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- PDB-2olz: Structure of human insulin in presence of thiocyanate at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 2olz
TitleStructure of human insulin in presence of thiocyanate at pH 7.0
Components
  • Insulin A
  • Insulin B
KeywordsHORMONE / R6 conformation
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
RESORCINOL / THIOCYANATE ION / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNorrman, M. / Schluckebier, G.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Crystallographic characterization of two novel crystal forms of human insulin induced by chaotropic agents and a shift in pH.
Authors: Norrman, M. / Schluckebier, G.
History
DepositionJan 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 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.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 1.4Apr 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
B: Insulin B
C: Insulin A
D: Insulin B
E: Insulin A
F: Insulin B
G: Insulin A
H: Insulin B
I: Insulin A
J: Insulin B
K: Insulin A
L: Insulin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,90623
Polymers34,90612
Non-polymers1,00011
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19890 Å2
ΔGint-215 kcal/mol
Surface area12880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.600, 60.800, 62.100
Angle α, β, γ (deg.)90.00, 116.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11G-613-

HOH

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Components

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Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
Insulin A


Mass: 2383.698 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide
Insulin B


Mass: 3433.953 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 5 types, 324 molecules

#3: Chemical
ChemComp-RCO / RESORCINOL / 1,3-BENZENEDIOL / 1,3-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15mM Na-SCN, 5%(v/v) ethanol, 200mM phosphate buffer pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.3 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 6, 2006
RadiationMonochromator: Double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 36828 / % possible obs: 92.2 % / Redundancy: 2.1 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 14.9
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 5.1 / Num. unique all: 4537 / % possible all: 48.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: insulin R6 conformation

Resolution: 1.7→19.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.434 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22147 1745 5 %RANDOM
Rwork0.1784 ---
obs0.18055 33178 94.83 %-
all-36828 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.962 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2354 0 62 313 2729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222485
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9653364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8765288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45824.5120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90515369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.71156
X-RAY DIFFRACTIONr_chiral_restr0.0970.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021900
X-RAY DIFFRACTIONr_nbd_refined0.2330.21347
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2223
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.216
X-RAY DIFFRACTIONr_mcbond_it0.8091.51474
X-RAY DIFFRACTIONr_mcangle_it1.50122356
X-RAY DIFFRACTIONr_scbond_it2.16731011
X-RAY DIFFRACTIONr_scangle_it3.4954.51008
LS refinement shellResolution: 1.7→1.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 107 -
Rwork0.255 1700 -
obs--67.45 %
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)
10.76810.37931.17771.05770.12922.0409-0.01110.1546-0.0337-0.08640.0228-0.052-0.12310.2315-0.0117-0.0226-0.01620.03250.032-0.0109-0.026333.4005-1.07819.6717
21.07870.42250.13270.1816-0.10281.50610.0098-0.0425-0.0151-0.05790.0716-0.02990.196-0.0642-0.08140.0095-0.0317-0.0016-0.03240.01410.010216.3075-13.291618.4668
31.20460.0372-0.34321.81940.73632.28760.05230.1839-0.1225-0.167-0.12210.1759-0.2367-0.38190.06980.03160.0504-0.03560.0178-0.0183-0.049212.41940.91091.083
40.5262-0.16130.06180.6691-0.01820.4627-0.0168-0.067-0.0245-0.0216-0.0043-0.0224-0.0017-0.03220.0211-0.03010.00560.01340.0044-0.00480.002323.9563-2.631127.3211
51.0551-0.34080.18160.6263-0.7480.9518-0.04560.0230.07630.0315-0.06090.0401-0.19540.1690.10650.1033-0.0460.0073-0.05250.0275-0.028925.348512.839510.5163
60.60480.43860.82382.88171.01891.41150.1277-0.0733-0.0252-0.3033-0.21610.1943-0.2324-0.34840.0884-0.04380.0606-0.03450.0595-0.0442-0.0015.35653.481615.5664
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
7X-RAY DIFFRACTION4GG1 - 211 - 21
8X-RAY DIFFRACTION4HH1 - 281 - 28
9X-RAY DIFFRACTION5II1 - 211 - 21
10X-RAY DIFFRACTION5JJ1 - 281 - 28
11X-RAY DIFFRACTION6KK1 - 211 - 21
12X-RAY DIFFRACTION6LL1 - 281 - 28

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