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- PDB-4ajz: Ligand controlled assembly of hexamers, dihexamers, and linear mu... -

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Basic information

Entry
Database: PDB / ID: 4ajz
TitleLigand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin
Components
  • INSULIN A CHAIN
  • INSULIN B CHAIN
KeywordsHORMONE
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / negative regulation of fatty acid metabolic process / nitric oxide-cGMP-mediated signaling / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / negative regulation of fatty acid metabolic process / nitric oxide-cGMP-mediated signaling / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / transport vesicle / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / Insulin receptor recycling / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / vasodilation / Golgi lumen / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / 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 / positive regulation of gene expression / regulation of DNA-templated transcription / 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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.4Dec 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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 A CHAIN
B: INSULIN B CHAIN
C: INSULIN A CHAIN
D: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6938
Polymers11,4334
Non-polymers2604
Water84747
1
A: INSULIN A CHAIN
B: INSULIN B CHAIN
hetero molecules

A: INSULIN A CHAIN
B: INSULIN B CHAIN
hetero molecules

A: INSULIN A CHAIN
B: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3469
Polymers17,1506
Non-polymers1963
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area5110 Å2
ΔGint-95.3 kcal/mol
Surface area10670 Å2
MethodPISA
2
C: INSULIN A CHAIN
D: INSULIN B CHAIN
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)17,73515
Polymers17,1506
Non-polymers5859
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area5600 Å2
ΔGint-149.1 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.550, 79.550, 38.970
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

21D-1030-

ZN

31D-1031-

CL

41B-2003-

HOH

51B-2009-

HOH

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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 (brewer's yeast) / References: UniProt: P01308
#2: Protein/peptide INSULIN B CHAIN


Mass: 3332.849 Da / Num. of mol.: 2 / Fragment: DELTA B30, RESIDUES 25-53
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308

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Non-polymers , 4 types, 51 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.08 Å3/Da / Density % sol: 40.74 % / Description: NONE
Crystal growMethod: microbatch / pH: 7.5
Details: MICROBATCH METHOD 5MM PHENOL, 0.4M NACL; 6% (V/V) ETHANOL, 100MM HEPES 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: May 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→33.93 Å / Num. obs: 7500 / % possible obs: 87.9 % / Observed criterion σ(I): 0 / Redundancy: 2.49 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.7
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.4 / % possible all: 52.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EV3

1ev3


Resolution: 1.8→33.92 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.647 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25477 731 9.7 %RANDOM
Rwork0.18924 ---
obs0.19545 6819 88.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.892 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0.41 Å20 Å2
2---0.82 Å20 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms785 0 10 47 842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02827
X-RAY DIFFRACTIONr_bond_other_d0.0050.02537
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9631125
X-RAY DIFFRACTIONr_angle_other_deg1.4543.0191295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.197599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14324.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21315129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.889152
X-RAY DIFFRACTIONr_chiral_restr0.1020.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02928
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02174
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 36 -
Rwork0.243 300 -
obs--51.45 %
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)
15.16711.3573-0.39731.70531.21935.1127-0.08270.41570.4444-0.3964-0.08920.4807-0.3259-0.45850.17190.259-0.0091-0.0650.2467-0.01190.3157-17.463-3.427-8.963
24.61.02890.70376.0705-0.40815.34340.17080.17040.0337-0.1844-0.07990.0969-0.0538-0.2457-0.0910.0542-0.0063-0.03130.0962-0.00020.1098-12.205-3.713-3.599
35.085-0.19481.97538.07481.1214.85520.0829-0.3307-0.21140.5076-0.008-0.05630.2323-0.2098-0.07490.1477-0.0366-0.0170.10310.06840.0943-3.417-16.1048.797
43.7678-0.13580.7557.86034.27765.42190.0008-0.2047-0.12430.2177-0.14940.41480.158-0.33290.14850.0812-0.0245-0.010.06950.04420.1056-7.101-9.843.521
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION2B1 - 29
3X-RAY DIFFRACTION3C1 - 21
4X-RAY DIFFRACTION4D1 - 29

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