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Basic information

Entry
Database: PDB / ID: 4ajx
TitleLigand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin
Components(INSULIN) x 2
KeywordsHORMONE
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 cellular amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / endosome lumen / positive regulation of 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 / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / regulation of protein localization / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
N-(16-Carboxyhexadecanoyl)-L-glutamic acid / IMIDAZOLE / RESORCINOL / Insulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSteensgaard, D.B. / Schluckebier, G. / Strauss, H.M. / Norrman, M. / Thomsen, J.K. / Friderichsen, A.V. / Havelund, S. / Jonassen, I.
CitationJournal: Biochemistry / Year: 2013
Title: Ligand Controlled Assembly of Hexamers, Dihexamers, and Linear Multihexamer Structures by the Engineered Acylated Insulin Degludec.
Authors: Steensgaard, D.B. / Schluckebier, G. / Strauss, H.M. / Norrman, M. / Thomsen, J.K. / Friderichsen, A.V. / Havelund, S. / Jonassen, I.
History
DepositionFeb 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Jun 24, 2015Group: Derived calculations
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INSULIN
B: INSULIN
C: INSULIN
D: INSULIN
E: INSULIN
F: INSULIN
G: INSULIN
H: INSULIN
I: INSULIN
J: INSULIN
K: INSULIN
L: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,17527
Polymers34,29912
Non-polymers1,87615
Water6,449358
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-94.4 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.310, 62.490, 57.270
Angle α, β, γ (deg.)90.00, 111.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
INSULIN


Mass: 2383.698 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308
#2: Protein/peptide
INSULIN


Mass: 3332.849 Da / Num. of mol.: 6 / Fragment: RESIDUES 25-53
Source method: isolated from a genetically manipulated source
Details: DELTA 30, SYNTHETICALLY MODIFIED AT LYS 29 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308

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Non-polymers , 6 types, 373 molecules

#3: Chemical ChemComp-16E / N-(16-Carboxyhexadecanoyl)-L-glutamic acid


Mass: 415.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H37NO7
#4: Chemical
ChemComp-RCO / RESORCINOL / 1,3-BENZENEDIOL / 1,3-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.29 Å3/Da / Density % sol: 46.33 % / Description: NONE
Crystal growpH: 7 / Details: 0.6 M IMIDAZOLE/MALONIC ACID PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→40.5 Å / Num. obs: 90966 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 11.72 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 19.15
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.51 / % possible all: 60.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_947)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EVR

1evr


Resolution: 1.2→40.497 Å / SU ML: 0.1 / σ(F): 1.99 / Phase error: 15.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1596 4449 5 %
Rwork0.1405 --
obs0.1415 89598 92.71 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.619 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4182 Å20 Å2-0.0188 Å2
2---0.3665 Å20 Å2
3---0.7847 Å2
Refinement stepCycle: LAST / Resolution: 1.2→40.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 123 358 2806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142672
X-RAY DIFFRACTIONf_angle_d1.6143625
X-RAY DIFFRACTIONf_dihedral_angle_d15.189963
X-RAY DIFFRACTIONf_chiral_restr0.098397
X-RAY DIFFRACTIONf_plane_restr0.008469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.21360.1955850.20561792X-RAY DIFFRACTION58
1.2136-1.22790.3409960.29261900X-RAY DIFFRACTION62
1.2279-1.24290.21631170.21842077X-RAY DIFFRACTION68
1.2429-1.25860.22211190.21032276X-RAY DIFFRACTION75
1.2586-1.27520.30671210.23972433X-RAY DIFFRACTION79
1.2752-1.29270.21821270.19442655X-RAY DIFFRACTION88
1.2927-1.31110.28891550.2262903X-RAY DIFFRACTION94
1.3111-1.33070.17721410.13123072X-RAY DIFFRACTION100
1.3307-1.35150.15631430.1193083X-RAY DIFFRACTION100
1.3515-1.37370.16891250.13112930X-RAY DIFFRACTION96
1.3737-1.39740.16311760.11772999X-RAY DIFFRACTION99
1.3974-1.42280.1341510.10933042X-RAY DIFFRACTION100
1.4228-1.45010.15961840.12073009X-RAY DIFFRACTION99
1.4501-1.47970.17621460.12443017X-RAY DIFFRACTION98
1.4797-1.51190.13561610.10053046X-RAY DIFFRACTION100
1.5119-1.54710.13751460.10612906X-RAY DIFFRACTION96
1.5471-1.58580.13351630.09563039X-RAY DIFFRACTION100
1.5858-1.62860.13131610.09353067X-RAY DIFFRACTION100
1.6286-1.67660.12341630.09813041X-RAY DIFFRACTION100
1.6766-1.73070.12191560.10063067X-RAY DIFFRACTION100
1.7307-1.79250.14111640.10763039X-RAY DIFFRACTION100
1.7925-1.86430.15151540.1163076X-RAY DIFFRACTION100
1.8643-1.94920.15331420.13792602X-RAY DIFFRACTION85
1.9492-2.05190.15241790.12373042X-RAY DIFFRACTION99
2.0519-2.18050.14561610.12522894X-RAY DIFFRACTION95
2.1805-2.34880.15141470.12952779X-RAY DIFFRACTION91
2.3488-2.58510.15931420.13693105X-RAY DIFFRACTION100
2.5851-2.95910.16631590.15163093X-RAY DIFFRACTION100
2.9591-3.72780.15141800.15253054X-RAY DIFFRACTION100
3.7278-40.52020.16751850.17163111X-RAY DIFFRACTION99

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