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- PDB-1b9e: HUMAN INSULIN MUTANT SERB9GLU -

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Basic information

Entry
Database: PDB / ID: 1b9e
TitleHUMAN INSULIN MUTANT SERB9GLU
Components(PROTEIN (INSULIN)) x 2
KeywordsHORMONE/GROWTH FACTOR / HORMONE / FAST-ACTING INSULIN / HORMONE-GROWTH FACTOR COMPLEX
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 / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, D.C. / Zeng, Z.H. / Yao, Z.P. / Li, H.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structure of an insulin dimer in an orthorhombic crystal: the structure analysis of a human insulin mutant (B9 Ser-->Glu).
Authors: Yao, Z.P. / Zeng, Z.H. / Li, H.M. / Zhang, Y. / Feng, Y.M. / Wang, D.C.
#1: Journal: Acta Biochem.Biophys.Sinica / Year: 1996
Title: Protein Engineering of Insulin: [B9 Glutamic Acid Human Insulin]
Authors: Liu, B. / Liang, Z.H. / Tang, Y.H. / Zhang, X.T. / Zhu, S.Q. / Feng, Y.M.
History
DepositionNov 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (INSULIN)
B: PROTEIN (INSULIN)
C: PROTEIN (INSULIN)
D: PROTEIN (INSULIN)


Theoretical massNumber of molelcules
Total (without water)11,7194
Polymers11,7194
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-37 kcal/mol
Surface area6910 Å2
MethodPISA
2
A: PROTEIN (INSULIN)
B: PROTEIN (INSULIN)

C: PROTEIN (INSULIN)
D: PROTEIN (INSULIN)


Theoretical massNumber of molelcules
Total (without water)11,7194
Polymers11,7194
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area3740 Å2
ΔGint-39 kcal/mol
Surface area6880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.560, 46.390, 51.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.990949, -0.078334, 0.109014), (-0.079595, 0.996801, -0.007253), (-0.108098, -0.015864, -0.994014)
Vector: 20.6941, 0.8964, 1.0884)

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Components

#1: Protein/peptide PROTEIN (INSULIN)


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


Mass: 3475.989 Da / Num. of mol.: 2 / Mutation: S9E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.3 Å3/Da / Density % sol: 46.19 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 3.5
Details: HANGING DROP, 0.1M AMMONIA CITRATE, 0.12% CHROMIUM DICHLORIDE (W/V), 10% ACETONE (V/V), 4% DIMETHYL FORMAMIDE (V/V), PH 3.8, pH 3.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 3.8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.03 M1dropHCl
30.1 Mammonium citrate1reservoir
40.12 %1reservoirCrCl2
510 %(v/v)acetone1reservoir
64 %dimethylformamide1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 3, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→27.3 Å / Num. obs: 3538 / % possible obs: 88.43 % / Redundancy: 3.83 % / Biso Wilson estimate: 28.83 Å2 / Rmerge(I) obs: 0.0854 / Net I/σ(I): 15.98
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.07 / % possible all: 88.4
Reflection
*PLUS
Num. measured all: 13549
Reflection shell
*PLUS
% possible obs: 87.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZN INSULIN DIMER

Resolution: 2.5→6.5 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.264 156 5 %RANDOM
Rwork0.165 ---
obs-3170 84.7 %-
Displacement parametersBiso mean: 24.35 Å2
Refinement stepCycle: LAST / Resolution: 2.5→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 0 0 45 861
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.637
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.48
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.422
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.58 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.304 15 5 %
Rwork0.244 315 -
obs--84.7 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6.5 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.48
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.422
LS refinement shell
*PLUS
Rfactor Rfree: 0.304 / % reflection Rfree: 5 % / Rfactor Rwork: 0.244

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