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- PDB-2omh: Structure of human insulin cocrystallized with ARG-12 peptide in ... -

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Basic information

Entry
Database: PDB / ID: 2omh
TitleStructure of human insulin cocrystallized with ARG-12 peptide in presence of urea
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin NPH-like crystal
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
FORMAMIDE / RESORCINOL / UREA / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsNorrman, M. / Schluckebier, G.
CitationJournal: EUR.J.PHARM.SCI. / Year: 2007
Title: Structural characterization of insulin NPH formulations.
Authors: Norrman, M. / Hubalek, F. / Schluckebier, G.
History
DepositionJan 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_asym_id / _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.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: 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
E: Insulin A chain
F: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,23718
Polymers17,4536
Non-polymers78412
Water2,972165
1
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
E: Insulin A chain
F: Insulin B chain
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)36,47536
Polymers34,90612
Non-polymers1,56924
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area21000 Å2
ΔGint-245 kcal/mol
Surface area13230 Å2
MethodPISA
2
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
E: Insulin A chain
F: Insulin B chain
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)36,47536
Polymers34,90612
Non-polymers1,56924
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)61.360, 61.360, 85.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein/peptide , 2 types, 6 molecules ACEBDF

#1: Protein/peptide Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 3 / 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.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 7 types, 177 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-RCO / RESORCINOL / 1,3-BENZENEDIOL / 1,3-DIHYDROXYBENZENE / Resorcinol


Mass: 110.111 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H6O2
#5: Chemical
ChemComp-URE / UREA / Urea


Mass: 60.055 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH4N2O
#6: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-ARF / FORMAMIDE / Formamide


Type: L-peptide NH3 amino terminus / Mass: 45.041 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH3NO
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 500mM NaCl, 2.5M urea, 1.2mg/ml ARG-12 peptide, 50mM resorcinol, 50mM phosphate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2004
RadiationMonochromator: Double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→50 Å / Num. all: 35834 / Num. obs: 34738 / % possible obs: 96.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.3
Reflection shellResolution: 1.36→1.4 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2933 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: insulin trimer R conformation

Resolution: 1.36→14.95 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.6 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22274 1739 5 %RANDOM
Rwork0.20022 ---
obs0.20136 32948 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.684 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.36→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 49 165 1377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221253
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.9721697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.375147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.38924.5961
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40215184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.699153
X-RAY DIFFRACTIONr_chiral_restr0.0910.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02970
X-RAY DIFFRACTIONr_nbd_refined0.2330.2603
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2885
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.290
X-RAY DIFFRACTIONr_metal_ion_refined0.1830.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.226
X-RAY DIFFRACTIONr_mcbond_it0.6561.5747
X-RAY DIFFRACTIONr_mcangle_it1.29121186
X-RAY DIFFRACTIONr_scbond_it1.8273521
X-RAY DIFFRACTIONr_scangle_it2.9114.5508
LS refinement shellResolution: 1.36→1.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 124 -
Rwork0.308 2414 -
obs--98.79 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6737-0.34520.6651.2117-0.1261.2633-0.06140.08330.0944-0.0680.05690.0091-0.0561-0.12980.0045-0.0330.02360.00440.00270.0317-0.0215-11.819611.716311.1571
21.181-0.2569-0.4151.3241-0.4272.46320.0656-0.05850.1240.15480.0198-0.0982-0.32230.2368-0.08540.0038-0.05270.0012-0.0047-0.0043-0.01623.675914.845327.772
31.44181.54080.47553.38630.24681.85820.04670.0437-0.2596-0.0796-0.0895-0.39380.22270.24760.0428-0.01640.01740.0411-0.02130.00470.03765.4007-3.18413.2292
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 211 - 21
2X-RAY DIFFRACTION1BB1 - 281 - 28
3X-RAY DIFFRACTION2CC1 - 211 - 21
4X-RAY DIFFRACTION2DD1 - 281 - 28
5X-RAY DIFFRACTION3EE1 - 211 - 21
6X-RAY DIFFRACTION3FF1 - 281 - 28

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