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- PDB-6s34: Zinc free, dimeric human insulin determined to 1.35 Angstrom reso... -

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Basic information

Entry
Database: PDB / ID: 6s34
TitleZinc free, dimeric human insulin determined to 1.35 Angstrom resolution
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin / cubic / human / zinc free
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 respiratory burst involved in inflammatory response / 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 / 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 / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / cognition / vasodilation / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsJohansson, E.
Citation
Journal: Not Published
Title: Zinc free, dimeric human insulin determined to 1.35 Angstrom resolution
Authors: Johansson, E.
#2: Journal: Protein Sci. / Year: 2020
Title: Insulin binding to the analytical antibody sandwich pair OXI-005 and HUI-018: Epitope mapping and binding properties.
Authors: Johansson, E. / Wu, X. / Yu, B. / Yang, Z. / Cao, Z. / Wiberg, C. / Jeppesen, C.B. / Poulsen, F.
#1: Journal: Nat Commun / Year: 2020
Title: Molecular engineering of safe and efficacious oral basal insulin.
Authors: Hubalek, F. / Refsgaard, H.H.F. / Gram-Nielsen, S. / Madsen, P. / Nishimura, E. / Munzel, M. / Brand, C.L. / Stidsen, C.E. / Claussen, C.H. / Wulff, E.M. / Pridal, L. / Ribel, U. / ...Authors: Hubalek, F. / Refsgaard, H.H.F. / Gram-Nielsen, S. / Madsen, P. / Nishimura, E. / Munzel, M. / Brand, C.L. / Stidsen, C.E. / Claussen, C.H. / Wulff, E.M. / Pridal, L. / Ribel, U. / Kildegaard, J. / Porsgaard, T. / Johansson, E. / Steensgaard, D.B. / Hovgaard, L. / Glendorf, T. / Hansen, B.F. / Jensen, M.K. / Nielsen, P.K. / Ludvigsen, S. / Rugh, S. / Garibay, P.W. / Moore, M.C. / Cherrington, A.D. / Kjeldsen, T.
History
DepositionJun 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _database_2.pdbx_DOI ..._citation.journal_abbrev / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[3]
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description ...Data collection / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / entity_src_gen / pdbx_initial_refinement_model
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8803
Polymers5,8182
Non-polymers621
Water1,18966
1
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)11,7596
Polymers11,6354
Non-polymers1242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_455-x-1/2,y,-z1
Buried area4340 Å2
ΔGint-34 kcal/mol
Surface area5870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.170, 78.170, 78.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Components on special symmetry positions
IDModelComponents
11A-130-

HOH

21B-219-

HOH

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Components

#1: Protein/peptide Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3433.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.42 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium Citrate, 0.1 M Sodium Hepes, pH 7.5, 20 % isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→39.08 Å / Num. obs: 17613 / % possible obs: 99.98 % / Redundancy: 19.5 % / Biso Wilson estimate: 18.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05849 / Rpim(I) all: 0.01357 / Rrim(I) all: 0.06007 / Net I/σ(I): 28.21
Reflection shellResolution: 1.35→1.398 Å / Redundancy: 18 % / Rmerge(I) obs: 1.61 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 1749 / CC1/2: 0.727 / Rpim(I) all: 0.3888 / Rrim(I) all: 1.656 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B2D

1b2d


Resolution: 1.35→39.08 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1774 876 4.7 %
Rwork0.1608 --
obs-17611 99.98 %
Displacement parametersBiso mean: 26.03 Å2
Refinement stepCycle: LAST / Resolution: 1.35→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms405 0 4 66 475
LS refinement shellResolution: 1.35→1.398 Å
RfactorNum. reflection% reflection
Rfree0.2477 90 4.9 %
Rwork0.2635 1748 -
obs--99.94 %

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