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- PDB-3zu1: Structure of LysB29(Nepsilon omega-carboxyheptadecanoyl) des(B30)... -

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Basic information

Entry
Database: PDB / ID: 3zu1
TitleStructure of LysB29(Nepsilon omega-carboxyheptadecanoyl) des(B30) Human Insulin
Components
  • INSULIN A CHAIN
  • INSULIN B CHAIN
KeywordsHORMONE
Function / homology
Function and homology information


Signaling by Insulin receptor / alpha-beta T cell activation / negative regulation of glycogen catabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior ...Signaling by Insulin receptor / alpha-beta T cell activation / negative regulation of glycogen catabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / positive regulation of cellular protein metabolic process / negative regulation of reactive oxygen species biosynthetic process / COPI-mediated anterograde transport / regulation of cellular amino acid metabolic process / regulation of protein localization to plasma membrane / Regulation of insulin secretion / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Signal attenuation / negative regulation of protein secretion / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of insulin receptor signaling pathway / neuron projection maintenance / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / negative regulation of acute inflammatory response / positive regulation of cell differentiation / regulation of transmembrane transporter activity / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / regulation of synaptic plasticity / positive regulation of brown fat cell differentiation / cognition / regulation of protein localization / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / acute-phase response / activation of protein kinase B activity / positive regulation of glucose import / vasodilation / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor binding / positive regulation of protein localization to nucleus / insulin receptor signaling pathway / glucose metabolic process / Golgi lumen / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / endoplasmic reticulum to Golgi vesicle-mediated transport / wound healing / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell migration / positive regulation of protein kinase B signaling / Golgi membrane / Amyloid fiber formation / G protein-coupled receptor signaling pathway / amyloid fibril formation / endoplasmic reticulum lumen / regulation of transcription, DNA-templated / positive regulation of gene expression / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
RESORCINOL / Insulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchluckebier, G. / Whittingham, J.
CitationJournal: To be Published
Title: Structure of Lysb29(Nepsilon Omega-Carboxyheptadecanoyl) Des(B30) Human Insulin
Authors: Schluckebier, G. / Whittingham, J.
History
DepositionJul 13, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,05710
Polymers11,6354
Non-polymers4226
Water1,36976
1
A: INSULIN A CHAIN
B: INSULIN B CHAIN
C: INSULIN A CHAIN
D: INSULIN B CHAIN
hetero molecules

A: INSULIN A CHAIN
B: INSULIN B CHAIN
C: INSULIN A CHAIN
D: INSULIN B CHAIN
hetero molecules

A: INSULIN A CHAIN
B: INSULIN B CHAIN
C: INSULIN A CHAIN
D: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,17230
Polymers34,90612
Non-polymers1,26618
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area21990 Å2
ΔGint-895.6 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)79.060, 79.060, 41.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-1030-

ZN

21B-1031-

CL

31D-1030-

ZN

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 21
2116C1 - 21
1126B1 - 24
2126D1 - 24
1226B26 - 29
2226D26 - 29

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.0026, 0.9999, -0.0162), (1, -0.0027, -0.0061), (-0.0062, -0.0162, -0.9999)
Vector: -0.0182, 0.4631, -0.5789)

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide INSULIN A CHAIN


Mass: 2383.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P01308
#2: Protein/peptide INSULIN B CHAIN


Mass: 3433.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: LYS B29, D29 CHEMICALLY MODIFIED WITH CARBOXY -HEPTADECANOYLIC ACID
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P01308

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Non-polymers , 4 types, 82 molecules

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


Mass: 110.111 Da / Num. of mol.: 2 / 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsINSULIN IS IN COMPLEX WITH ZINC (ZN) AND RESORCINOL (RCO).

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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: 2.14 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 7.5
Details: 100MM HEPES, 300MM NA-CITRATE, 24% 2-PROPANOL PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 22850 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 2.07 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.3
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 1.65 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / % possible all: 84.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EV3
Resolution: 1.6→21.88 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.156 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ACYLATED LYSINE (B29 AND D29) DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1249 10 %RANDOM
Rwork0.165 ---
obs0.17 11270 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.54 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å2-0.7 Å20 Å2
2---1.4 Å20 Å2
3---2.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→21.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms748 0 20 76 844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022831
X-RAY DIFFRACTIONr_bond_other_d0.0010.02727
X-RAY DIFFRACTIONr_angle_refined_deg1.9471.9771141
X-RAY DIFFRACTIONr_angle_other_deg1.01731682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19424.11834
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44615122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.425152
X-RAY DIFFRACTIONr_chiral_restr0.1330.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02940
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02178
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.231.5512
X-RAY DIFFRACTIONr_mcbond_other0.391.5220
X-RAY DIFFRACTIONr_mcangle_it2.0362825
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1623319
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6034.5312
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A282loose positional0.435
12C282loose positional0.435
21B327loose positional0.545
22D327loose positional0.545
11A282loose thermal1.1610
12C282loose thermal1.1610
21B327loose thermal1.1510
22D327loose thermal1.1510
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 90 -
Rwork0.34 839 -
obs--98.41 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.80891.6602-3.63315.2939-2.72538.94790.05280.6969-0.3867-0.4198-0.06970.519-0.1644-0.21120.01690.1774-0.0199-0.0970.2174-0.05380.1782-15.9066-3.0158-9.1749
210.9561-2.5739-6.3156.73871.44239.6111-0.01770.1446-0.6761-0.205-0.13270.39110.3468-0.00650.15040.09630.0117-0.05470.0923-0.01070.0776-9.3583-6.0106-4.3244
35.9121-0.65771.81578.27311.2237.49010.0008-0.5196-0.47570.78630.12930.50680.0632-0.3503-0.130.2827-0.02130.0520.1460.12430.2352-3.2611-15.99048.7466
46.4324-3.8674-1.61512.61886.60859.5126-0.1757-0.3386-0.55760.4547-0.07860.73410.252-0.46780.25430.08620.00520.02550.11220.05540.0812-6.5263-9.2054.2408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION2B1 - 28
3X-RAY DIFFRACTION3C1 - 21
4X-RAY DIFFRACTION4D1 - 28

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