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- PDB-3fhp: A neutron crystallographic analysis of a porcine 2Zn insulin at 2... -

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Basic information

Entry
Database: PDB / ID: 3fhp
TitleA neutron crystallographic analysis of a porcine 2Zn insulin at 2.0 A resolution
Components(Insulin) x 2
KeywordsHORMONE / 2Zn insulin / neutron crystallography / protonation / H/D exchange / Carbohydrate metabolism / Cleavage on pair of basic residues / Glucose metabolism / Secreted
Function / homology
Function and homology information


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 / glycoprotein biosynthetic process / response to L-arginine ...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 / glycoprotein biosynthetic process / response to L-arginine / positive regulation of lipoprotein lipase activity / lactate biosynthetic process / lipoprotein biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / COPI-mediated anterograde transport / lipid biosynthetic process / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / positive regulation of DNA replication / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / negative regulation of lipid catabolic process / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / wound healing / insulin receptor binding / negative regulation of protein catabolic process / hormone activity / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / 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 / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / 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
DEUTERATED WATER / Insulin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIwai, W. / Kurihara, K. / Yamada, T. / Kobayashi, Y. / Ohnishi, Y. / Tanaka, I. / Takahashi, H. / Niimura, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: A neutron crystallographic analysis of T6 porcine insulin at 2.1 A resolution
Authors: Iwai, W. / Yamada, T. / Kurihara, K. / Ohnishi, Y. / Kobayashi, Y. / Tanaka, I. / Takahashi, H. / Kuroki, R. / Tamada, T. / Niimura, N.
History
DepositionDec 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 21, 2013Group: Other
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Jun 13, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.5Jul 18, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_scattering_type
Revision 1.6Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,7066
Polymers11,5754
Non-polymers1312
Water1,60389
1
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)35,11818
Polymers34,72612
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 area20840 Å2
ΔGint-263.4 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.849, 82.849, 34.173
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

31B-87-

DOD

41D-89-

DOD

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Components

#1: Protein/peptide Insulin / / Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: UNP residues 88-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01315
#2: Protein/peptide Insulin / / Insulin B chain


Mass: 3403.927 Da / Num. of mol.: 2 / Fragment: UNP residues 25-54
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01315
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 6.3
Details: 2.3mg/ml insulin, 50mM sodium citrate, 6mM zinc acetate, 17% acetone, pH6.3, LIQUID DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: JRR-3M / Beamline: 1G-B / Wavelength: 2.6 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 8, 2006
RadiationMonochromator: ELLASTICALLY BENT SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.6 Å / Relative weight: 1
ReflectionResolution: 2→80 Å / Num. all: 4824 / Num. obs: 4824 / % possible obs: 23.2 % / Redundancy: 2.2 % / Biso Wilson estimate: 8.2 Å2 / Rmerge(I) obs: 0.147
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.393 / Num. unique all: 4824 / % possible all: 81.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
XFITdata reduction
CNS1.1refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4INS

4ins


Resolution: 2→41.43 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 484314.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.247 208 5.2 %RANDOM
Rwork0.168 ---
obs0.168 4030 68.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.8544 Å2 / ksol: 0.06 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å21.58 Å20 Å2
2--0.38 Å20 Å2
3----0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→41.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 2 89 897
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
NEUTRON DIFFRACTIONc_bond_d0.008
NEUTRON DIFFRACTIONc_bond_d_na
NEUTRON DIFFRACTIONc_bond_d_prot
NEUTRON DIFFRACTIONc_angle_d
NEUTRON DIFFRACTIONc_angle_d_na
NEUTRON DIFFRACTIONc_angle_d_prot
NEUTRON DIFFRACTIONc_angle_deg1.7
NEUTRON DIFFRACTIONc_angle_deg_na
NEUTRON DIFFRACTIONc_angle_deg_prot
NEUTRON DIFFRACTIONc_dihedral_angle_d22.8
NEUTRON DIFFRACTIONc_dihedral_angle_d_na
NEUTRON DIFFRACTIONc_dihedral_angle_d_prot
NEUTRON DIFFRACTIONc_improper_angle_d7.75
NEUTRON DIFFRACTIONc_improper_angle_d_na
NEUTRON DIFFRACTIONc_improper_angle_d_prot
NEUTRON DIFFRACTIONc_mcbond_it1.51.5
NEUTRON DIFFRACTIONc_mcangle_it2.352
NEUTRON DIFFRACTIONc_scbond_it1.522
NEUTRON DIFFRACTIONc_scangle_it2.322.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.075 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 13 8 %
Rwork0.202 150 -
obs--16 %
Xplor file
Refine-IDSerial noParam fileTopol file
NEUTRON DIFFRACTION1pro3.parampro2.top
NEUTRON DIFFRACTION2sol.paramsol.top
NEUTRON DIFFRACTION3ion.paramion.top

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