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- PDB-3jsd: Insulin's biosynthesis and activity have opposing structural requ... -

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Basic information

Entry
Database: PDB / ID: 3jsd
TitleInsulin's biosynthesis and activity have opposing structural requirements: a new factor in neonatal diabetes mellitus
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / diabetes mellitus / Insulin's biosynthesis / proinsulin / insulin hexamer / Carbohydrate metabolism / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Glucose metabolism / Secreted
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / 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/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
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWeiss, M.A. / Wan, Z.L. / Dodson, E.J. / Liu, M. / Xu, B. / Hua, Q.X. / Turkenburg, M. / Whittingham, J. / Nakagawa, S.H. / Huang, K. ...Weiss, M.A. / Wan, Z.L. / Dodson, E.J. / Liu, M. / Xu, B. / Hua, Q.X. / Turkenburg, M. / Whittingham, J. / Nakagawa, S.H. / Huang, K. / Hu, S.Q. / Jia, W.H. / Wang, S.H. / Brange, J. / Whittaker, J. / Arvan, P. / Katsoyannis, P.G. / Dodson, G.G.
Citation
Journal: To be Published
Title: Insulin's biosynthesis and activity have opposing structural requirements: a new factor in neonatal diabetes mellitus
Authors: Weiss, M.A. / Wan, Z.L. / Dodson, E.J. / Liu, M. / Xu, B. / Hua, Q.X. / Turkenburg, M. / Whittingham, J. / Nakagawa, S.H. / Huang, K. / Hu, S.Q. / Jia, W.H. / Wang, S.H. / Brange, J. / ...Authors: Weiss, M.A. / Wan, Z.L. / Dodson, E.J. / Liu, M. / Xu, B. / Hua, Q.X. / Turkenburg, M. / Whittingham, J. / Nakagawa, S.H. / Huang, K. / Hu, S.Q. / Jia, W.H. / Wang, S.H. / Brange, J. / Whittaker, J. / Arvan, P. / Katsoyannis, P.G. / Dodson, G.G.
#1: Journal: Philos.Trans.R.Soc.Lond.B Biol.Sci. / Year: 1988
Title: The structure of 2Zn pig insulin crystals at 1.5 A resolution.
Authors: Baker, E.N. / Blundell, T.L. / Cutfield, J.F. / Cutfield, S.M. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D.M. / Hubbard, R.E. / Isaacs, N.W. / Reynolds, C.D.
#2: Journal: Nature / Year: 1976
Title: Structure of insulin in 4-zinc insulin.
Authors: Bentley, G. / Dodson, E. / Dodson, G. / Hodgkin, D. / Mercola, D.
#3: 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.
#4: Journal: J.Biol.Chem. / Year: 2006
Title: Toward the active conformation of insulin: stereospecific modulation of a structural switch in the B chain.
Authors: Hua, Q.X. / Nakagawa, S. / Hu, S.Q. / Jia, W. / Wang, S. / Weiss, M.A.
History
DepositionSep 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9599
Polymers11,6634
Non-polymers2965
Water32418
1
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules

A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules

A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,87827
Polymers34,99012
Non-polymers88815
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17300 Å2
ΔGint-140.7 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.843, 80.843, 38.842
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-31-

ZN

21B-32-

CL

31D-31-

ZN

41D-32-

CL

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: UNP residues 90-110 / Source method: obtained synthetically / Details: biosynthetic sequence / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3447.979 Da / Num. of mol.: 2 / Fragment: UNP residues 25-54 / Source method: obtained synthetically / Details: biosynthetic sequence / References: UniProt: P01308

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Non-polymers , 4 types, 23 molecules

#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 / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.27 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 0.02M Tris-HCl, 0.05M Sodium citrate, 5% Acetone, 0.03% Phenol, 0.01% Zinc acetate, pH 8.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 25, 1998
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→17.37 Å / Num. all: 7390 / Num. obs: 3190 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.071
Reflection shellResolution: 2.5→2.66 Å / Rmerge(I) obs: 0.254 / Num. unique all: 455 / % possible all: 95.2

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Processing

Software
NameClassification
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TRZ

1trz


Resolution: 2.5→17.37 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.274 344 -RANDOM
Rwork0.206 ---
obs0.206 3190 97.6 %-
all-3190 --
Displacement parametersBiso mean: 51.7 Å2
Baniso -1Baniso -2Baniso -3
1--10.31 Å20 Å20 Å2
2---10.31 Å20 Å2
3---20.61 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→17.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 11 18 841
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d5.32
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.5-2.660.294600.2520.03945595.2
2.66-17.370.2743440.2060.015319097.6

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