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- PDB-2vk0: Crystal structure form ultalente insulin microcrystals -

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Basic information

Entry
Database: PDB / ID: 2vk0
TitleCrystal structure form ultalente insulin microcrystals
Components
  • INSULIN A CHAIN
  • INSULIN B CHAIN
KeywordsHORMONE / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM / MICRO FOCUS BEAMLINE / INSULIN / SECRETED / MICRO CRYSTAL / CLEAVAGE ON PAIR OF BASIC RESIDUES / DISEASE MUTATION / DIABETES MELLITUS
Function / homology
Function and homology information


Signaling by Insulin receptor / alpha-beta T cell activation / negative regulation of glycogen catabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior ...Signaling by Insulin receptor / alpha-beta T cell activation / negative regulation of glycogen catabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / positive regulation of cellular protein metabolic process / negative regulation of reactive oxygen species biosynthetic process / COPI-mediated anterograde transport / regulation of cellular amino acid metabolic process / regulation of protein localization to plasma membrane / Regulation of insulin secretion / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Signal attenuation / negative regulation of protein secretion / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of insulin receptor signaling pathway / neuron projection maintenance / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / negative regulation of acute inflammatory response / positive regulation of cell differentiation / regulation of transmembrane transporter activity / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / regulation of synaptic plasticity / positive regulation of brown fat cell differentiation / cognition / regulation of protein localization / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / acute-phase response / activation of protein kinase B activity / positive regulation of glucose import / vasodilation / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor binding / positive regulation of protein localization to nucleus / insulin receptor signaling pathway / glucose metabolic process / Golgi lumen / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / endoplasmic reticulum to Golgi vesicle-mediated transport / wound healing / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell migration / positive regulation of protein kinase B signaling / Golgi membrane / Amyloid fiber formation / G protein-coupled receptor signaling pathway / amyloid fibril formation / endoplasmic reticulum lumen / regulation of transcription, DNA-templated / positive regulation of gene expression / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
4-HYDROXY-BENZOIC ACID METHYL ESTER / Insulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWagner, A. / Diez, J. / Schulze-Briese, C. / Schluckebier, G.
CitationJournal: Proteins / Year: 2009
Title: Crystal Structure of Ultralente--A Microcrystalline Insulin Suspension.
Authors: Wagner, A. / Diez, J. / Schulze-Briese, C. / Schluckebier, G.
History
DepositionDec 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 3, 2011Group: Database references / Derived calculations / Other

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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)12,0499
Polymers11,6354
Non-polymers4145
Water1,18966
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)36,14727
Polymers34,90612
Non-polymers1,24115
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area18950 Å2
ΔGint-568 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)81.030, 81.030, 33.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-1031-

ZN

21D-1030-

ZN

31B-2025-

HOH

41D-2003-

HOH

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Components

#1: Protein/peptide INSULIN A CHAIN


Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: RESIDUES 90-110
Source method: isolated from a genetically manipulated source
Details: ULTRALENTE INSULIN CRYSTALS / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P01308
#2: Protein/peptide INSULIN B CHAIN


Mass: 3433.953 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-54
Source method: isolated from a genetically manipulated source
Details: ULTRALENTE INSULIN CRYSTALS / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P01308
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MPB / 4-HYDROXY-BENZOIC ACID METHYL ESTER / Methylparaben


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.78 Å3/Da / Density % sol: 30.48 %
Description: DATA COLLECTION FROM MICRO CRYSTAL 25-X-25 X 8 MICROMETER
Crystal growpH: 5.5 / Details: pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9786
DetectorType: MARRESEARCH / Detector: CCD / Details: MICRO FOCUS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.2→24.1 Å / Num. obs: 13231 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.7 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY MSO

Resolution: 2.2→40.52 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.865 / SU B: 19.805 / SU ML: 0.267 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.653 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 209 5 %RANDOM
Rwork0.24 ---
obs0.242 3958 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms766 0 15 66 847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021805
X-RAY DIFFRACTIONr_bond_other_d0.0040.02520
X-RAY DIFFRACTIONr_angle_refined_deg0.971.9851087
X-RAY DIFFRACTIONr_angle_other_deg1.0343.0191248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34124.86537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82315124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.774152
X-RAY DIFFRACTIONr_chiral_restr0.3170.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02888
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02166
X-RAY DIFFRACTIONr_nbd_refined0.1580.2207
X-RAY DIFFRACTIONr_nbd_other0.1760.2525
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2381
X-RAY DIFFRACTIONr_nbtor_other0.0860.2399
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.234
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.0920.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0660.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1641.5631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.1892764
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.2723419
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.3734.5323
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.37 15
Rwork0.316 300
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.3724-2.79821.49725.0566-4.52996.86720.305-0.16310.21211.9059-0.4780.7190.2207-0.07970.17310.0522-0.02890.09690.1002-0.0699-0.0243-17.55273.22617.1512
26.5864-1.79171.04414.7851-0.84157.5693-0.0384-0.2890.00130.7324-0.0442-0.4818-0.039-0.53110.0825-0.01420.00160.017-0.10.0266-0.0106-12.22155.50022.1411
313.1219-0.2588-1.33412.36961.20193.4586-0.28331.0346-0.2392-0.79440.23310.5489-0.1054-0.43970.05020.2819-0.076-0.0230.02350.05570.0391-3.477516.7617-9.1115
410.3195-0.90080.99036.98852.49615.63340.04130.4760.0896-0.40380.03930.0799-0.1596-0.1436-0.0805-0.0097-0.02370.0485-0.08640.0612-0.0645-5.324311.0453-4.3057
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION2B1 - 30
3X-RAY DIFFRACTION3C1 - 21
4X-RAY DIFFRACTION4D1 - 30

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