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- PDB-5wdm: An ultra-stable single-chain insulin analog resists thermal inact... -

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Basic information

Entry
Database: PDB / ID: 5wdm
TitleAn ultra-stable single-chain insulin analog resists thermal inactivation and exhibits biological signaling duration equivalent to the native protein
ComponentsSingle-chain insulin analog
KeywordsHORMONE / single chain / hexamer / designed insulin
Function / homology
Function and homology information


cellular response to oxygen-containing compound / 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 / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion ...cellular response to oxygen-containing compound / 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 / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / positive regulation of protein autophosphorylation / 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 / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / Signal attenuation / fatty acid homeostasis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of insulin receptor signaling pathway / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / COPI-mediated anterograde transport / transport vesicle / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / Insulin receptor recycling / 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 nitric-oxide synthase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / regulation of transmembrane transporter activity / positive regulation of glycolytic process / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / endosome lumen / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / positive regulation of cell differentiation / Regulation of insulin secretion / insulin receptor binding / wound healing / negative regulation of protein catabolic process / hormone activity / regulation of synaptic plasticity / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / cognition / glucose metabolic process / vasodilation / insulin receptor signaling pathway / glucose homeostasis / cell-cell signaling / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / positive regulation of cell growth / 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 / 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-like, subunit E / Insulin-like / 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 ...Insulin-like, subunit E / Insulin-like / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsYee, V.C. / Aldabbagh, K. / Peng, Y.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: An ultra-stable single-chain insulin analog resists thermal inactivation and exhibits biological signaling duration equivalent to the native protein.
Authors: Glidden, M.D. / Aldabbagh, K. / Phillips, N.B. / Carr, K. / Chen, Y.S. / Whittaker, J. / Phillips, M. / Wickramasinghe, N.P. / Rege, N. / Swain, M. / Peng, Y. / Yang, Y. / Lawrence, M.C. / ...Authors: Glidden, M.D. / Aldabbagh, K. / Phillips, N.B. / Carr, K. / Chen, Y.S. / Whittaker, J. / Phillips, M. / Wickramasinghe, N.P. / Rege, N. / Swain, M. / Peng, Y. / Yang, Y. / Lawrence, M.C. / Yee, V.C. / Ismail-Beigi, F. / Weiss, M.A.
History
DepositionJul 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single-chain insulin analog
B: Single-chain insulin analog
C: Single-chain insulin analog
D: Single-chain insulin analog
E: Single-chain insulin analog
F: Single-chain insulin analog


Theoretical massNumber of molelcules
Total (without water)39,1766
Polymers39,1766
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-46 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.382, 85.771, 45.696
Angle α, β, γ (deg.)90.000, 110.890, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ASN / End label comp-ID: ASN

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLNGLNchain AAA4 - 574 - 57
2GLNGLNchain BBB4 - 574 - 57
3HISHISchain CCC5 - 575 - 57
4GLNGLNchain DDD4 - 574 - 57
5GLNGLNchain EEE4 - 574 - 57
6HISHISchain FFF5 - 575 - 57

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Components

#1: Protein
Single-chain insulin analog


Mass: 6529.333 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A6XGL2, UniProt: P01308*PLUS
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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 15% PEG 8000, and 0.1 M Tris HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 2.8→38.22 Å / Num. obs: 7718 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 63.13 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.2
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.309

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSOct 15data reduction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GUJ

1guj


Resolution: 2.803→38.22 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 36.59
RfactorNum. reflection% reflection
Rfree0.3142 743 9.66 %
Rwork0.251 --
obs0.2572 7694 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.83 Å2 / Biso mean: 71.1315 Å2 / Biso min: 5.57 Å2
Refinement stepCycle: final / Resolution: 2.803→38.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 0 0 2155
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072212
X-RAY DIFFRACTIONf_angle_d1.0982956
X-RAY DIFFRACTIONf_chiral_restr0.047321
X-RAY DIFFRACTIONf_plane_restr0.005384
X-RAY DIFFRACTIONf_dihedral_angle_d15.202766
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1612X-RAY DIFFRACTION16.249TORSIONAL
12B1612X-RAY DIFFRACTION16.249TORSIONAL
13C1612X-RAY DIFFRACTION16.249TORSIONAL
14D1612X-RAY DIFFRACTION16.249TORSIONAL
15E1612X-RAY DIFFRACTION16.249TORSIONAL
16F1612X-RAY DIFFRACTION16.249TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8029-3.01930.38661760.29321328150497
3.0193-3.3230.36911540.27931393154799
3.323-3.80340.31591250.262114021527100
3.8034-4.79050.30991410.237514051546100
4.7905-38.22380.28381470.23914231570100

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