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- PDB-2om1: Structure of human insulin in presence of thiocyanate at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 2om1
TitleStructure of human insulin in presence of thiocyanate at pH 6.5
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / R6 conformation
Function / homology
Function and homology information


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 / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...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 / regulation of protein secretion / Insulin processing / 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 / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / 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
RESORCINOL / THIOCYANATE ION / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
G: Insulin A chain
H: Insulin B chain
I: Insulin A chain
J: Insulin B chain
K: Insulin A chain
L: Insulin B chain
Q: Insulin A chain
R: Insulin B chain
S: Insulin A chain
T: Insulin B chain
U: Insulin A chain
V: Insulin B chain
X: Insulin A chain
Y: Insulin B chain
1: Insulin A chain
2: Insulin B chain
3: Insulin A chain
4: Insulin B chain
a: Insulin A chain
b: Insulin B chain
c: Insulin A chain
d: Insulin B chain
e: Insulin A chain
f: Insulin B chain
g: Insulin A chain
h: Insulin B chain
i: Insulin A chain
j: Insulin B chain
k: Insulin A chain
l: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,53367
Polymers104,71836
Non-polymers2,81531
Water13,601755
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
G: Insulin A chain
H: Insulin B chain
I: Insulin A chain
J: Insulin B chain
K: Insulin A chain
L: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,81422
Polymers34,90612
Non-polymers90810
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20080 Å2
ΔGint-219 kcal/mol
Surface area12730 Å2
MethodPISA, PQS
2
Q: Insulin A chain
R: Insulin B chain
S: Insulin A chain
T: Insulin B chain
U: Insulin A chain
V: Insulin B chain
X: Insulin A chain
Y: Insulin B chain
1: Insulin A chain
2: Insulin B chain
3: Insulin A chain
4: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,90623
Polymers34,90612
Non-polymers1,00011
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20290 Å2
ΔGint-217 kcal/mol
Surface area12700 Å2
MethodPISA, PQS
3
a: Insulin A chain
b: Insulin B chain
c: Insulin A chain
d: Insulin B chain
e: Insulin A chain
f: Insulin B chain
g: Insulin A chain
h: Insulin B chain
i: Insulin A chain
j: Insulin B chain
k: Insulin A chain
l: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,81422
Polymers34,90612
Non-polymers90810
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20310 Å2
ΔGint-223 kcal/mol
Surface area12450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.000, 219.480, 224.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
111-1009-

HOH

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Components

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Protein/peptide , 2 types, 36 molecules ACEGIKQSUX13acegikBDFHJLRTVY24...

#1: Protein/peptide
Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 18 / 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.: 18 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 5 types, 786 molecules

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


Mass: 110.111 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C6H6O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 6 / 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.: 755 / 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: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15mM Na-SCN, 5%(v/v) ethanol, 200mM phosphate buffer, pH 6.5, 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: 1.97→50 Å / Num. all: 103274 / Num. obs: 102732 / % possible obs: 99.5 % / Redundancy: 8.6 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.7
Reflection shellResolution: 1.97→2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.45 / Num. unique all: 4480 / % possible all: 89.2

