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- PDB-1q4v: CRYSTAL STRUCTURE OF ALLO-ILEA2-INSULIN, AN INACTIVE CHIRAL ANALO... -

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Entry
Database: PDB / ID: 1q4v
TitleCRYSTAL STRUCTURE OF ALLO-ILEA2-INSULIN, AN INACTIVE CHIRAL ANALOGUE: IMPLICATIONS FOR THE MECHANISM OF RECEPTOR
Components(Insulin) x 2
KeywordsHORMONE/GROWTH FACTOR / allo-Ile-A2-insulin / protein unfolding / insulin receptor / 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 / activation of protein kinase B activity / negative regulation of respiratory burst involved in inflammatory response / 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 / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / 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 across plasma membrane / 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 / cognition / vasodilation / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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
PHENOL / : / Insulin
Similarity search - Component
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWan, Z.L. / Xu, B. / Chu, Y.C. / Katsoyannis, P.G. / Weiss, M.A.
Citation
Journal: Biochemistry / Year: 2003
Title: Crystal structure of allo-Ile(A2)-insulin, an inactive chiral analogue: implications for the mechanism of receptor binding.
Authors: Wan, Z.L. / Xu, B. / Chu, Y.C. / Katsoyannis, P.G. / Weiss, M.A.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: CHIRAL MUTAGENESIS OF INSULIN'S HIDDEN RECEPTOR-BINDING SURFACE: STRUCTURE OF AN ALLO-ISOLEUCINE (A2) ANALOGUE
Authors: Xu, B. / Hua, Q.X. / NAKAGAWA, S.H. / JIA, W. / CHU, Y.C. / KASOYANNIS, P.G. / WEISS, M.A.
#2: Journal: Protein Sci. / Year: 2002
Title: A CAVITY-FORMING MUTATION IN INSULIN INDUCES SEGMENTAL UNFOLDING OF A SURROUNDING ALPHA-HELIX
Authors: XU, B. / HUA, Q.X. / NAKAGAWA, S.H. / JIA, W. / CHU, Y.C. / KATSOYANNIS, P.G. / WEISS, M.A.
#3: 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.
#4: Journal: Trends Biochem.Sci. / Year: 1999
Title: IS PROTEIN FOLDING HIERARCHIC? I. LOCAL STRUCTURE AND PEPTIDE FOLDING
Authors: BALDWIN, R.L. / ROSE, G.D.
#5: Journal: Trends Biochem.Sci. / Year: 1999
Title: IS PROTEIN FOLDING HIERARCHIC? II. FOLDING INTERMEDIATES AND TRANSITION STATES
Authors: BALDWIN, R.L. / ROSE, G.D.
History
DepositionAug 4, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionAug 19, 2003ID: 1PC1
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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_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 1.4Nov 20, 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
B: Insulin
C: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8607
Polymers11,6354
Non-polymers2253
Water1,15364
1
A: Insulin
B: Insulin
hetero molecules

A: Insulin
B: Insulin
hetero molecules

A: Insulin
B: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6499
Polymers17,4536
Non-polymers1963
Water1086
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 area5440 Å2
ΔGint-100 kcal/mol
Surface area10190 Å2
MethodPISA
2
C: Insulin
D: Insulin
hetero molecules

C: Insulin
D: Insulin
hetero molecules

C: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,93212
Polymers17,4536
Non-polymers4796
Water1086
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 area6330 Å2
ΔGint-105 kcal/mol
Surface area10480 Å2
MethodPISA
3
A: Insulin
B: Insulin
C: Insulin
D: Insulin
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)35,58121
Polymers34,90612
Non-polymers6759
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 area18730 Å2
ΔGint-255 kcal/mol
Surface area13710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.487, 80.487, 37.939
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-102-

ZN

DetailsThe crystallographic asymmetry unit of insulin consists of two monomers each consisting two heterochains. The entry presents coordinates for monomer 1 (chain indicators A and B)and monomer 2 (chain indicators C and D). There are two zinc ions per insulin hexamer located on the three-fold axis. The conformations of two monomers are different the result of B changed in conformation of the first residues of the B-chain. The biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -y,x-y,z and -x+y,-x,z

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Components

#1: Protein/peptide Insulin


Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: INSULIN A CHAIN / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN Homo Sapiens (human).
References: GenBank: AAA59172, UniProt: P01308*PLUS
#2: Protein/peptide Insulin


Mass: 3433.953 Da / Num. of mol.: 2 / Fragment: INSULIN B CHAIN / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN Homo Sapiens (human).
References: GenBank: AAA59172, UniProt: P01308*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: Tris, sodium citrate, acetone, phenol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
20.02 M1dropHCl
30.02 MTris-HCl1reservoir
40.05 Msodium citrate1reservoir
55 %acetone1reservoir
60.03 %phenol1reservoir
70.01 %zinc acetate1reservoirpH8.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 12, 2001 / Details: mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→23.24 Å / Num. obs: 5897 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.07 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 43.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 4.1 / Num. unique all: 543 / % possible all: 89.3
Reflection
*PLUS
Lowest resolution: 23.2 Å / Num. obs: 5892
Reflection shell
*PLUS
% possible obs: 89.3 % / Redundancy: 1.27 % / Num. unique obs: 543

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TRZ

1trz


Resolution: 2→23.24 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 613 10.4 %RANDOM
Rwork0.219 ---
obs-5892 98.7 %-
Solvent computationSolvent model: Flat model / Bsol: 37.6603 Å2 / ksol: 0.29202 e/Å3
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å22.43 Å20 Å2
2---2.18 Å20 Å2
3---6.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→23.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 9 64 883
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.378 89 9.6 %
Rwork0.331 753 -
obs-753 80.6 %
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 23.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Lowest resolution: 2.07 Å

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