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- PDB-5ems: Crystal Structure of an iodinated insulin analog -

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Basic information

Entry
Database: PDB / ID: 5ems
TitleCrystal Structure of an iodinated insulin analog
Components(Insulin) x 2
KeywordsHORMONE / insulin / non-standard modification / protein design / protein engineering
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / IRS activation / Insulin processing / negative regulation of NAD(P)H oxidase activity / Insulin receptor recycling / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / IRS activation / Insulin processing / negative regulation of NAD(P)H oxidase activity / Insulin receptor recycling / 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 respiratory burst / positive regulation of peptide hormone secretion / negative regulation of respiratory burst involved in inflammatory response / alpha-beta T cell activation / negative regulation of gluconeogenesis / positive regulation of protein metabolic process => GO:0051247 / negative regulation of acute inflammatory response / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / COPI-mediated anterograde transport / regulation of protein localization to plasma membrane / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Signal attenuation / negative regulation of protein secretion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of nitric oxide mediated signal transduction / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / positive regulation of insulin receptor signaling pathway / Regulation of insulin secretion / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / transport vesicle / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of brown fat cell differentiation / positive regulation of mitotic nuclear division / regulation of transmembrane transporter activity / positive regulation of long-term synaptic potentiation / regulation of synaptic plasticity / positive regulation of cell differentiation / cognition / activation of protein kinase B activity / positive regulation of cytokine production / positive regulation of protein secretion / positive regulation of glucose import / acute-phase response / negative regulation of proteolysis / hormone activity / positive regulation of nitric-oxide synthase activity / vasodilation / insulin receptor binding / insulin receptor signaling pathway / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / wound healing / Golgi lumen / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / positive regulation of phosphatidylinositol 3-kinase signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / positive regulation of NF-kappaB transcription factor activity / positive regulation of protein kinase B signaling / positive regulation of MAPK cascade / protease binding / G protein-coupled receptor signaling pathway / positive regulation of cell migration / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / endoplasmic reticulum lumen / 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 / insulin-like growth factor / relaxin family. / Insulin-like / Insulin/IGF/Relaxin family / Insulin family signature. / Insulin-like superfamily / Insulin, conserved site
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLawrence, M.C. / Pandyarajan, V. / Wan, Z. / Weiss, M.A.
Funding support United States, Australia, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK04949 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK079233 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)F30 DK094685-04 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007250 United States
National Health and Medical Research Council (NHMRC, Australia)1005896 Australia
National Health and Medical Research Council (NHMRC, Australia)1058233 Australia
National Health and Medical Research Council (NHMRC, Australia)361646 Australia
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Extending Halogen-based Medicinal Chemistry to Proteins: IODO-INSULIN AS A CASE STUDY.
Authors: El Hage, K. / Pandyarajan, V. / Phillips, N.B. / Smith, B.J. / Menting, J.G. / Whittaker, J. / Lawrence, M.C. / Meuwly, M. / Weiss, M.A.
History
DepositionNov 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Jan 11, 2017Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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)36,33222
Polymers35,56512
Non-polymers76610
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18580 Å2
ΔGint-235 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.430, 61.630, 58.580
Angle α, β, γ (deg.)90.00, 111.38, 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 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide
Insulin /


Mass: 3543.827 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 4 types, 85 molecules

#3: Chemical
ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O
#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 / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate, 0.08% zinc acetate, 2% phenol

