area6030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.900, 78.900, 78.900
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-212-

HOH

21B-238-

HOH

-
Components

#1: Protein/peptide INSULIN (PH 10)


Mass: 2339.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P01317
#2: Protein/peptide INSULIN (PH 10)


Mass: 3403.927 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P01317
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-DCE / 1,2-DICHLOROETHANE / ETHYLENE DICHLORIDE / 1,2-Dichloroethane


Mass: 98.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4Cl2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE 1,2-DICHLOROETHANE IS BOUND IS CIS CONFORMATION IN A SYMMETRIC POSITION ACROSS THE ...THE 1,2-DICHLOROETHANE IS BOUND IS CIS CONFORMATION IN A SYMMETRIC POSITION ACROSS THE CRYSTALLOGRAPHIC TWO-FOLD AXIS BETWEEN THE TWO INSULIN DIMER-FORMING MOLECULES.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.47 %
Crystal grow
*PLUS
pH: 9.2 / Method: microdialysis
Details: referred to 'Dodson, E.J.', (1978) J.Mol.Biol., 125, 387-396
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
20.2 M12Na2HPO4
30.01 MNa3EDTA11

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 10 Å / Num. obs: 6281 / % possible obs: 100 % / Num. measured all: 24331 / Rmerge(I) obs: 0.095

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.191 / Highest resolution: 1.9 Å
Details: IN 1BPH AND 1CPH, THE SIDE CHAIN OF GLU A 4 CAN ADOPT TWO ALTERNATIVE POSITIONS WHICH OVERLAP. THEIR RELATIVE WEIGHT AND THE ATOMIC POSITIONS OF THE SECOND CONFORMER ARE NOT ACCURATELY ...Details: IN 1BPH AND 1CPH, THE SIDE CHAIN OF GLU A 4 CAN ADOPT TWO ALTERNATIVE POSITIONS WHICH OVERLAP. THEIR RELATIVE WEIGHT AND THE ATOMIC POSITIONS OF THE SECOND CONFORMER ARE NOT ACCURATELY DETERMINED. IN 1APH, 1BPH, AND 1DPH, THE SIDE CHAIN OF GLU B 21 IS DISORDERED. IT HAS BEEN MODELED AS SUPERPOSITION OF TWO CONFORMATIONS BUT ATOMIC POSITIONS FOR THESE CONFORMATIONS ARE PROBABLY NOT VERY ACCURATE. THE MAIN AND SIDE CHAIN OF ALA B 30 (C-TERMINAL RESIDUE OF CHAIN B) CAN ADOPT TWO SEPARATE CONFORMATIONS AND IS DISORDERED IN EACH OF THESE CONFORMATIONS, WHICH LIMITED THE ACCURACY OF DETERMINATION OF ATOMIC POSITIONS FOR THE CONFORMERS OF ALA B 30. IN 1APH AND 1CPH, SINGLE ALTERNATIVE CONFORMERS ARE PREDOMINANT BUT, DUE TO DISORDER, THEY ARE ASSIGNED PARTIAL OCCUPANCIES. IN 1BPH AND 1DPH, BOTH ALTERNATIVE CONFORMERS ARE INCLUDED IN THE ENTRY.
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms410 0 5 66 481
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.9 Å / Rfactor all: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.051
X-RAY DIFFRACTIONp_planar_d0.063

+
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