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- PDB-2omg: Structure of human insulin cocrystallized with protamine and urea -

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Basic information

Entry
Database: PDB / ID: 2omg
TitleStructure of human insulin cocrystallized with protamine and urea
Components
  • (Insulin A chain) x 2
  • 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 / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / 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 / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / positive regulation of protein autophosphorylation / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / Signal attenuation / fatty acid homeostasis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of insulin receptor signaling pathway / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / COPI-mediated anterograde transport / transport vesicle / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / Insulin receptor recycling / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of nitric-oxide synthase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / regulation of transmembrane transporter activity / positive regulation of glycolytic process / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / endosome lumen / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / positive regulation of cell differentiation / Regulation of insulin secretion / insulin receptor binding / wound healing / negative regulation of protein catabolic process / hormone activity / regulation of synaptic plasticity / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / cognition / glucose metabolic process / vasodilation / insulin receptor signaling pathway / glucose homeostasis / cell-cell signaling / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / positive regulation of cell growth / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / 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-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 / UREA / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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.conn_type_id / _struct_conn.id / _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
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_validate_close_contact / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end

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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)18,47718
Polymers17,6686
Non-polymers80912
Water1,78399
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)36,95336
Polymers35,33612
Non-polymers1,61724
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area22630 Å2
ΔGint-237 kcal/mol
Surface area13340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.660, 61.660, 85.540
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 , 3 types, 6 molecules AEBDFC

#1: Protein/peptide Insulin A chain


Mass: 2426.722 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: 3476.978 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
#3: Protein/peptide Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 6 types, 111 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CRS / M-CRESOL


Mass: 108.138 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8O
#6: Chemical
ChemComp-URE / UREA


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


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


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


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 60mM m-cresol, 3M urea, 1.0 mg/ml protamine sulphate, 400mM NaCl, 40mM 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: I911-5 / Wavelength: 0.969 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2004
RadiationMonochromator: Double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. all: 27022 / Num. obs: 25119 / % possible obs: 93 % / Redundancy: 8 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.4
Reflection shellResolution: 1.52→1.6 Å / Redundancy: 6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.9 / Num. unique all: 4630 / % possible all: 74.7

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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: 1.52→25.88 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.502 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20947 1276 5.1 %RANDOM
Rwork0.18253 ---
obs0.18391 23837 95.99 %-
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: 28.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.52→25.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 66 99 1328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211253
X-RAY DIFFRACTIONr_bond_other_d0.0020.02817
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.9771686
X-RAY DIFFRACTIONr_angle_other_deg0.9453.0191929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7695143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98724.560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4515181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.404153
X-RAY DIFFRACTIONr_chiral_restr0.1030.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02316
X-RAY DIFFRACTIONr_nbd_refined0.2890.2354
X-RAY DIFFRACTIONr_nbd_other0.1950.2851
X-RAY DIFFRACTIONr_nbtor_refined0.2050.2616
X-RAY DIFFRACTIONr_nbtor_other0.090.2609
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2940.271
X-RAY DIFFRACTIONr_metal_ion_refined0.1840.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3050.224
X-RAY DIFFRACTIONr_mcbond_it0.9351.5753
X-RAY DIFFRACTIONr_mcbond_other0.2871.5298
X-RAY DIFFRACTIONr_mcangle_it1.66721180
X-RAY DIFFRACTIONr_scbond_it2.613515
X-RAY DIFFRACTIONr_scangle_it4.0544.5505
LS refinement shellResolution: 1.52→1.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 76 -
Rwork0.215 1521 -
obs--84.59 %
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)
17.5981.601-0.66612.8342-0.69283.4967-0.1777-0.42-0.2810.26830.1094-0.01180.0545-0.2190.0684-0.1202-0.02710.0203-0.09850.038-0.134318.70618.914110.341
23.1839-0.56770.43612.7503-1.34617.88410.13040.3821-0.2195-0.5161-0.0564-0.25510.66880.4167-0.074-0.05110.04140.0172-0.0708-0.0015-0.089934.133115.7081-6.6276
33.346-4.041-0.45118.38950.73233.6303-0.0517-0.2170.64590.34210.0052-0.8335-0.47950.33630.0465-0.0682-0.0336-0.0864-0.08560.0146-0.006136.018834.08237.9448
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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