[English] 日本語
Yorodumi
- PDB-2omq: VEALYL peptide derived from human insulin chain B, residues 12-17 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2omq
TitleVEALYL peptide derived from human insulin chain B, residues 12-17
ComponentsVEALYL peptide derived from human insulin chain B, residues 12-17
KeywordsPROTEIN FIBRIL / steric zipper / anti-parallel beta-sheet
Function / homology
Function and homology information


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 / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...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 / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / 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-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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIvanova, M. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Nature / Year: 2007
Title: Atomic structures of amyloid cross-beta spines reveal varied steric zippers.
Authors: Sawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M.I. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H.T. / Madsen, A. / Riekel, C. / Eisenberg, D.
History
DepositionJan 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 25, 2014Group: Other
Revision 1.4Apr 22, 2015Group: Structure summary
Revision 1.5Oct 18, 2017Group: Refinement description / Category: software
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VEALYL peptide derived from human insulin chain B, residues 12-17
B: VEALYL peptide derived from human insulin chain B, residues 12-17
C: VEALYL peptide derived from human insulin chain B, residues 12-17
D: VEALYL peptide derived from human insulin chain B, residues 12-17


Theoretical massNumber of molelcules
Total (without water)2,8274
Polymers2,8274
Non-polymers00
Water724
1
A: VEALYL peptide derived from human insulin chain B, residues 12-17
B: VEALYL peptide derived from human insulin chain B, residues 12-17
C: VEALYL peptide derived from human insulin chain B, residues 12-17
D: VEALYL peptide derived from human insulin chain B, residues 12-17

A: VEALYL peptide derived from human insulin chain B, residues 12-17
B: VEALYL peptide derived from human insulin chain B, residues 12-17
C: VEALYL peptide derived from human insulin chain B, residues 12-17
D: VEALYL peptide derived from human insulin chain B, residues 12-17


Theoretical massNumber of molelcules
Total (without water)5,6558
Polymers5,6558
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Unit cell
Length a, b, c (Å)18.425, 9.613, 21.975
Angle α, β, γ (deg.)90.880, 96.120, 100.930
Int Tables number1
Space group name H-MP1
DetailsA steric zipper can be generated by repeated unit cell translations of the asymmetric unit along the b axis.

-
Components

#1: Protein/peptide
VEALYL peptide derived from human insulin chain B, residues 12-17


Mass: 706.827 Da / Num. of mol.: 4 / Fragment: residues 12-17 / Source method: obtained synthetically / References: UniProt: P01308*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 2.5
Details: 2mM peptide in 100 mM NaCl and 50 mM phosphate. Crystals can be more easily reproduced by dissolving peptide to 2 mM in water at room temperature, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9466
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9466 Å / Relative weight: 1
ReflectionResolution: 1.7→90 Å / Num. obs: 820 / % possible obs: 93 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.172 / Χ2: 1.065 / Net I/σ(I): 3.9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.830.4132991.071191.7
1.83-2.020.322961.094188.6
2.02-2.310.2413111.086196.6
2.31-2.910.1912961.049193.1
2.91-900.1113211.039195.3

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: polyalanine beta strands with ideal geometry

Resolution: 2→21.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.375 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 40 4.9 %RANDOM
Rwork0.201 ---
obs0.205 820 83.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.338 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20.41 Å20.99 Å2
2--0.34 Å2-0.09 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2→21.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms200 0 0 4 204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023200
X-RAY DIFFRACTIONr_bond_other_d00.02208
X-RAY DIFFRACTIONr_angle_refined_deg2.2712.106272
X-RAY DIFFRACTIONr_angle_other_deg3.1193472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.878520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.309258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0761532
X-RAY DIFFRACTIONr_chiral_restr0.0360.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02204
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0236
X-RAY DIFFRACTIONr_nbd_refined0.2240.228
X-RAY DIFFRACTIONr_nbd_other0.2530.2159
X-RAY DIFFRACTIONr_nbtor_refined0.2140.281
X-RAY DIFFRACTIONr_nbtor_other0.1360.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2870.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.210
X-RAY DIFFRACTIONr_mcbond_it5.5741.5120
X-RAY DIFFRACTIONr_mcbond_other01.556
X-RAY DIFFRACTIONr_mcangle_it6.9522188
X-RAY DIFFRACTIONr_scbond_it7.371380
X-RAY DIFFRACTIONr_scangle_it10.1864.584
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.267 49 -
obs--84.48 %

+
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