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- PDB-6h3m: The crystal structure of a human seleno-insulin analog -

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Basic information

Entry
Database: PDB / ID: 6h3m
TitleThe crystal structure of a human seleno-insulin analog
Components(Insulin) x 2
KeywordsHORMONE / Insulin / selenocysteine / analog / human
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 / negative regulation of respiratory burst involved in inflammatory response / activation of protein kinase B activity / 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 / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / 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 / 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 / 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 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 / SAD / Resolution: 1.821 Å
AuthorsLansky, S. / Weil-Ktorza, O. / Metanis, N. / Shoham, G.
CitationJournal: Chemistry / Year: 2019
Title: Substitution of an Internal Disulfide Bridge with a Diselenide Enhances both Foldability and Stability of Human Insulin.
Authors: Weil-Ktorza, O. / Rege, N. / Lansky, S. / Shalev, D.E. / Shoham, G. / Weiss, M.A. / Metanis, N.
History
DepositionJul 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
F: Insulin
H: Insulin
J: Insulin
L: Insulin
E: Insulin
G: Insulin
I: Insulin
K: Insulin
N: Insulin
P: Insulin
Q: Insulin
R: Insulin


Theoretical massNumber of molelcules
Total (without water)47,29216
Polymers47,29216
Non-polymers00
Water2,522140
1
A: Insulin
J: Insulin


Theoretical massNumber of molelcules
Total (without water)5,9112
Polymers5,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Insulin
E: Insulin


Theoretical massNumber of molelcules
Total (without water)5,9112
Polymers5,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Insulin
D: Insulin


Theoretical massNumber of molelcules
Total (without water)5,9112
Polymers5,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Insulin
K: Insulin


Theoretical massNumber of molelcules
Total (without water)5,9112
Polymers5,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
H: Insulin
G: Insulin


Theoretical massNumber of molelcules
Total (without water)5,9112
Polymers5,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
L: Insulin
I: Insulin


Theoretical massNumber of molelcules
Total (without water)5,9112
Polymers5,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
N: Insulin
Q: Insulin


Theoretical massNumber of molelcules
Total (without water)5,9112
Polymers5,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
P: Insulin
R: Insulin


Theoretical massNumber of molelcules
Total (without water)5,9112
Polymers5,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.011, 42.344, 61.453
Angle α, β, γ (deg.)100.58, 98.70, 117.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
Insulin


Mass: 2477.488 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide
Insulin


Mass: 3433.953 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
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: 1.8 Å3/Da / Density % sol: 31.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.8 M NaCl, 35 mM NaCitrate, 0.5 mM ZnAcetate, 0.3 M Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 28501 / % possible obs: 96.2 % / Redundancy: 5.22 % / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.67
Reflection shellResolution: 1.82→1.93 Å / Redundancy: 5.04 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 4398 / CC1/2: 0.84 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.821→35.982 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 1422 4.99 %
Rwork0.1896 --
obs0.1915 28475 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.821→35.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 0 140 3315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133277
X-RAY DIFFRACTIONf_angle_d1.4914433
X-RAY DIFFRACTIONf_dihedral_angle_d12.8071908
X-RAY DIFFRACTIONf_chiral_restr0.089486
X-RAY DIFFRACTIONf_plane_restr0.009566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8213-1.88640.34071290.28632475X-RAY DIFFRACTION88
1.8864-1.9620.29971420.25732696X-RAY DIFFRACTION96
1.962-2.05130.28121430.2232722X-RAY DIFFRACTION96
2.0513-2.15940.25861400.20462683X-RAY DIFFRACTION96
2.1594-2.29470.27091450.19242747X-RAY DIFFRACTION97
2.2947-2.47180.22421430.19492722X-RAY DIFFRACTION97
2.4718-2.72050.27571420.1942705X-RAY DIFFRACTION97
2.7205-3.11390.23881450.19442749X-RAY DIFFRACTION98
3.1139-3.92240.19791470.1732792X-RAY DIFFRACTION99
3.9224-35.98920.20051460.17432762X-RAY DIFFRACTION99

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