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Processing

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

Resolution: 1.97→19.99 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.662 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21165 5132 5 %RANDOM
Rwork0.17463 ---
obs0.17646 97508 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.836 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.97→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7135 0 174 755 8064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227511
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.96810167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0555872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35724.485359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.205151137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3581518
X-RAY DIFFRACTIONr_chiral_restr0.1190.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025740
X-RAY DIFFRACTIONr_nbd_refined0.2350.23802
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25310
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2614
X-RAY DIFFRACTIONr_metal_ion_refined0.1580.222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.234
X-RAY DIFFRACTIONr_mcbond_it0.9551.54457
X-RAY DIFFRACTIONr_mcangle_it1.78927130
X-RAY DIFFRACTIONr_scbond_it2.4733054
X-RAY DIFFRACTIONr_scangle_it3.9884.53034
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 322 -
Rwork0.217 6629 -
obs--93.13 %
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)
11.06870.01241.08570.59650.3161.25750.0574-0.08970.00660.0008-0.02490.0860.003-0.0856-0.0325-0.04330.0132-0.00850.02370.0197-0.0087-47.1125-58.37938.9814
20.1984-0.05660.14370.83980.3970.90220.0236-0.0093-0.01350.0089-0.0088-0.0526-0.1093-0.0513-0.01470.0088-0.01550.0048-0.01460.0019-0.028-33.9578-50.029611.7085
31.0983-0.73780.56681.1880.1341.80590.1036-0.0479-0.14950.0025-0.02980.04440.1483-0.1273-0.0738-0.0164-0.0139-0.0324-0.06470.03730.0431-36.9105-78.97669.5826
42.03990.63260.5372.2129-0.39990.30040.03830.0413-0.1658-0.21080.00680.00810.04310.0714-0.04520.0079-0.00030.0001-0.0294-0.0203-0.0292-33.6907-68.3979-1.8675
52.1520.59430.35713.28821.0290.4110.1296-0.1644-0.07670.3551-0.0969-0.10490.1537-0.0459-0.03270.0678-0.0356-0.0401-0.00340.042-0.0882-33.9026-63.909226.4424
60.40250.2542-0.50742.5784-0.61881.51460.025-0.0339-0.0740.1915-0.0982-0.2516-0.05540.08120.0731-0.0312-0.0014-0.0678-0.0410.04490.0356-21.5639-68.631317.456
70.3258-0.00310.33071.0184-0.12421.65040.0304-0.05180.0558-0.01030.01310.06410.0977-0.1448-0.0435-0.02790.00160.01070.02020.0175-0.0355-37.0606-27.043739.1536
80.61040.339-0.10410.22820.0860.53660.0443-0.03410.133-0.0097-0.0311-0.01280.01490.0446-0.0132-0.0393-0.00180.0139-0.00520.0220.0229-18.0621-14.770837.0499
91.1137-0.1336-0.16362.01470.62790.20910.01510.04450.0316-0.21960.0248-0.0675-0.00260.0174-0.03990.0327-0.00870.02130.00940.0169-0.0681-24.8239-28.794620.4029
100.84340.3465-0.6410.62890.42121.4504-0.0203-0.0062-0.0448-0.02060.0001-0.02520.13790.00480.02020.0289-0.0012-0.0095-0.0310.0081-0.0449-30.0721-40.997335.3253
111.24940.4815-0.72831.02210.22620.73170.056-0.10020.01860.08-0.0514-0.06560.07140.0641-0.00460.00040.0154-0.00450.03250.0154-0.0702-19.3464-25.699248.4494
120.77840.66680.44351.9791-0.22241.0702-0.05370.0758-0.091-0.10740.0169-0.1970.11350.03930.0367-0.02680.02360.0488-0.00250.0081-0.0078-11.005-31.174828.1842
131.1326-0.5437-0.39823.0303-1.32351.5491-0.0183-0.14670.1849-0.0942-0.0284-0.2296-0.04310.05550.0467-0.0275-0.0001-0.0325-0.07740.04720.064311.167716.482319.8333
142.5772-0.7357-0.69562.05890.18350.18790.0516-0.13840.23440.0845-0.0445-0.31160.079-0.0873-0.0071-0.0410.0065-0.03210.0040.03580.00915.8329-3.233130.8074
151.65831.18030.44433.3077-1.17151.15890.0625-0.15010.22860.1669-0.02980.3471-0.081-0.0395-0.0328-0.06230.00490.0492-0.0407-0.00960.067-5.22335.225431.0291
161.8452-0.2237-0.14571.2738-0.28520.38110.0182-0.0005-0.1054-0.10060.01270.0665-0.0019-0.0226-0.0309-0.0354-0.0050.0008-0.02650.01770.00633.7226-11.309524.4247
170.9611-0.1639-1.28594.3552-0.58041.9626-0.00810.02660.0731-0.37380.05330.51740.126-0.069-0.0451-0.0208-0.0047-0.1175-0.08920.05660.0832-5.97937.000215.2363
182.71040.72140.6143.1946-0.56730.7277-0.11650.04340.086-0.6581-0.1235-0.42240.11650.00950.240.08180.02850.1069-0.06790.08360.004916.19253.423812.1754
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
13X-RAY DIFFRACTION7QM1 - 211 - 21
14X-RAY DIFFRACTION7RN1 - 281 - 28
15X-RAY DIFFRACTION8SO1 - 211 - 21
16X-RAY DIFFRACTION8TP1 - 281 - 28
17X-RAY DIFFRACTION9UQ1 - 211 - 21
18X-RAY DIFFRACTION9VR1 - 281 - 28
19X-RAY DIFFRACTION10XS1 - 211 - 21
20X-RAY DIFFRACTION10YT1 - 281 - 28
21X-RAY DIFFRACTION111U1 - 211 - 21
22X-RAY DIFFRACTION112V1 - 281 - 28
23X-RAY DIFFRACTION123W1 - 211 - 21
24X-RAY DIFFRACTION124X1 - 281 - 28
25X-RAY DIFFRACTION13aY1 - 211 - 21
26X-RAY DIFFRACTION13bZ1 - 281 - 28
27X-RAY DIFFRACTION14cAA1 - 211 - 21
28X-RAY DIFFRACTION14dBA1 - 281 - 28
29X-RAY DIFFRACTION15eCA1 - 211 - 21
30X-RAY DIFFRACTION15fDA1 - 281 - 28
31X-RAY DIFFRACTION16gEA1 - 211 - 21
32X-RAY DIFFRACTION16hFA1 - 281 - 28
33X-RAY DIFFRACTION17iGA1 - 211 - 21
34X-RAY DIFFRACTION17jHA1 - 281 - 28
35X-RAY DIFFRACTION18kIA1 - 211 - 21
36X-RAY DIFFRACTION18lJA1 - 281 - 28

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