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- PDB-1qiy: HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR COMPLEXED ... -

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Basic information

Entry
Database: PDB / ID: 1qiy
TitleHUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR COMPLEXED WITH PHENOL
Components
  • INSULIN A CHAIN
  • INSULIN B CHAIN
KeywordsHORMONE / GLUCOSE METABOLISM / DIABETES / INSULIN MUTANT
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / 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 / positive regulation of protein autophosphorylation / 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 / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / Signal attenuation / fatty acid homeostasis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of insulin receptor signaling pathway / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / COPI-mediated anterograde transport / transport vesicle / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / Insulin receptor recycling / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of nitric-oxide synthase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / regulation of transmembrane transporter activity / positive regulation of glycolytic process / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / endosome lumen / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / positive regulation of cell differentiation / Regulation of insulin secretion / insulin receptor binding / wound healing / negative regulation of protein catabolic process / hormone activity / regulation of synaptic plasticity / positive regulation of neuron projection development / 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 / protease binding / positive regulation of cell growth / 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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTang, L. / Whittingham, J.L. / Verma, C.S. / Caves, L.S.D. / Dodson, G.G.
CitationJournal: Biochemistry / Year: 1999
Title: Structural Consequences of the B5 Histidine --> Tyrosine Mutation in Human Insulin Characterized by X-Ray Crystallography and Conformational Analysis.
Authors: Tang, L. / Whittingham, J.L. / Verma, C.S. / Caves, L.S.D. / Dodson, G.G.
History
DepositionJun 18, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 1, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
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_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_asym_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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
E: INSULIN A CHAIN
F: INSULIN B CHAIN
G: INSULIN A CHAIN
H: INSULIN B CHAIN
I: INSULIN A CHAIN
J: INSULIN B CHAIN
K: INSULIN A CHAIN
L: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,82222
Polymers35,05612
Non-polymers76610
Water1,63991
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19990 Å2
ΔGint-238.9 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.100, 62.080, 48.350
Angle α, β, γ (deg.)90.00, 109.87, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE ASYMMETRIC UNIT CONTAINS A 2ZN INSULIN HEXAMER,CONSISTING OF THREE EQUIVALENT DIMERS RELATED BY A NON-CRYSTALLOGRAPHIC 3-FOLD SYMMETRY AXIS. THE ZINC AND CHLORIDE IONS ARE LOCATED ON THIS 3-FOLD AXIS.

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Components

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Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
INSULIN A CHAIN / B5TYR_R6_PHN


Mass: 2383.698 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308
#2: Protein/peptide
INSULIN B CHAIN / B5TYR_R6_PHN


Mass: 3458.980 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308

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Non-polymers , 4 types, 101 molecules

#3: Chemical
ChemComp-IPH / 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


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


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN B, HIS 29 TO TYR ENGINEERED RESIDUE IN CHAIN D, HIS 29 TO TYR ...ENGINEERED RESIDUE IN CHAIN B, HIS 29 TO TYR ENGINEERED RESIDUE IN CHAIN D, HIS 29 TO TYR ENGINEERED RESIDUE IN CHAIN F, HIS 29 TO TYR ENGINEERED RESIDUE IN CHAIN H, HIS 29 TO TYR ENGINEERED RESIDUE IN CHAIN J, HIS 29 TO TYR ENGINEERED RESIDUE IN CHAIN L, HIS 29 TO TYR
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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.8
Details: CRYSTALLISATION IN BATCH, 10 MG B5 TYR INSULIN DISSOLVED IN 2 ML 0.02M HCL. TO THIS ADDED 0.1 ML 0.12M ZINC ACETATE, 1.5 ML 0.2 M TRI-SODIUM CITRATE, 0.4 ML 2.5% (AQ.) PHENOL AND 120 MG NACL. ...Details: CRYSTALLISATION IN BATCH, 10 MG B5 TYR INSULIN DISSOLVED IN 2 ML 0.02M HCL. TO THIS ADDED 0.1 ML 0.12M ZINC ACETATE, 1.5 ML 0.2 M TRI-SODIUM CITRATE, 0.4 ML 2.5% (AQ.) PHENOL AND 120 MG NACL. PH ADJUSTED TO 6.5-7.8 .
Crystal grow
*PLUS
Method: batch method / PH range low: 7.8 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
20.02 M112 mlHCl
30.12 Mzinc acetate110.1 ml
40.2 Mtrisodium citrate111.5 ml
52.5 %phenol110.4 ml
1insulin11
611NaCl

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MULTIWIRE SIEMENS / Detector: AREA DETECTOR / Date: Jan 15, 1993
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→36.8 Å / Num. obs: 13832 / % possible obs: 92 % / Redundancy: 1.8 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 10
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 5 / % possible all: 95.5
Reflection shell
*PLUS
% possible obs: 95.5 %

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Processing

Software
NameClassification
PROLSQrefinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: R6 (NATIVE) INSULIN

Resolution: 2.3→36.8 Å / σ(F): 0
Details: THE FOLLOWING SIDECHAINS HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER, A4, A14, B13, B21, B29, B30, C4, D1, E5, F1, F21, F25, G4, H13, H21, J21, L1, L21, L30 THE FOLLOWING CHAIN ...Details: THE FOLLOWING SIDECHAINS HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER, A4, A14, B13, B21, B29, B30, C4, D1, E5, F1, F21, F25, G4, H13, H21, J21, L1, L21, L30 THE FOLLOWING CHAIN TERMINAL RESIDUES HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER, D29-D30, F29-F30, H29-H30, J29-J30
RfactorNum. reflection% reflection
Rwork0.186 --
all-13832 -
obs-13832 92 %
Displacement parametersBiso mean: 35.9 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 46 91 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.73
X-RAY DIFFRACTIONp_mcangle_it45
X-RAY DIFFRACTIONp_scbond_it7.37
X-RAY DIFFRACTIONp_scangle_it8.610
X-RAY DIFFRACTIONp_plane_restr0.0170.025
X-RAY DIFFRACTIONp_chiral_restr0.140.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.3
X-RAY DIFFRACTIONp_multtor_nbd0.2610.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2790.3
X-RAY DIFFRACTIONp_planar_tor3.17
X-RAY DIFFRACTIONp_staggered_tor19.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor13.420
X-RAY DIFFRACTIONp_special_tor

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