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- PDB-3gky: The Structural Basis of an ER Stress-Associated Bottleneck in a P... -

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Basic information

Entry
Database: PDB / ID: 3gky
TitleThe Structural Basis of an ER Stress-Associated Bottleneck in a Protein Folding Landscape
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / protein folding / ER stress-associated / TR transition receptor binding / Carbohydrate metabolism / Cleavage on pair of basic residues / Diabetes mellitus / Disease mutation / Disulfide bond / Glucose metabolism / Pharmaceutical / Secreted
Function / homology
Function and homology information


positive regulation of lipoprotein lipase activity / Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / response to L-arginine ...positive regulation of lipoprotein lipase activity / Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / response to L-arginine / lactate biosynthetic process / positive regulation of glucose metabolic process / positive regulation of fatty acid biosynthetic process / glycoprotein biosynthetic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / 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 / lipid biosynthetic process / positive regulation of respiratory burst / negative regulation of acute inflammatory response / TORC1 signaling / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / positive regulation of insulin receptor signaling pathway / negative regulation of respiratory burst involved in inflammatory response / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of mitotic nuclear division / positive regulation of glycolytic process / positive regulation of DNA replication / acute-phase response / positive regulation of cytokine production / positive regulation of D-glucose import across plasma membrane / positive regulation of protein secretion / insulin receptor binding / positive regulation of translation / wound healing / hormone activity / positive regulation of neuron projection development / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / vasodilation / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / protease binding / positive regulation of canonical NF-kappaB signal transduction / 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 / negative regulation of gene expression / positive regulation of cell population proliferation / : / 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, M. / Wan, Z.L. / Chu, Y.C. / Alddin, H. / Klaproth, B. / Weiss, M.A.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Crystal structure of a "nonfoldable" insulin: IMPAIRED FOLDING EFFICIENCY DESPITE NATIVE ACTIVITY.
Authors: Liu, M. / Wan, Z.L. / Chu, Y.C. / Aladdin, H. / Klaproth, B. / Choquette, M. / Hua, Q.X. / Mackin, R.B. / Rao, J.S. / De Meyts, P. / Katsoyannis, P.G. / Arvan, P. / Weiss, M.A.
#1: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1988
Title: The structure of 2zn pig insulin crystal at 1.5 A resolution
Authors: Baker, E.N. / Blujdell, T.L. / Cutfield, J.F. / Cutfield, S.M. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D. / Isaacs, N.W. / Reynolds, C.D.
#2: Journal: Nature / Year: 1976
Title: Structure of insulin in 4-zinc insulin
Authors: Bentley, G. / Dodson, E. / Dodson, G. / Hodgkin, D. / Mercola, D.
#3: Journal: Nature / Year: 1989
Title: Phenol stabilizes more helix in a new symmetrical zinc insulin hexamer
Authors: Derewenda, U. / Derewenda, Z. / Dodson, E. / Dodson, G. / Reynold, C. / Smith, G. / Sparks, C. / Swenson, D.
#4: Journal: J.Biol.Chem. / Year: 2006
Title: Toward the active conformation of insulin: stereospecific modulation of a structural swith in the B chain
Authors: Hua, Q.X. / Nakagawa, S. / Hu, S.Q. / Jia, W. / Wang, S. / Weiss, M.A.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 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 / 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_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 16, 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)11,9179
Polymers11,6214
Non-polymers2965
Water2,252125
1
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules

A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules

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)35,75127
Polymers34,86412
Non-polymers88815
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area19390 Å2
ΔGint-314 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.225, 78.225, 36.712
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

21B-32-

CL

31D-31-

ZN

41D-32-

CL

51D-36-

HOH

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide Insulin A chain


Mass: 2406.714 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: biosynthetic sequence / Source: (synth.) Sus scrofa (pig) / References: UniProt: P01315
#2: Protein/peptide Insulin B chain


Mass: 3403.927 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: biosynthetic sequence / Source: (synth.) Sus scrofa (pig) / References: UniProt: P01315

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Non-polymers , 4 types, 130 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.85 Å3/Da / Density % sol: 33.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 0.02 M Tris, 0.05 M sodium citrate, 5% acetone, 0.03% phenol, 0.01% zinc acetate, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.948 Å
DetectorDetector: CCD / Date: Feb 11, 2004 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 1.8→22.58 Å / Num. all: 7752 / Num. obs: 7299 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 390252.65 / Redundancy: 6.4 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.5
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 7.4 / Num. unique all: 1027 / % possible all: 90.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TRZ

1trz


Resolution: 1.8→22.58 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 789 -Random
Rwork0.209 ---
all-7752 --
obs-7299 94.2 %-
Displacement parametersBiso mean: 39.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å21.1 Å20 Å2
2---1.62 Å20 Å2
3---3.24 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→22.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms822 0 11 125 958
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d0.6
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.311 133 -
Rwork0.297 --
obs-1027 90.1 %

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