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- PDB-6p4z: Structure of gadolinium-caged cobalt (III) insulin hexamer -

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Basic information

Entry
Database: PDB / ID: 6p4z
TitleStructure of gadolinium-caged cobalt (III) insulin hexamer
Components(Insulin chain ...) x 2
KeywordsHORMONE / contrast agent / environmentally sensitive / gadolinium / insulin hexamer / proteins
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / 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 / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / 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 / 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/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
: / GADOLINIUM ATOM / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTran, T.H. / Taylor, S.K. / Stojanovic, M.N. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM) United States
CitationJournal: ChemBioChem / Year: 2018
Title: Insulin Hexamer-Caged Gadolinium Ion as MRI Contrast-o-phore
Authors: Taylor, S.K. / Tran, T.H. / Liu, M.Z. / Harris, P.E. / Sun, Y. / Jambawalikar, S.R. / Tong, L. / Stojanovic, M.N.
History
DepositionMay 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Structure summary / Category: audit_author / struct / Item: _struct.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,9468
Polymers11,6354
Non-polymers3114
Water86548
1
A: Insulin chain A
B: Insulin chain B
C: Insulin chain A
D: Insulin chain B
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)35,83824
Polymers34,90612
Non-polymers93212
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 area19390 Å2
ΔGint-257 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.400, 81.400, 33.700
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-

CO

21D-101-

CL

31D-102-

CO

41D-215-

HOH

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Components

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Insulin chain ... , 2 types, 4 molecules ACBD

#1: Protein/peptide Insulin chain A


Mass: 2383.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide Insulin chain B


Mass: 3433.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308

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Non-polymers , 4 types, 52 molecules

#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Gd / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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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: 33.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 18% (w/v) PEG 12,000 and 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→23.5 Å / Num. obs: 7216 / % possible obs: 92.9 % / Redundancy: 2.3 % / Net I/σ(I): 13.5
Reflection shellResolution: 1.8→1.9 Å / Num. unique obs: 1153

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→23.498 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.25
RfactorNum. reflection% reflection
Rfree0.2386 373 5.17 %
Rwork0.1811 --
obs0.1839 7216 92.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→23.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 0 4 48 805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008774
X-RAY DIFFRACTIONf_angle_d0.7941054
X-RAY DIFFRACTIONf_dihedral_angle_d3.112438
X-RAY DIFFRACTIONf_chiral_restr0.043118
X-RAY DIFFRACTIONf_plane_restr0.006133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7969-2.05680.30131350.21272292X-RAY DIFFRACTION95
2.0568-2.59090.24041180.19372336X-RAY DIFFRACTION94
2.5909-23.50020.22031200.16722215X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 12.1086 Å / Origin y: 2.4825 Å / Origin z: 10.9343 Å
111213212223313233
T0.1391 Å2-0.013 Å2-0.0106 Å2-0.1916 Å20.0115 Å2--0.1687 Å2
L1.5474 °2-0.2834 °2-0.0293 °2-3.3218 °21.0473 °2--1.5919 °2
S-0.0416 Å °-0.0286 Å °0.08 Å °0.1013 Å °0.0443 Å °-0.0523 Å °-0.0141 Å °0.0936 Å °0.0037 Å °
Refinement TLS groupSelection details: all

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