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- PDB-1j73: Crystal structure of an unstable insulin analog with native activity. -

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Basic information

Entry
Database: PDB / ID: 1j73
TitleCrystal structure of an unstable insulin analog with native activity.
Components
  • insulin a
  • insulin b
KeywordsHORMONE/GROWTH FACTOR / A8-Diaminobutyric Acid human insulin / hormone-receptor interface / HORMONE-GROWTH FACTOR COMPLEX
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 respiratory burst involved in inflammatory response / activation of protein kinase B activity / negative regulation of protein secretion / 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 / 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 / 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 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 protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / 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
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWan, Z. / Zhao, M. / Nakagawa, S. / Jia, W. / Weiss, M.A.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Non-standard insulin design: structure-activity relationships at the periphery of the insulin receptor.
Authors: Weiss, M.A. / Wan, Z. / Zhao, M. / Chu, Y.C. / Nakagawa, S.H. / Burke, G.T. / Jia, W. / Hellmich, R. / Katsoyannis, P.G.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Diabetes-associated mutations in a beta-cell transcription factor destabilize an antiparallel "mini-zipper" in a dimerization interface
Authors: Hua, Q.X. / Zhao, M. / Narayana, N. / Nakagawa, S.H. / Jia, W.H. / Weiss, M.A.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: The Relationship Between Insulin Bioactivity and Structure in the NH2-terminal A-chain Helix
Authors: Olsen, H.B. / Ludvigsen, S. / Kaarsholm, N.C.
#3: Journal: J.Mol.Biol. / Year: 1996
Title: Mapping the Functional Surface of Insulin by Design: Structure and Function of a Novel A-chain Analogue
Authors: Hua, Q.X. / Hu, S.Q. / Frank, B.H. / Jia, W.H. / Chu, Y.C. / Wang, S.H. / Burke, G.T. / Kaysoyannis, P.G. / Weiss, M.A.
#4: Journal: Biophys.Chem. / Year: 1994
Title: A Proposed Interaction Model of the Insulin Molecule with its Receptor
Authors: Liang, D.C. / Chang, W.R. / Wan, Z.L. / Vijayan, N.M.
History
DepositionMay 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 400COMPOUND THE CONFORMATIONS OF TWO MONOMERS ARE DIFFERENT AS THE RESULT OF A CHANGE IN CONFORMATION ...COMPOUND THE CONFORMATIONS OF TWO MONOMERS ARE DIFFERENT AS THE RESULT OF A CHANGE IN CONFORMATION OF THE FIRST EIGHT RESIDUES OF THE B-CHAINS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: insulin a
B: insulin b
C: insulin a
D: insulin b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7646
Polymers11,6334
Non-polymers1312
Water1,71195
1
A: insulin a
B: insulin b
C: insulin a
D: insulin b
hetero molecules

A: insulin a
B: insulin b
C: insulin a
D: insulin b
hetero molecules

A: insulin a
B: insulin b
C: insulin a
D: insulin b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,29218
Polymers34,90012
Non-polymers3926
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 area17750 Å2
ΔGint-264 kcal/mol
Surface area14220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.220, 79.220, 36.884
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-31-

ZN

21D-31-

ZN

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Components

#1: Protein/peptide insulin a


Mass: 2382.713 Da / Num. of mol.: 2 / Mutation: T8(DAB) / Source method: obtained synthetically
Details: The protein was chemically synthesized. The sequence is naturally found in Homo sapiens(human).
References: UniProt: P01308
#2: Protein/peptide insulin b


Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The protein was chemically synthesized. The sequence is naturally found in Homo sapiens(human).
References: UniProt: P01308
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.91 Å3/Da / Density % sol: 35.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: Tris, phonel, acetone, sodium citrate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
20.02 M1dropHCl
30.1 MTris-HCl1reservoir
40.1 Msodium citrate1reservoirpH7.8
50.02 %zinc acetate1reservoir
68 %acetate1reservoir
70.5 %phenol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 26, 1998 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. all: 5681 / Num. obs: 5448 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 2→2.03 Å / Redundancy: 611 % / Rmerge(I) obs: 0.097 / % possible all: 100
Reflection
*PLUS
% possible obs: 93 % / Rmerge(I) obs: 0.056

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementResolution: 2→10 Å / σ(F): 2 / σ(I): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.273 500 9.2 %random
Rwork0.205 ---
all-5681 --
obs-5448 --
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 2 95 907
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 9.2 % / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.46
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.089

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