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- PDB-1ev6: Structure of the monoclinic form of the M-cresol/insulin R6 hexamer -

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Basic information

Entry
Database: PDB / ID: 1ev6
TitleStructure of the monoclinic form of the M-cresol/insulin R6 hexamer
Components(INSULIN) x 2
KeywordsHORMONE/GROWTH FACTOR / R6 Hexameric Insulin / HORMONE-GROWTH FACTOR COMPLEX
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 / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / 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 / Resolution: 1.9 Å
AuthorsSmith, G.D. / Ciszak, E. / Magrum, L.A. / Pangborn, W.A. / Blessing, R.H.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2000
Title: R6 Hexameric Insulin Complexed with m-Cresol or Resorcinol
Authors: Smith, G.D. / Ciszak, E. / Magrum, L.A. / Pangborn, W.A. / Blessing, R.H.
#1: Journal: Nature / Year: 1989
Title: Phenol Stabilizes more Helix in a New Symmetrical Zinc Insulin Hexamer
Authors: Derewenda, U. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D. / Smith, G.D. / Sparks, C. / Swenson, D.
#2: Journal: Proteins / Year: 1992
Title: Structure of a Rhombohedral R6 Insulin/Phenol Complex
Authors: Smith, G.D. / Dodson, G.G.
History
DepositionApr 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INSULIN
B: INSULIN
C: INSULIN
D: INSULIN
E: INSULIN
F: INSULIN
G: INSULIN
H: INSULIN
I: INSULIN
J: INSULIN
K: INSULIN
L: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,88824
Polymers34,90612
Non-polymers98212
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19540 Å2
ΔGint-234 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.247, 61.739, 47.467
Angle α, β, γ (deg.)90.00, 111.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
INSULIN


Mass: 2383.698 Da / Num. of mol.: 6 / Fragment: RESIDUES 87-107 / Source method: obtained synthetically
Details: This sequence occurs naturally in homo sapiens (human)
References: UniProt: P01308
#2: Protein/peptide
INSULIN


Mass: 3433.953 Da / Num. of mol.: 6 / Fragment: RESIDUES 25-54 / Source method: obtained synthetically
Details: This sequence occurs naturally in homo sapiens (human)
References: UniProt: P01308

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Non-polymers , 5 types, 242 molecules

#3: Chemical
ChemComp-CRS / M-CRESOL


Mass: 108.138 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C7H8O
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 298 K / Method: slow cooling / pH: 6.5
Details: 30 mg insulin, 3.0 ml 0.02 M HCl, 0.3 ml 0.15 M Zinc Acetate, 1.5 ml 0.2 M Sodium Citrate, 1.2 ml 5% m-Cresol in ethanol, pH 6.5, SLOW COOLING, temperature 298.0K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
20.02 M113.0mlHCl
30.15 Mzinc acetate110.3ml
40.2 Msodium citrate111.5ml
55 %m-cresol in ethanol111.2ml
1insulin1130mg

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 18, 2000 / Details: OSMIC CONFOCAL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→20.95 Å / Num. all: 28441 / Num. obs: 28441 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.15 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 40.6
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 5.4 / % possible all: 92.6
Reflection
*PLUS
Num. measured all: 174925
Reflection shell
*PLUS
% possible obs: 92.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
CNS1phasing
RefinementResolution: 1.9→20.95 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2490 9.9 %random
Rwork0.195 ---
all0.195 25127 --
obs0.195 25127 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.11 Å2 / ksol: 0.292 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å21.98 Å2
2---5.09 Å20 Å2
3---5.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→20.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 69 240 2717
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.862
X-RAY DIFFRACTIONc_mcangle_it2.742.5
X-RAY DIFFRACTIONc_scbond_it2.592.5
X-RAY DIFFRACTIONc_scangle_it3.823
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 388 9.5 %
Rwork0.271 3678 -
obs--93.9 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
X-RAY DIFFRACTIONc_mcbond_it2
X-RAY DIFFRACTIONc_scbond_it2.5
X-RAY DIFFRACTIONc_mcangle_it2.5
X-RAY DIFFRACTIONc_scangle_it3
LS refinement shell
*PLUS
Rfactor Rfree: 0.333 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.271 / Rfactor obs: 0.271

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