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- PDB-4cy7: Crystal structure of human insulin analogue (NMe-AlaB8)-insulin c... -

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Basic information

Entry
Database: PDB / ID: 4cy7
TitleCrystal structure of human insulin analogue (NMe-AlaB8)-insulin crystal form II
Components
  • INSULIN A CHAIN
  • INSULIN B CHAIN
KeywordsHORMONE / DIABETES
Function / homology
Function and homology information


negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of feeding behavior / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / 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 feeding behavior / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / 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 / 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 / activation of protein kinase B activity / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / regulation of protein localization to plasma membrane / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / transport vesicle / nitric oxide-cGMP-mediated signaling / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / endosome lumen / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / negative regulation of protein catabolic process / hormone activity / positive regulation of neuron projection development / regulation of synaptic plasticity / 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 / 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 / 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
ACETATE ION / Insulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKosinova, L. / Veverka, V. / Novotna, P. / Collinsova, M. / Urbanova, M. / Jiracek, J. / Moody, N.R. / Turkenburg, J.P. / Brzozowski, A.M. / Zakova, L.
CitationJournal: Biochemistry / Year: 2014
Title: An Insight Into Structural and Biological Relevance of the T/R Transition of the B-Chain N-Terminus in Human Insulin.
Authors: Kosinova, L. / Veverka, V. / Novotna, P. / Collinsova, M. / Urbanova, M. / Moody, N.R. / Turkenburg, J.P. / Jiracek, J. / Brzozowski, A.M. / Zakova, L.
History
DepositionApr 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 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 A CHAIN
B: INSULIN B CHAIN
C: INSULIN A CHAIN
D: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8476
Polymers11,6914
Non-polymers1552
Water2,720151
1
A: INSULIN A CHAIN
B: INSULIN B CHAIN
hetero molecules

C: INSULIN A CHAIN
D: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8476
Polymers11,6914
Non-polymers1552
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area3590 Å2
ΔGint-50 kcal/mol
Surface area7010 Å2
MethodPISA
2
C: INSULIN A CHAIN
D: INSULIN B CHAIN
hetero molecules

A: INSULIN A CHAIN
B: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8476
Polymers11,6914
Non-polymers1552
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
MethodPISA
Unit cell
Length a, b, c (Å)44.300, 46.190, 51.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide INSULIN A CHAIN


Mass: 2383.698 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308
#2: Protein/peptide INSULIN B CHAIN


Mass: 3462.006 Da / Num. of mol.: 2 / Mutation: YES / Source method: obtained synthetically
Details: GLY8 IS SUBSTITUTED TO ALA AND N-PEPTIDE ATOM OF ALA8 IS METHYLATED
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.36 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 4 / Details: 0.0375 M NA2SO4, PH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.4→32 Å / Num. obs: 21186 / % possible obs: 98.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.4 / Net I/σ(I): 22.3
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.7 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MSO

1mso


Resolution: 1.4→31.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.063 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY RESIDUES B29-B30 ARE DISORDERED AND NOT MODELLED. THE TWO MOLECULES IN THE ASYMMETRIC UNIT DO NOT FORM ANY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY RESIDUES B29-B30 ARE DISORDERED AND NOT MODELLED. THE TWO MOLECULES IN THE ASYMMETRIC UNIT DO NOT FORM ANY PHYSIOLOGICAL DIMERS. THE PHYSIOLOGICAL DIMERS ARE FORMED BY CRYSTALLOGRAPHIC SYMMETRY. THE AB MOLECULE FORM DIMER WITH CRYSTALLOGRAPHIC SYMMETRY RELATED CD MOLECULE BY - XPLUSHALF,-Y,ZPLUSHALF THE CD MOLECULE FORM DIMER WITH CRYSTALLOGRAPHIC SYMMETRY RELATED AB MOLECULE BY THE SAME SYM OPERATOR
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 1086 5.1 %RANDOM
Rwork0.17958 ---
obs0.1806 20063 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2---0.31 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.4→31.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms786 0 9 151 946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.019848
X-RAY DIFFRACTIONr_bond_other_d0.0010.02758
X-RAY DIFFRACTIONr_angle_refined_deg2.5371.9521157
X-RAY DIFFRACTIONr_angle_other_deg1.24931724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9495103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0423.84639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16615125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.152153
X-RAY DIFFRACTIONr_chiral_restr0.2190.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02213
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9441.611416
X-RAY DIFFRACTIONr_mcbond_other1.8811.594414
X-RAY DIFFRACTIONr_mcangle_it2.652.38517
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6892432
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.402→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 72 -
Rwork0.253 1451 -
obs--98.07 %

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