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- PDB-5uqa: Insulin with proline analog FzP at position B28 in the R6 state -

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Basic information

Entry
Database: PDB / ID: 5uqa
TitleInsulin with proline analog FzP at position B28 in the R6 state
Components(Insulin, chain ...) x 2
KeywordsHORMONE / Insulin Hormone
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
ACETONE / PHENOL / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31000248093 Å
AuthorsLieblich, S.A. / Fang, K.Y. / Tirrell, D.A.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: To Be Published
Title: Insulin with proline analog FzP at position B28 in the R6 state
Authors: Lieblich, S.A. / Fang, K.Y. / Tirrell, D.A.
History
DepositionFeb 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin, chain A
B: Insulin, chain B
C: Insulin, chain A
D: Insulin, chain B
E: Insulin, chain A
F: Insulin, chain B
G: Insulin, chain A
H: Insulin, chain B
I: Insulin, chain A
J: Insulin, chain B
K: Insulin, chain A
L: Insulin, chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,06830
Polymers35,01412
Non-polymers1,05518
Water4,324240
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20320 Å2
ΔGint-282 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.936, 61.258, 60.39
Angle α, β, γ (deg.)90.0, 111.694, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Insulin, chain ... , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
Insulin, chain A /


Mass: 2383.698 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide
Insulin, chain B /


Mass: 3451.944 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308

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Non-polymers , 7 types, 258 molecules

#3: Chemical
ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O
#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: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-ACN / ACETONE / Acetone


Mass: 58.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H6O
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.3M Tris pH8, 17mM Zinc Acetate, 1% Phenol, 0.3875M Sodium Citrate, 2.1% Acetone
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Room temp
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2016
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.31→35.5 Å / Num. obs: 74398 / Biso Wilson estimate: 16.1420287196 Å2
Reflection shellResolution: 1.31→1.326 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2587 / % possible all: 97.6

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Processing

Software
NameVersionClassification
phenix.refine1.9_1692+SVNrefinement
PHENIX1.9_1692+SVNrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EV6

1ev6


Resolution: 1.31000248093→35.5276984754 Å / SU ML: 0.137401211013 / Cross valid method: THROUGHOUT / σ(F): 1.33281516724 / Phase error: 17.937196213
RfactorNum. reflection% reflectionSelection details
Rfree0.182111798874 3749 5.03911395468 %RANDOM
Rwork0.152410704119 70649 --
obs0.15392757289 74398 97.4280401247 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.4386011946 Å2
Refinement stepCycle: LAST / Resolution: 1.31000248093→35.5276984754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 0 62 240 2586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005808429587542514
X-RAY DIFFRACTIONf_angle_d1.102876142593395
X-RAY DIFFRACTIONf_chiral_restr0.082681555987386
X-RAY DIFFRACTIONf_plane_restr0.0034482858675433
X-RAY DIFFRACTIONf_dihedral_angle_d12.8255193781859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.32660.2940439031751310.2594284877832587X-RAY DIFFRACTION96.1103253182
1.3266-1.3440.2631246884161370.2320384048522573X-RAY DIFFRACTION96.5443534022
1.344-1.36250.2784987940171320.2263941268952569X-RAY DIFFRACTION96.7406876791
1.3625-1.38190.3047464768141480.2220434293922607X-RAY DIFFRACTION96.9046781569
1.3819-1.40250.2254510080891370.1917912715192597X-RAY DIFFRACTION96.881644224
1.4025-1.42450.254471551621240.1826743781122619X-RAY DIFFRACTION96.7548500882
1.4245-1.44780.2243796011571290.1710696818852529X-RAY DIFFRACTION96.5492190338
1.4478-1.47280.1720754030571110.1590302324192653X-RAY DIFFRACTION96.8126094571
1.4728-1.49960.1643718110621420.1410194301442476X-RAY DIFFRACTION94.3763518385
1.4996-1.52840.1797798704191530.1364537080962557X-RAY DIFFRACTION95.9292035398
1.5284-1.55960.1695396741721290.1282652088492644X-RAY DIFFRACTION97.6064765927
1.5596-1.59350.1688961921031310.1269990256732630X-RAY DIFFRACTION97.8730946473
1.5935-1.63060.1810356209051450.1297713873112614X-RAY DIFFRACTION97.8715856687
1.6306-1.67140.1759639900361470.122812621552614X-RAY DIFFRACTION97.6999292286
1.6714-1.71660.1599686205671210.1198654132832632X-RAY DIFFRACTION98.0413105413
1.7166-1.76710.1635378170121560.1302016325562591X-RAY DIFFRACTION98.0371163455
1.7671-1.82410.1756025970561360.135136265792667X-RAY DIFFRACTION98.1786339755
1.8241-1.88930.1857979627471490.1328030550582550X-RAY DIFFRACTION95.8451704545
1.8893-1.96490.1757663164641570.1351114946352650X-RAY DIFFRACTION98.9076814658
1.9649-2.05430.185434063991250.1425528817562674X-RAY DIFFRACTION99.2553191489
2.0543-2.16260.1544032816561430.1461460113172665X-RAY DIFFRACTION99.1175432404
2.1626-2.29810.1951057056711340.1443637510732646X-RAY DIFFRACTION98.8268752222
2.2981-2.47550.2006725846781510.1567204497352685X-RAY DIFFRACTION98.8842398884
2.4755-2.72450.1883166642031350.1577202148572541X-RAY DIFFRACTION94.927279177
2.7245-3.11860.1723291555271460.1629778878162695X-RAY DIFFRACTION99.2315752707
3.1186-3.92830.17141721410.1515415673342700X-RAY DIFFRACTION99.2662473795
3.9283-35.54080.1755092059691590.1582311908772684X-RAY DIFFRACTION97.4297464016

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