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- PDB-4efx: Highly biologically active insulin with additional disulfide bond -

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Basic information

Entry
Database: PDB / ID: 4efx
TitleHighly biologically active insulin with additional disulfide bond
Components(Insulin) x 2
KeywordsHORMONE
Function / homology
Function and homology information


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 ...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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsNorrman, M. / Vinther, T.N.
CitationJournal: Protein Sci. / Year: 2013
Title: Insulin analog with additional disulfide bond has increased stability and preserved activity.
Authors: Vinther, T.N. / Norrman, M. / Ribel, U. / Huus, K. / Schlein, M. / Steensgaard, D.B. / Pedersen, T.A. / Pettersson, I. / Ludvigsen, S. / Kjeldsen, T. / Jensen, K.J. / Hubalek, F.
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 20, 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: Insulin
B: Insulin
C: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2366
Polymers11,1054
Non-polymers1312
Water59433
1
A: Insulin


Theoretical massNumber of molelcules
Total (without water)2,3741
Polymers2,3741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2442
Polymers3,1791
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Insulin


Theoretical massNumber of molelcules
Total (without water)2,3741
Polymers2,3741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2442
Polymers3,1791
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Insulin
B: Insulin
C: Insulin
D: Insulin
hetero molecules

A: Insulin
B: Insulin
C: Insulin
D: Insulin
hetero molecules

A: Insulin
B: Insulin
C: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,70718
Polymers33,31412
Non-polymers3926
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17610 Å2
ΔGint-161 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.367, 79.367, 34.228
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-101-

ZN

21D-101-

ZN

31D-209-

HOH

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Components

#1: Protein/peptide Insulin / Insulin A chain


Mass: 2373.683 Da / Num. of mol.: 2 / Mutation: A10C, B4C
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 / Insulin B chain


Mass: 3178.683 Da / Num. of mol.: 2
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.87 Å3/Da / Density % sol: 34.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15M DL-Malic Acid, 20% w/v PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 5517 / Num. obs: 5517 / % possible obs: 97 % / Redundancy: 5.3 % / Rsym value: 0.049 / Net I/σ(I): 31.6
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 205 / Rsym value: 0.202 / % possible all: 57.4

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0119refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house monomer model

Resolution: 1.98→39.69 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.871 / SU B: 9.035 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.278 289 5.2 %RANDOM
Rwork0.207 ---
obs0.21 5284 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.98→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 0 2 33 794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02787
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.9441072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.754596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.55824.59537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48615114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.726151
X-RAY DIFFRACTIONr_chiral_restr0.1230.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02599
LS refinement shellResolution: 1.978→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 20 -
Rwork0.293 356 -
obs--90.17 %

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