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- PDB-6gv0: Insulin glulisine -

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Basic information

Entry
Database: PDB / ID: 6gv0
TitleInsulin glulisine
Components(Insulin) x 2
KeywordsHORMONE / Insulin glulisine insulin analogue
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 / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / nitric oxide-cGMP-mediated signaling / IRS activation / Insulin processing / 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 / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / nitric oxide-cGMP-mediated signaling / 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 / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / positive regulation of nitric oxide mediated signal transduction / fatty acid homeostasis / regulation of protein localization to plasma membrane / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic 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 / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / activation of protein kinase B activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / Regulation of insulin secretion / acute-phase response / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / positive regulation of nitric-oxide synthase activity / positive regulation of cell differentiation / negative regulation of proteolysis / regulation of transmembrane transporter activity / wound healing / regulation of synaptic plasticity / insulin receptor binding / negative regulation of protein catabolic process / hormone activity / cognition / positive regulation of neuron projection development / Golgi lumen / positive regulation of protein localization to nucleus / vasodilation / glucose metabolic process / regulation of protein localization / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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 / regulation of DNA-templated transcription / positive regulation of gene expression / 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
FORMIC ACID / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsChayen, N.E. / Helliwell, J.R. / Solomon-Gamsu, H.V. / Govada, L. / Morgan, M. / Gillis, R.B. / Adams, G.
CitationJournal: Sci Rep / Year: 2021
Title: Analysis of insulin glulisine at the molecular level by X-ray crystallography and biophysical techniques.
Authors: Gillis, R.B. / Solomon, H.V. / Govada, L. / Oldham, N.J. / Dinu, V. / Jiwani, S.I. / Gyasi-Antwi, P. / Coffey, F. / Meal, A. / Morgan, P.S. / Harding, S.E. / Helliwell, J.R. / Chayen, N.E. / Adams, G.G.
History
DepositionJun 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_related_exp_data_set / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Insulin
B: Insulin
I: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8888
Polymers11,6654
Non-polymers2234
Water1,36976
1
G: Insulin
B: Insulin
I: Insulin
D: Insulin
hetero molecules

G: Insulin
B: Insulin
I: Insulin
D: Insulin
hetero molecules

G: Insulin
B: Insulin
I: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,66524
Polymers34,99612
Non-polymers66912
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 area20950 Å2
ΔGint-265 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.440, 82.440, 33.650
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

31B-219-

HOH

41D-225-

HOH

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Components

#1: Protein/peptide Insulin /


Mass: 2383.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P01308
#2: Protein/peptide Insulin /


Mass: 3448.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P01308
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 1.96 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2-0.4M Mg-formate 0.1M BisTris buffer / PH range: 5.5-6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.26→41.22 Å / Num. obs: 22986 / % possible obs: 100 % / Redundancy: 4 % / Net I/σ(I): 27
Reflection shellResolution: 1.26→1.28 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3228 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ey9

4ey9


Resolution: 1.26→24.486 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 20.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1518 1130 4.92 %RANDOM
Rwork0.1279 ---
obs0.1292 22984 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.26→24.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms796 0 8 76 880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023883
X-RAY DIFFRACTIONf_angle_d1.8871197
X-RAY DIFFRACTIONf_dihedral_angle_d15.369323
X-RAY DIFFRACTIONf_chiral_restr0.125133
X-RAY DIFFRACTIONf_plane_restr0.012155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2601-1.31740.31291330.26592723X-RAY DIFFRACTION99
1.3174-1.38690.23381430.1812730X-RAY DIFFRACTION99
1.3869-1.47370.19071440.13272735X-RAY DIFFRACTION100
1.4737-1.58750.15051150.10062756X-RAY DIFFRACTION100
1.5875-1.74720.1321550.09372715X-RAY DIFFRACTION100
1.7472-20.12891300.10032745X-RAY DIFFRACTION100
2-2.51930.14641680.11872715X-RAY DIFFRACTION100
2.5193-24.49060.15211420.13862735X-RAY DIFFRACTION100

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