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Data collection

DiffractionMean temperature: 233 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40.85 Å / Num. obs: 13255 / % possible obs: 95.6 % / Redundancy: 4.76 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 18.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZNJ
Resolution: 2.3→40.847 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 1330 10.03 %
Rwork0.1626 --
obs0.1696 11926 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→40.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 46 75 2426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082411
X-RAY DIFFRACTIONf_angle_d1.0893234
X-RAY DIFFRACTIONf_dihedral_angle_d12.56796
X-RAY DIFFRACTIONf_chiral_restr0.051350
X-RAY DIFFRACTIONf_plane_restr0.006415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.32391070.2471978X-RAY DIFFRACTION78
2.3822-2.47750.30071290.2071151X-RAY DIFFRACTION92
2.4775-2.59030.25921300.18951165X-RAY DIFFRACTION95
2.5903-2.72680.33881350.18761200X-RAY DIFFRACTION96
2.7268-2.89760.31811340.1921204X-RAY DIFFRACTION99
2.8976-3.12130.28581390.19031239X-RAY DIFFRACTION100
3.1213-3.43520.24381350.16851242X-RAY DIFFRACTION100
3.4352-3.9320.19741360.14141239X-RAY DIFFRACTION100
3.932-4.95250.17071460.12911235X-RAY DIFFRACTION100
4.9525-40.85370.1931390.14461273X-RAY DIFFRACTION99
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)
18.0317-0.1511-0.68376.1314-2.00836.1787-0.1747-0.85470.38360.6966-0.1331-0.735-0.38710.76610.24820.36510.0297-0.13850.529-0.09280.4008-5.08383.414757.6567
23.282-4.9638-2.85918.2933.0855.4659-0.303-0.2581-0.05110.43050.1534-0.42230.62290.44550.18820.31940.0047-0.05740.2492-0.00640.4047-11.273-2.191153.1423
33.38680.1176-1.41199.1-3.52782.3892-0.1701-0.0893-0.6119-0.96030.10820.33370.3794-0.01010.1490.438-0.012-0.01530.23460.0260.3391-17.3679-18.390147.2766
46.474-1.9576-1.07493.82651.11763.2617-0.2487-0.3243-0.40040.5327-0.0488-0.13160.56980.43190.38680.37360.02610.02650.32460.03730.3132-13.4056-10.149248.8043
56.37750.3549-0.61495.2947-0.50922.97290.09020.23960.7545-0.0058-0.2766-0.1994-0.7664-0.14430.02770.3298-0.0239-0.0080.28770.13410.4458-14.32917.138133.8272
64.5425-0.1396-2.05873.67920.32372.7578-0.2164-0.0760.55050.1262-0.0738-0.0891-0.17890.23440.22360.26940.0321-0.01610.29690.04020.4353-10.10729.995137.4427
73.64563.01832.21414.85621.85455.02690.22580.5741-0.09980.29250.2474-0.70830.4520.532-0.51880.26860.0454-0.01620.4436-0.00380.61133.2811-2.279837.0966
83.59022.96811.74427.82225.65588.40220.12270.12990.3937-0.28790.0828-0.3862-0.37330.4428-0.22220.24420.03380.02980.28590.0380.4912-4.4482.454835.0215
95.7104-1.23133.98865.24772.59618.1488-0.0057-0.4505-0.13790.4419-0.09960.67060.2183-0.84780.03210.25350.03820.10470.36340.00920.3732-32.4233-0.777748.7411
107.45363.30693.67175.15262.74934.9282-0.1460.26850.1120.1999-0.16350.7107-0.1251-0.14450.33540.195-0.02260.02690.3249-0.03630.2894-27.046-0.04240.8898
112.5839-0.4117-1.77018.0427-0.68617.28170.34170.92510.2371-0.9083-0.32670.3319-0.1072-0.65760.00020.32260.0909-0.05990.4251-0.01770.3249-22.4608-2.014423.6534
124.1133-3.41950.34293.72860.31735.38380.17670.7699-0.0742-0.0495-0.28370.6088-0.0702-0.25280.10270.2649-0.0187-0.01570.353-0.00760.3473-23.5905-3.15332.7744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'
7X-RAY DIFFRACTION7chain 'G'
8X-RAY DIFFRACTION8chain 'H'
9X-RAY DIFFRACTION9chain 'I'
10X-RAY DIFFRACTION10chain 'J'
11X-RAY DIFFRACTION11chain 'K'
12X-RAY DIFFRACTION12chain 'L'

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