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- PDB-3ilg: Crystal structure of humnan insulin Sr+2 complex -

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Basic information

Entry
Database: PDB / ID: 3ilg
TitleCrystal structure of humnan insulin Sr+2 complex
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / Insulin / conformational state / metal binding / Carbohydrate metabolism / Cleavage on pair of basic residues / Diabetes mellitus / 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
STRONTIUM ION / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRaghavendra, N. / Pattabhi, V. / Rajan, S.S.
CitationJournal: To be Published
Title: Metal induced conformational changes in human insulin: Crystal structures of Sr+2, Ni+2 and Cu+2 complexes of human insulin
Authors: Raghavendra, N. / Pattabhi, V. / Rajan, S.S.
History
DepositionAug 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8116
Polymers11,6354
Non-polymers1752
Water1,02757
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)35,43218
Polymers34,90612
Non-polymers5266
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 area19940 Å2
ΔGint-231 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.298, 81.298, 33.734
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-31-

SR

21D-31-

SR

31B-38-

HOH

41B-47-

HOH

51D-32-

HOH

61D-41-

HOH

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Components

#1: Protein/peptide Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3433.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
#3: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1.84 Å3/Da / Density % sol: 33.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M Sodium Citrate, 1M Ammonium Sulphate, 0.1M Strontium Chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 2008 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 6573 / Num. obs: 6243 / % possible obs: 99 % / Redundancy: 5.3 % / Biso Wilson estimate: 36.08 Å2 / Rmerge(I) obs: 0.0672 / Rsym value: 0.0573 / Net I/σ(I): 8.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.1745 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6573 / Rsym value: 0.1643 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MSO

1mso


Resolution: 1.9→16.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.883 / SU B: 4.222 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27804 303 4.6 %RANDOM
Rwork0.19154 ---
obs0.19529 6243 99.76 %-
all-6573 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.11 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→16.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 2 57 869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022832
X-RAY DIFFRACTIONr_angle_refined_deg1.671.9541130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15824.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52515130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.056152
X-RAY DIFFRACTIONr_chiral_restr0.1020.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02636
X-RAY DIFFRACTIONr_nbd_refined0.2450.2402
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.252
X-RAY DIFFRACTIONr_metal_ion_refined0.3960.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3720.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3960.222
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3950.26
X-RAY DIFFRACTIONr_mcbond_it1.2431.5504
X-RAY DIFFRACTIONr_mcangle_it2.2752810
X-RAY DIFFRACTIONr_scbond_it3.2913337
X-RAY DIFFRACTIONr_scangle_it4.6384.5320
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0.27804 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 17 -
Rwork0.262 479 -
obs-479 100 %

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