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- PDB-7qac: The T2 structure of polycrystalline cubic human insulin -

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Basic information

Entry
Database: PDB / ID: 7qac
TitleThe T2 structure of polycrystalline cubic human insulin
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / cubic / human / insulin / T2
Function / homology
Function and homology information


negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / positive regulation of insulin receptor signaling pathway / negative regulation of respiratory burst involved in inflammatory response / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of D-glucose import across plasma membrane / positive regulation of protein secretion / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / regulation of synaptic plasticity / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / receptor ligand activity / 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)
MethodPOWDER DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsKaravassili, F. / Triandafillidis, D.P. / Valmas, A. / Spiliopoulou, M. / Fili, S. / Kontou, P. / Bowler, M.W. / Von Dreele, R.B. / Fitch, A. / Margiolaki, I.
Funding supportEuropean Union, Greece, 2items
OrganizationGrant numberCountry
General Secretariat for Research and Technology (GSRT)European Union
Hellenic Foundation for Research and Innovation (HFRI)3051 Greece
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: The T 2 structure of polycrystalline cubic human insulin.
Authors: Triandafillidis, D.P. / Karavassili, F. / Spiliopoulou, M. / Valmas, A. / Athanasiadou, M. / Nikolaras, G. / Fili, S. / Kontou, P. / Bowler, M.W. / Chasapis, C.T. / Von Dreele, R.B. / Fitch, ...Authors: Triandafillidis, D.P. / Karavassili, F. / Spiliopoulou, M. / Valmas, A. / Athanasiadou, M. / Nikolaras, G. / Fili, S. / Kontou, P. / Bowler, M.W. / Chasapis, C.T. / Von Dreele, R.B. / Fitch, A.N. / Margiolaki, I.
History
DepositionNov 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Aug 16, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.accession_code
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 1 REMARK 250 REFINEMENT. REMARK 250 PROGRAM : GSAS REMARK 250 AUTHORS : LARSON & VON DREELE REMARK ... REMARK 250 REFINEMENT. REMARK 250 PROGRAM : GSAS REMARK 250 AUTHORS : LARSON & VON DREELE REMARK 250 REMARK 250 DATA USED IN REFINEMENT REMARK 250 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 250 RESOLUTION RANGE LOW (ANGSTROMS) : 39.43 REMARK 250 POWDER DIFFRACTION DATA. REMARK 250 REMARK 250 FIT TO DATA USED IN REFINEMENT REMARK 250 NUMBER OF POWDER PATTERNS : 6 REMARK 250 PROFILE R VALUES (%) : 7.70 11.54 12.16 8.80 7.61 2.12 REMARK 250 WEIGHTED PROFILE R VALUES (%) : 10.98 14.75 15.17 12.12 10.95 3.34 REMARK 250 F**2 R VALUES (%) : 42.02 38.68 44.09 38.89 35.52 24.00 REMARK 250 NUMBERS OF POWDER PATTERN POINTS : 8256 7003 7002 7002 7002 4740 REMARK 250 NUMBERS OF REFLECTIONS : 3816 2345 2349 2345 2305 4998 REMARK 250 TOTAL NUMBER OF POWDER POINTS : 41005 REMARK 250 REMARK 250 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 250 PROTEIN ATOMS : REMARK 250 NUCLEIC ACID ATOMS : REMARK 250 HETEROGEN ATOMS : REMARK 250 SOLVENT ATOMS : REMARK 250 REMARK 250 MODEL REFINEMENT. REMARK 250 NUMBER OF LEAST-SQUARES PARAMETERS : 786 REMARK 250 NUMBER OF RESTRAINTS : 1951 REMARK 250 LEAST-SQUARES MATRIX BAND WIDTH : 50 REMARK 250 MARQUARDT COEFFICIENT : 8.30 REMARK 250 REMARK 250 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. NUMBER. REMARK 250 INTERATOMIC DISTANCES (A) :0.015 506 REMARK 250 BOND ANGLES (DEG) : 1.43 702 REMARK 250 CHIRAL VOLUMES (A**3) :0.036 52 REMARK 250 TORSION ANGLE RESTRAINTS (E) : 1.00 98 REMARK 250 DISTANCES FROM RESTRAINT PLANES (A) :0.020 149 REMARK 250 TORSION PSEUDOPOTENTIAL RESTRAINTS (E) : 3.84 68 REMARK 250 ANTI-BUMPING DISTANCE RESTRAINTS (A) :0.123 186 REMARK 250 HYDROGEN BOND DISTANCE RESTRAINTS (A) :0.293 212

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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


Theoretical massNumber of molelcules
Total (without water)5,8182
Polymers5,8182
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-13 kcal/mol
Surface area3910 Å2
Components on special symmetry positions
IDModelComponents
11B-120-

HOH

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Components

#1: Protein/peptide Insulin A chain


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: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3433.953 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: POWDER DIFFRACTION / Number of used crystals: 6

