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- PDB-2om0: Structure of human insulin in presence of urea at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 2om0
TitleStructure of human insulin in presence of urea 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 / 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 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 / UREA / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 6, 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)108,02678
Polymers104,71836
Non-polymers3,30842
Water11,313628
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)36,12928
Polymers34,90612
Non-polymers1,22316
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20830 Å2
ΔGint-234 kcal/mol
Surface area12870 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)36,00926
Polymers34,90612
Non-polymers1,10314
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20600 Å2
ΔGint-237 kcal/mol
Surface area12750 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)35,88824
Polymers34,90612
Non-polymers98212
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20320 Å2
ΔGint-242 kcal/mol
Surface area12640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.936, 219.318, 223.674
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, 670 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-URE / UREA


Mass: 60.055 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH4N2O
#5: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 3.45 Å3/Da / Density % sol: 64.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M NaCl, 3M urea, 100mM 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: I911-2 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 10, 2005
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: 2.05→50 Å / Num. all: 91370 / Num. obs: 91251 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.6
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.2 / Num. unique all: 6331 / % possible all: 100

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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: 2.05→28.31 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.007 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22714 4536 5 %RANDOM
Rwork0.18428 ---
obs0.18638 86749 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.194 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7115 0 204 628 7947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227542
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9710213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.895876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43724.505364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.482151132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9671519
X-RAY DIFFRACTIONr_chiral_restr0.1420.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025829
X-RAY DIFFRACTIONr_nbd_refined0.2180.23561
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25239
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.2472
X-RAY DIFFRACTIONr_metal_ion_refined0.1610.221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.340.229
X-RAY DIFFRACTIONr_mcbond_it1.211.54629
X-RAY DIFFRACTIONr_mcangle_it1.86227158
X-RAY DIFFRACTIONr_scbond_it2.61633379
X-RAY DIFFRACTIONr_scangle_it3.7684.53050
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 329 -
Rwork0.213 6376 -
obs--100 %
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)
12.2729-0.3903-2.01551.5947-0.31072.06960.0601-0.0430.09560.04260.0149-0.10030.0220.2398-0.075-0.11030.00110.00780.0551-0.0222-0.045517.562958.39618.9342
20.6615-0.0442-0.13041.0387-0.37481.41920.0532-0.0523-0.03480.05740.00080.00930.10810.0211-0.0541-0.0512-0.0242-0.0018-0.0192-0.0136-0.0754.422749.940511.5592
31.8035-1.5922-0.84022.43840.45562.37040.1144-0.06110.36880.0637-0.0574-0.1855-0.13070.0446-0.0569-0.0765-0.03840.0554-0.0948-0.05260.02367.534278.83469.6468
43.76891.6517-0.9283.87190.69411.18910.02450.23650.3117-0.29330.04910.0334-0.0458-0.0686-0.0736-0.084-0.00020.0155-0.02730.0206-0.07124.368368.5757-2.1186
51.72180.2685-0.35513.3212-0.81490.48580.1134-0.18940.15030.2615-0.11160.1097-0.1120.0606-0.00180.0409-0.05110.04060.007-0.0515-0.08064.335863.778326.367
60.9967-0.19640.38832.75370.7171.50810.0226-0.10160.12250.2963-0.1220.45790.0384-0.16120.0994-0.0675-0.03080.1028-0.0359-0.06830.0287-7.979568.544117.2644
70.28510.45530.73892.2238-0.46583.7257-0.0135-0.0526-0.12020.0353-0.0035-0.2177-0.00890.57020.017-0.0981-0.0036-0.01020.0736-0.0158-0.07287.621227.136439.0781
82.85560.74220.15381.18310.26391.99880.0249-0.0898-0.3231-0.049-0.02630.0430.0541-0.05080.0014-0.0804-0.0065-0.0311-0.0437-0.0081-0.0409-11.359914.713736.9968
92.73910.4167-0.46893.07-1.2750.5621-0.04870.1467-0.0246-0.40120.06130.04860.1325-0.0161-0.01270.0231-0.0289-0.039-0.001-0.03-0.1357-4.769228.727420.3129
102.10010.7953-0.00791.7515-1.1742.37520.0831-0.08490.10340.0924-0.07910.0519-0.22570.1755-0.004-0.0201-0.0304-0.0106-0.0365-0.0113-0.11870.471740.975535.1826
112.04270.30791.16092.4386-0.58522.04560.013-0.2205-0.02970.1583-0.03980.1554-0.0548-0.12080.0268-0.06360.00860.00580.0456-0.019-0.1111-10.294225.662148.4575
121.98211.1349-0.60733.38910.94312.58-0.15660.12860.1908-0.22570.01630.4594-0.2281-0.15210.1403-0.06190.0089-0.0931-0.04360.0071-0.0227-18.627831.048528.1071
131.9099-0.60220.63585.12632.58142.0779-0.0169-0.0781-0.21740.0268-0.24060.28880.1401-0.20390.2575-0.1195-0.03210.058-0.082-0.06980.0461-40.5388-16.574319.7823
144.7106-1.0761.85334.8766-0.85721.9670.0875-0.4732-0.110.2903-0.10420.5572-0.0178-0.24890.0166-0.1202-0.01340.06390.0251-0.0840.0211-45.13773.024930.8829
152.52022.2814-0.7195.48221.80492.42370.1589-0.2621-0.51920.3251-0.1185-0.83730.11160.0124-0.0404-0.1223-0.0066-0.0854-0.0770.02230.1459-24.1189-5.365231.063
163.27210.2170.77962.83380.88772.301-0.00830.00120.136-0.1372-0.07150.0204-0.14970.02420.0798-0.0968-0.0041-0.0164-0.063-0.0324-0.0288-33.148311.208524.4374
171.36220.29021.16737.55890.71982.4676-0.01880.0423-0.1167-0.61930.0837-1.0888-0.16550.1157-0.0648-0.0797-0.03430.1638-0.1079-0.07440.1316-23.3868-7.115115.2782
184.71941.4054-1.12766.67491.82312.0262-0.28280.15820.0459-1.1327-0.08280.8121-0.2013-0.30380.36560.04690.0186-0.1726-0.0669-0.0879-0.0286-45.6492-3.545712.0617
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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