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- PDB-1imx: 1.8 Angstrom crystal structure of IGF-1 -

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Basic information

Entry
Database: PDB / ID: 1imx
Title1.8 Angstrom crystal structure of IGF-1
ComponentsInsulin-like Growth Factor 1A
KeywordsHORMONE/GROWTH FACTOR / insulin/relaxin / detergent / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / proteoglycan biosynthetic process / positive regulation of glycoprotein biosynthetic process / myotube cell development / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration ...glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / proteoglycan biosynthetic process / positive regulation of glycoprotein biosynthetic process / myotube cell development / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / negative regulation of neuroinflammatory response / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / negative regulation of vascular associated smooth muscle cell apoptotic process / bone mineralization involved in bone maturation / IRS-related events triggered by IGF1R / positive regulation of cell growth involved in cardiac muscle cell development / exocytic vesicle / positive regulation of transcription regulatory region DNA binding / cell activation / positive regulation of calcineurin-NFAT signaling cascade / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of Ras protein signal transduction / myoblast differentiation / positive regulation of insulin-like growth factor receptor signaling pathway / myoblast proliferation / muscle organ development / negative regulation of interleukin-1 beta production / positive regulation of DNA binding / negative regulation of release of cytochrome c from mitochondria / positive regulation of cardiac muscle hypertrophy / positive regulation of smooth muscle cell migration / positive regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / negative regulation of smooth muscle cell apoptotic process / negative regulation of tumor necrosis factor production / epithelial to mesenchymal transition / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / SHC-related events triggered by IGF1R / positive regulation of osteoblast differentiation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / activation of protein kinase B activity / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / positive regulation of epithelial cell proliferation / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / skeletal system development / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of smooth muscle cell proliferation / insulin receptor binding / growth factor activity / wound healing / regulation of protein phosphorylation / hormone activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / integrin binding / Platelet degranulation / response to heat / regulation of gene expression / Ras protein signal transduction / cell population proliferation / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / positive regulation of cell migration / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Insulin-like growth factor I / Insulin-like, subunit E / Insulin-like / Insulin-like growth factor / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. ...Insulin-like growth factor I / Insulin-like, subunit E / Insulin-like / Insulin-like growth factor / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Insulin-like growth factor I / Insulin-like growth factor I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.82 Å
AuthorsVajdos, F.F. / Ultsch, M. / Schaffer, M.L. / Deshayes, K.D. / Liu, J. / Skelton, N.J. / de Vos, A.M.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal structure of human insulin-like growth factor-1: detergent binding inhibits binding protein interactions.
Authors: Vajdos, F.F. / Ultsch, M. / Schaffer, M.L. / Deshayes, K.D. / Liu, J. / Skelton, N.J. / de Vos, A.M.
History
DepositionMay 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin-like Growth Factor 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6063
Polymers7,6641
Non-polymers9422
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.831, 71.055, 65.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Insulin-like Growth Factor 1A / IGF-1


Mass: 7663.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01343, UniProt: P05019*PLUS
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-CPQ / N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE / DEOXY-BIGCHAP


Mass: 862.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H75N3O15 / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, deoxy big CHAPS, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.15 M1dropNaCl
220 mMsodium acetate1drop
310 mg/mlprotein1drop
424 %PEG33501reservoir
50.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9197, 1.5406, 0.9199, 0.8610
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 4, 2001
RadiationMonochromator: double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91971
21.54061
30.91991
40.8611
ReflectionResolution: 1.82→20 Å / Num. all: 6982 / Num. obs: 6871 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 16.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.5 / % possible all: 99.1
Reflection
*PLUS
% possible obs: 98.2 % / Num. measured all: 44573
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.29

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNX2000refinement
RefinementMethod to determine structure: MAD / Resolution: 1.82→19 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 864194.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 558 8.1 %RANDOM
Rwork0.245 ---
all-7015 --
obs-6871 97.9 %-
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.68 Å20 Å20 Å2
2---1.65 Å20 Å2
3---5.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.82→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms431 0 61 47 539
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.861.5
X-RAY DIFFRACTIONc_mcangle_it3.162
X-RAY DIFFRACTIONc_scbond_it2.682
X-RAY DIFFRACTIONc_scangle_it4.212.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 54 6.1 %
Rwork0.274 825 -
obs--74.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DBC.PARDBC.TOP
Software
*PLUS
Name: CNX2000 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 8.1 % / Rfactor obs: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.054
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.335 / % reflection Rfree: 6.1 % / Rfactor Rwork: 0.274

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