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- PDB-5usp: Insulin with proline analog Pip at position B28 in the T2 state -

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Basic information

Entry
Database: PDB / ID: 5usp
TitleInsulin with proline analog Pip at position B28 in the T2 state
Components
  • Insulin Chain A
  • Insulin Chain B
KeywordsHORMONE / Insulin
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 / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / 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 / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / 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 / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / Golgi lumen / vasodilation / 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 / molecular replacement / Resolution: 1.174 Å
AuthorsLieblich, S.A. / Fang, K.Y. / Tirrell, D.A.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: To Be Published
Title: Insulin with proline analog Pip at position B28 in the T2 state
Authors: Lieblich, S.A. / Fang, K.Y. / Tirrell, D.A.
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin Chain A
B: Insulin Chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8553
Polymers5,8322
Non-polymers231
Water1,27971
1
A: Insulin Chain A
B: Insulin Chain B
hetero molecules

A: Insulin Chain A
B: Insulin Chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7096
Polymers11,6634
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_455-x-1/2,y,-z1
Buried area4070 Å2
ΔGint-37 kcal/mol
Surface area5400 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-15 kcal/mol
Surface area3280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.047, 78.047, 78.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-101-

NA

21B-227-

HOH

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Components

#1: Protein/peptide Insulin Chain A


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: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide Insulin Chain B


Mass: 3447.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.4 Å3/Da / Density % sol: 63.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 275mM Sodium Citrate, 100mM Hepes pH 8.0 / Temp details: Room tempreature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2016
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.17→39.02 Å / Num. obs: 26487 / % possible obs: 99.7 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.02 / Rrim(I) all: 0.066 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.17-1.195.40.756211980.6690.3420.83593.3
6.43-39.0210.50.0560.9940.0190.05999.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.17 Å39.02 Å
Translation1.17 Å39.02 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T2A

3t2a


Resolution: 1.174→39.02 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.33
RfactorNum. reflection% reflection
Rfree0.1526 1307 4.93 %
Rwork0.1385 --
obs0.1391 26485 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.01 Å2 / Biso mean: 22.126 Å2 / Biso min: 9.9 Å2
Refinement stepCycle: final / Resolution: 1.174→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms390 0 1 71 462
Biso mean--65.8 39.82 -
Num. residues----50
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008436
X-RAY DIFFRACTIONf_angle_d1.07596
X-RAY DIFFRACTIONf_chiral_restr0.0569
X-RAY DIFFRACTIONf_plane_restr0.00476
X-RAY DIFFRACTIONf_dihedral_angle_d14.002161
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1737-1.22070.22331560.2092687284398
1.2207-1.27620.16771350.168627962931100
1.2762-1.34350.16451510.146827542905100
1.3435-1.42770.14351510.126727932944100
1.4277-1.53790.12781300.110828052935100
1.5379-1.69270.13871380.111828202958100
1.6927-1.93760.14161640.116427692933100
1.9376-2.44120.16531200.136128502970100
2.4412-39.0450.15071620.148729043066100

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