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.5164.98
23.5164.98
33.5164.98
43.5164.98
53.5164.98
63.5164.98
Crystal grow
Temperature (K)Crystal-IDMethodpHDetailsPH range
2931batch mode8.5613.494 mg/ml insulin, 0.818 mM zinc acetate, 10.563 mM sodium thiocyanate, 0.4 M sodium potassium phosphate (Na2HPO4/KH2PO4)8.69 - 8.43
2932batch mode7.8813.494 mg/ml insulin, 0.818 mM zinc acetate, 10.563 mM sodium thiocyanate, 0.4 M sodium potassium phosphate (Na2HPO4/KH2PO4)8.06 - 7.70
2933batch mode8.0213.494 mg/ml insulin, 0.818 mM zinc acetate, 10.563 mM sodium thiocyanate, 0.4 M sodium potassium phosphate (Na2HPO4/KH2PO4)8.30 - 7.74
2934batch mode8.1713.494 mg/ml insulin, 0.818 mM zinc acetate, 10.563 mM sodium thiocyanate, 0.4 M sodium potassium phosphate (Na2HPO4/KH2PO4)8.50 - 7.84
2935batch mode8.2613.494 mg/ml insulin, 0.818 mM zinc acetate, 10.563 mM sodium thiocyanate, 0.4 M sodium potassium phosphate (Na2HPO4/KH2PO4)8.70 - 7.82
2936batch mode8.1713.494 mg/ml insulin, 0.818 mM zinc acetate, 10.563 mM sodium thiocyanate, 0.4 M sodium potassium phosphate (Na2HPO4/KH2PO4)8.50 - 7.84

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22932N
32933N
42934N
52935N
62936N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)Take-off angle (°)TargetVoltage (kV)
SYNCHROTRONESRF ID2211.29974
SYNCHROTRONESRF ID2221.299868
SYNCHROTRONESRF ID2231.299995
SYNCHROTRONESRF ID2241.299995
SYNCHROTRONESRF ID2251.299995
SEALED TUBEMALVERN PANALYTICAL EMPYREAN TUBE61.540598, 1.54426040Cu45
Detector
TypeIDDetectorDateDetails
Cyberstar LaBr31SCINTILLATIONDec 8, 20159 Si(111) analyzer crystals with 9 detectors
Cyberstar LaBr32SCINTILLATIONDec 14, 20169 Si(111) analyzer crystals with 9 detectors
Cyberstar LaBr33SCINTILLATIONDec 14, 20169 Si(111) analyzer crystals with 9 detectors
Cyberstar LaBr34SCINTILLATIONDec 14, 20169 Si(111) analyzer crystals with 9 detectors
Cyberstar LaBr35SCINTILLATIONDec 14, 20169 Si(111) analyzer crystals with 9 detectors
Malvern Panalytical PIXcel 1D6PIXELDec 11, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength (Å)Wavelength-IDWavelength
1SINGLE WAVELENGTHMx-ray1.299741
2SINGLE WAVELENGTHMx-ray1.2998682
3SINGLE WAVELENGTHMx-ray1.2999953
4SINGLE WAVELENGTHMx-ray1.2999954
5SINGLE WAVELENGTHMx-ray1.2999955
6SINGLE WAVELENGTHMx-ray61.540598,1.544260
Radiation wavelength
IDWavelength (Å)Relative weight
11.299741
21.2998681
31.2999951
41.2999951
51.2999951
61.5405981
71.544260.5
Reflection
Resolution (Å)Num. allNum. obsObserved criterion σ(I)Entry-IDDiffraction-ID
2.288-39.433816381627QAC1
2.705-39.432345234527QAC2
2.702-39.432349234927QAC3
2.705-39.432345234527QAC4
2.718-39.432305230527QAC5
2.643-55.7634998499827QAC6

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Processing

Software
NameClassification
GSASrefinement
PRODDdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9INS

9ins


Resolution: 2.29→39 Å / Goodness of fit all: 2.06 / Num. parameters: 786 / Num. restraintsaints: 1951 / % reflection obs: 100 % / WRfactor all: 0.0694 / Cross valid method: NONE / Pd Marquardt correlation coeff: 8.3 / Pd LS matrix band width: 50 / Pd num. of points: 41005 / Pd num. of powder patterns: 6
Refinement stepCycle: LAST / Resolution: 2.288→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms405 0 0 62 467
Refine LS restraints
Refine-IDTypeDev idealNumber
POWDER DIFFRACTIONbond_d0.015506
POWDER DIFFRACTIONangle_d1.43702
POWDER DIFFRACTIONchiral0.03652
POWDER DIFFRACTIONsingtor198
POWDER DIFFRACTIONplanar_d0.02149
POWDER DIFFRACTIONmulttor3.8468
POWDER DIFFRACTIONhydrog_d0.293212

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