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- PDB-4gbi: Crystal structure of aspart insulin at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 4gbi
TitleCrystal structure of aspart insulin at pH 6.5
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / T3R3
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.502 Å
AuthorsLima, L.M.T.R. / Favero-Retto, M.P. / Palmieri, L.C.
CitationJournal: Biophys.Chem. / Year: 2013
Title: A T3R3 hexamer of the human insulin variant B28Asp.
Authors: Palmieri, L.C. / Favero-Retto, M.P. / Lourenco, D. / Lima, L.M.
History
DepositionJul 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Aug 22, 2018Group: Data collection / Database references / Structure summary
Category: entity / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_mutation / _struct_ref_seq_dif.details
Revision 1.3Sep 13, 2023Group: 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,08910
Polymers11,6714
Non-polymers4186
Water362
1
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)36,26830
Polymers35,01412
Non-polymers1,25418
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area23980 Å2
ΔGint-922 kcal/mol
Surface area10230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.290, 78.290, 36.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11D-101-

ZN

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: UNP residues 90-110 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3451.926 Da / Num. of mol.: 2 / Fragment: UNP residues 25-54 / Source method: isolated from a natural source / Details: P28D Aspart variant / Source: (natural) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-CRS / M-CRESOL / M-Cresol


Mass: 108.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.87 Å3/Da / Density % sol: 34.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 uL mother liquor (0.1 M MES, pH 6.5, 1.6 M magnesium sulfate heptahydrate) + 2 uL protein (aspart insulin, 100 U/mL), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.461
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 17, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.461 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.68
11K, H, -L20.32
ReflectionResolution: 2.502→39.145 Å / Num. all: 2607 / Num. obs: 2607 / % possible obs: 89.3 % / Redundancy: 1.7 % / Rsym value: 0.076 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.502-2.641.60.4716363960.4792.5
2.64-2.81.60.3781.66053670.37890.6
2.8-2.991.70.2292.95593350.22990.1
2.99-3.231.70.1525.15433200.15289.6
3.23-3.541.70.1235.44802890.12392.3
3.54-3.951.70.0710.14602720.0787.2
3.95-4.561.70.04216.93792250.04289.6
4.56-5.591.70.03817.33331910.03888
5.59-7.911.70.043172651530.04388.4
7.91-24.9681.80.04113.6109590.04163.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZEH

1zeh


Resolution: 2.502→39.145 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.1777 / WRfactor Rwork: 0.1234 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8539 / SU B: 12.257 / SU ML: 0.232 / SU Rfree: 0.0668 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 232 8.9 %RANDOM
Rwork0.1525 ---
obs0.1578 2602 89.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 106.16 Å2 / Biso mean: 52.5013 Å2 / Biso min: 24.73 Å2
Baniso -1Baniso -2Baniso -3
1--8.33 Å2-0 Å2-0 Å2
2---8.33 Å2-0 Å2
3---16.67 Å2
Refinement stepCycle: LAST / Resolution: 2.502→39.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 20 2 825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02839
X-RAY DIFFRACTIONr_bond_other_d0.0020.02541
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.961134
X-RAY DIFFRACTIONr_angle_other_deg1.1253.0191296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.252597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.21124.76242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.62315131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.847152
X-RAY DIFFRACTIONr_chiral_restr0.110.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02183
LS refinement shellResolution: 2.502→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 17 -
Rwork0.136 179 -
all-196 -
obs--90.74 %

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