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- PDB-1uz9: Crystallographic and solution studies of N-lithocholyl insulin: a... -

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Basic information

Entry
Database: PDB / ID: 1uz9
TitleCrystallographic and solution studies of N-lithocholyl insulin: a new generation of prolonged-acting insulins.
Components(INSULIN) x 2
KeywordsINSULIN / DIABETES MELLITUS / INSULIN FAMILY / HORMONE DISEASE MUTATION
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / 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 / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / 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 / Insulin processing / regulation of protein secretion / 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 / regulation of amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of gluconeogenesis / negative regulation of lipid catabolic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of protein autophosphorylation / Insulin receptor recycling / transport vesicle / insulin-like growth factor receptor binding / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / endosome lumen / Regulation of insulin secretion / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / positive regulation of neuron projection development / cognition / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / cell-cell signaling / insulin receptor signaling pathway / glucose homeostasis / regulation of protein localization / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / regulation of DNA-templated transcription / positive regulation of gene expression / 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
M-CRESOL / Chem-UZ9 / Insulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWhittingham, J.L. / Jonassen, I. / Havelund, S. / Roberts, S.M. / Dodson, E.J. / Verma, C.S. / Wilkinson, A.J. / Dodson, G.G.
CitationJournal: Biochemistry / Year: 2004
Title: Crystallographic and Solution Studies of N-Lithocholyl Insulin: A New Generation of Prolonged-Acting Human Insulins
Authors: Whittingham, J.L. / Jonassen, I. / Havelund, S. / Roberts, S.M. / Dodson, E.J. / Verma, C.S. / Wilkinson, A.J. / Dodson, G.G.
History
DepositionMar 8, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 / pdbx_struct_conn_angle / struct_conn
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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4286
Polymers5,7172
Non-polymers7124
Water90150
1
A: INSULIN
B: INSULIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)38,57036
Polymers34,29912
Non-polymers4,27024
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)51.790, 51.790, 68.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-1030-

ZN

21B-1031-

CL

31A-2004-

HOH

41B-2028-

HOH

DetailsTHE DODECAMER IS OF THE A-B HEXAMER TYPE WITH 6 A AND 6B CHAINS LINKED BY DISULFIDE BONDS THAT CAN BE GENERATEDBY APPLICATION OF SYMMETRY OPERATORS 2, 3, 10, 11 AND 12FROM REMARK 290 ABOVE.

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Components

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Protein/peptide , 2 types, 2 molecules AB

#1: Protein/peptide INSULIN


Mass: 2383.698 Da / Num. of mol.: 1 / Fragment: INSULIN A CHAIN, RESIDUES 90-110 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308
#2: Protein/peptide INSULIN


Mass: 3332.849 Da / Num. of mol.: 1 / Fragment: INSULIN B CHAIN, RESIDUES 25-53 / Source method: obtained synthetically
Details: PEPTIDE LINK BETWEEN B 29 SIDE CHAIN AND LITHOCHOLYL GROUP
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308

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Non-polymers , 5 types, 54 molecules

#3: Chemical ChemComp-CRS / M-CRESOL


Mass: 108.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O
#4: Chemical ChemComp-UZ9 / (2S)-2-AMINO-6-({(4R)-4-[(10R,13S)-10,13-DIMETHYL-3-OXOHEXADECAHYDRO-1H-CYCLOPENTA[A]PHENANTHREN-17-YL]PENTANOYL}AMINO)HEXANOIC ACID


Mass: 502.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50N2O4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsINSULIN DECREASES BLOOD GLUCOSE CONCENTRATION AND INCREASES CELL PERMEABILITY TO MONOSACCHARIDES, ...INSULIN DECREASES BLOOD GLUCOSE CONCENTRATION AND INCREASES CELL PERMEABILITY TO MONOSACCHARIDES, AMINO ACIDS AND FATTY ACIDS. IT ACCELERATES GLYCOLYSIS, THE PENTOSE PHOSPHATE CYCLE, AND GLYCOGEN SYNTHESIS IN LIVER.

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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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 8
Details: 0.5 M TRIS-HCL PH 8.0 0.1M TRI-SODIUM CITRATE, 2MM ZINC ACETATE, 0.05% W/V M-CRESOL

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.58→24 Å / Num. obs: 7689 / % possible obs: 98 % / Redundancy: 5.9 % / Biso Wilson estimate: 19.13 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 33
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 5 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 14 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XDA

1xda


Resolution: 1.6→24 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.48 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.206 353 5 %RANDOM
Rwork0.179 ---
obs0.18 7336 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms388 0 46 50 484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021456
X-RAY DIFFRACTIONr_bond_other_d0.0040.02403
X-RAY DIFFRACTIONr_angle_refined_deg1.8212.073626
X-RAY DIFFRACTIONr_angle_other_deg2.6563946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.716550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.1070.272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0110.02484
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0293
X-RAY DIFFRACTIONr_gen_planes_other0.250.2105
X-RAY DIFFRACTIONr_nbd_refined0.2430.2462
X-RAY DIFFRACTIONr_nbd_other0.1110.2258
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.460.230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0070.21
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4630.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2771.5252
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2312407
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6043204
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8724.5218
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: 1.59→1.63 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.227 21
Rwork0.148 530

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