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- PDB-5bpo: Human insulin with intra-chain chemical crosslink between modifie... -

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Basic information

Entry
Database: PDB / ID: 5bpo
TitleHuman insulin with intra-chain chemical crosslink between modified B27 and B29
Components(Insulin) x 2
KeywordsHORMONE / Chemical crosslink / B24-B29 / specificity
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 / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / positive regulation of insulin receptor signaling pathway / negative regulation of respiratory burst involved in inflammatory response / 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 across plasma membrane / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / regulation of synaptic plasticity / negative regulation of protein catabolic process / 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 phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of canonical NF-kappaB 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBrzozowski, A.M. / Turkenburg, J.P. / Jiracek, J. / Zakova, L.
CitationJournal: Sci Rep / Year: 2016
Title: Rational steering of insulin binding specificity by intra-chain chemical crosslinking.
Authors: Vikova, J. / Collinsova, M. / Kletvikova, E. / Budesinsky, M. / Kaplan, V. / Zakova, L. / Veverka, V. / Hexnerova, R. / Avino, R.J. / Strakova, J. / Selicharova, I. / Vanek, V. / Wright, D.W. ...Authors: Vikova, J. / Collinsova, M. / Kletvikova, E. / Budesinsky, M. / Kaplan, V. / Zakova, L. / Veverka, V. / Hexnerova, R. / Avino, R.J. / Strakova, J. / Selicharova, I. / Vanek, V. / Wright, D.W. / Watson, C.J. / Turkenburg, J.P. / Brzozowski, A.M. / Jiracek, J.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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


Theoretical massNumber of molelcules
Total (without water)11,6494
Polymers11,6494
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-38 kcal/mol
Surface area6280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.103, 45.968, 43.929
Angle α, β, γ (deg.)90.00, 128.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Insulin


Mass: 2383.698 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Sequence occurs naturally / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide Insulin


Mass: 3440.928 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3 / Details: 0.05 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→34.38 Å / Num. obs: 8033 / % possible obs: 97.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 3 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
xia2data reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mso

1mso


Resolution: 1.9→34.38 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.43 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3041 448 5.6 %RANDOM
Rwork0.23534 ---
obs0.23929 7579 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.275 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å2-0.72 Å2
2--0.97 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms778 0 0 94 872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.019836
X-RAY DIFFRACTIONr_bond_other_d0.0030.02732
X-RAY DIFFRACTIONr_angle_refined_deg2.1331.9711142
X-RAY DIFFRACTIONr_angle_other_deg1.22331686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0275103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53124.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54715119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.912151
X-RAY DIFFRACTIONr_chiral_restr0.1390.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02972
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02213
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_it2.3132.326403
X-RAY DIFFRACTIONr_mcbond_other2.2872.319402
X-RAY DIFFRACTIONr_mcangle_it3.2223.44500
X-RAY DIFFRACTIONr_mcangle_other3.2223.447501
X-RAY DIFFRACTIONr_scbond_it2.162.562433
X-RAY DIFFRACTIONr_scbond_other2.1582.565434
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1943.8640
X-RAY DIFFRACTIONr_long_range_B_refined6.419.8571033
X-RAY DIFFRACTIONr_long_range_B_other5.84119.521984
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 20 -
Rwork0.228 524 -
obs--92.05 %

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