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- PDB-1tgr: Crystal Structure of mini-IGF-1(2) -

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Basic information

Entry
Database: PDB / ID: 1tgr
TitleCrystal Structure of mini-IGF-1(2)
ComponentsInsulin-like growth factor IA
KeywordsHORMONE/GROWTH FACTOR / IGF-I / IGF-1 / Disulfide Isomerization / recepter binding / 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 / bone mineralization involved in bone maturation / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / positive regulation of cell growth involved in cardiac muscle cell development / negative regulation of vascular associated smooth muscle cell apoptotic process / IRS-related events triggered by IGF1R / exocytic vesicle / cell activation / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of transcription regulatory region DNA binding / 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 cardiac muscle hypertrophy / positive regulation of activated T cell proliferation / positive regulation of smooth muscle cell migration / negative regulation of release of cytochrome c from mitochondria / negative regulation of amyloid-beta formation / negative regulation of smooth muscle cell apoptotic process / negative regulation of tumor necrosis factor production / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / epithelial to mesenchymal transition / positive regulation of DNA binding / 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 / positive regulation of glycolytic process / activation of protein kinase B activity / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / skeletal system development / positive regulation of epithelial cell proliferation / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of smooth muscle cell proliferation / regulation of protein phosphorylation / insulin-like growth factor receptor binding / growth factor activity / wound healing / insulin receptor binding / hormone activity / cellular response to amyloid-beta / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / integrin binding / Platelet degranulation / response to heat / regulation of gene expression / cell population proliferation / Ras protein signal transduction / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / 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/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. ...Insulin-like growth factor I / Insulin-like, subunit E / Insulin-like / Insulin-like growth factor / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Insulin-like growth factor I / Insulin-like growth factor I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD or SIRAS / Resolution: 1.42 Å
AuthorsLiang, D.C. / Yun, C.H. / Chang, W.R.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: 1.42A crystal structure of mini-IGF-1(2): an analysis of the disulfide isomerization property and receptor binding property of IGF-1 based on the three-dimensional structure
Authors: Yun, C.H. / Tang, Y.H. / Feng, Y.M. / An, X.M. / Chang, W.R. / Liang, D.C.
History
DepositionMay 29, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin-like growth factor IA
B: Insulin-like growth factor IA


Theoretical massNumber of molelcules
Total (without water)11,6942
Polymers11,6942
Non-polymers00
Water2,612145
1
A: Insulin-like growth factor IA


Theoretical massNumber of molelcules
Total (without water)5,8471
Polymers5,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Insulin-like growth factor IA


Theoretical massNumber of molelcules
Total (without water)5,8471
Polymers5,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Insulin-like growth factor IA

A: Insulin-like growth factor IA

A: Insulin-like growth factor IA

A: Insulin-like growth factor IA

B: Insulin-like growth factor IA

B: Insulin-like growth factor IA

B: Insulin-like growth factor IA

B: Insulin-like growth factor IA


Theoretical massNumber of molelcules
Total (without water)46,7748
Polymers46,7748
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_444x-1/2,y-1/2,z-1/21
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation7_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation8_455x-1/2,-y+1/2,-z+1/21
Buried area12880 Å2
ΔGint-36 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.86, 61.98, 70.82
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-63-

HOH

21B-112-

HOH

DetailsThe mini-IGF-1(2) dimer is formed during crystallization. It is not a physiological dimer.

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Components

#1: Protein Insulin-like growth factor IA / mini-IGF-1 isomer 2


Mass: 5846.783 Da / Num. of mol.: 2 / Fragment: residues 1-52 / Mutation: T29K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: DH12S / Gene: E.coli / Plasmid: PVT102-U-ALPHAMFL-MINI-IGF-1 / Cell line (production host): Saccharomyces cerevisiae / Production host: Escherichia coli (E. coli) / Strain (production host): XV700-6B(leu2,ura3,pep4) / References: UniProt: P01343, UniProt: P05019*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.6 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.65
Details: Citrate, ethanol, pH 6.65, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 30, 2003 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. all: 23469 / Num. obs: 23375 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 16.7
Reflection shellResolution: 1.42→1.45 Å / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD or SIRAS / Resolution: 1.42→8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.003 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1262 5.1 %RANDOM
Rwork0.196 ---
all0.213 23469 --
obs0.198 23375 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.695 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20.37 Å20.31 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.42→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 0 145 955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021899
X-RAY DIFFRACTIONr_bond_other_d0.0030.02785
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.991217
X-RAY DIFFRACTIONr_angle_other_deg0.85531835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4625116
X-RAY DIFFRACTIONr_chiral_restr0.0840.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021053
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02208
X-RAY DIFFRACTIONr_nbd_refined0.2310.2202
X-RAY DIFFRACTIONr_nbd_other0.2420.2876
X-RAY DIFFRACTIONr_nbtor_other0.0840.2485
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3690.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.216
X-RAY DIFFRACTIONr_mcbond_it0.8951.5556
X-RAY DIFFRACTIONr_mcangle_it1.5722889
X-RAY DIFFRACTIONr_scbond_it2.4363343
X-RAY DIFFRACTIONr_scangle_it3.6574.5328
LS refinement shellResolution: 1.42→1.456 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.223 84
Rwork0.246 1655
obs-1655

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