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- PDB-3kr3: Crystal structure of IGF-II antibody complex -

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Basic information

Entry
Database: PDB / ID: 3kr3
TitleCrystal structure of IGF-II antibody complex
Components
  • Insulin-like growth factor IIInsulin-like growth factor 2
  • antibody-Fab (heavy chain)
  • antibody-Fab (light chain)
KeywordsIMMUNE SYSTEM / Antibody-target complex / Carbohydrate metabolism / Glucose metabolism / Glycoprotein / Growth factor / Hormone / Mitogen / Osteogenesis / Secreted
Function / homology
Function and homology information


spongiotrophoblast cell proliferation / positive regulation of skeletal muscle tissue growth / negative regulation of muscle cell differentiation / embryonic placenta morphogenesis / regulation of muscle cell differentiation / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / genomic imprinting / positive regulation of organ growth / exocrine pancreas development ...spongiotrophoblast cell proliferation / positive regulation of skeletal muscle tissue growth / negative regulation of muscle cell differentiation / embryonic placenta morphogenesis / regulation of muscle cell differentiation / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / genomic imprinting / positive regulation of organ growth / exocrine pancreas development / positive regulation of multicellular organism growth / positive regulation of vascular endothelial cell proliferation / positive regulation of activated T cell proliferation / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of cell division / embryonic placenta development / positive regulation of glycogen biosynthetic process / SHC-related events triggered by IGF1R / positive regulation of insulin receptor signaling pathway / striated muscle cell differentiation / insulin-like growth factor receptor binding / protein serine/threonine kinase activator activity / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / animal organ morphogenesis / growth factor activity / insulin receptor binding / hormone activity / osteoblast differentiation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / glucose metabolic process / positive regulation of peptidyl-tyrosine phosphorylation / integrin binding / Platelet degranulation / insulin receptor signaling pathway / in utero embryonic development / positive regulation of MAPK cascade / receptor ligand activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell population proliferation / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Insulin-like growth factor II E-peptide, C-terminal / Insulin-like growth factor II / Insulin-like growth factor II E-peptide / Insulin-like, subunit E / Insulin-like / Insulin-like growth factor / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. ...Insulin-like growth factor II E-peptide, C-terminal / Insulin-like growth factor II / Insulin-like growth factor II E-peptide / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Insulin-like growth factor II
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPeat, T.S. / Newman, J. / Adams, T.E.
CitationJournal: Mol.Cancer Ther. / Year: 2010
Title: A human monoclonal antibody against insulin-like growth factor-II blocks the growth of human hepatocellular carcinoma cell lines in vitro and in vivo.
Authors: Dransfield, D.T. / Cohen, E.H. / Chang, Q. / Sparrow, L.G. / Bentley, J.D. / Dolezal, O. / Xiao, X. / Peat, T.S. / Newman, J. / Pilling, P.A. / Phan, T. / Priebe, I. / Brierley, G.V. / ...Authors: Dransfield, D.T. / Cohen, E.H. / Chang, Q. / Sparrow, L.G. / Bentley, J.D. / Dolezal, O. / Xiao, X. / Peat, T.S. / Newman, J. / Pilling, P.A. / Phan, T. / Priebe, I. / Brierley, G.V. / Kastrapeli, N. / Kopacz, K. / Martik, D. / Wassaf, D. / Rank, D. / Conley, G. / Huang, Y. / Adams, T.E. / Cosgrove, L.
History
DepositionNov 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Insulin-like growth factor II
H: antibody-Fab (heavy chain)
L: antibody-Fab (light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8987
Polymers57,6503
Non-polymers2484
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-22 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.667, 106.921, 110.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Insulin-like growth factor II / Insulin-like growth factor 2 / IGF-II / Somatomedin-A


Mass: 7484.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF-II, IGF2, PP1446 / Production host: Escherichia coli (E. coli) / References: UniProt: P01344
#2: Antibody antibody-Fab (heavy chain)


Mass: 26615.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody antibody-Fab (light chain)


Mass: 23550.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 52.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.3
Details: 18.5% PEG 6000, 118mM CaCl2, 10% (v/v) PCB buffer (propionate-cacodylate-bis-tris propane buffer), pH 5.3, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95363 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95363 Å / Relative weight: 1
ReflectionResolution: 2.2→37.4 Å / Num. all: 31276 / Num. obs: 26600 / % possible obs: 89.6 %
Reflection shellResolution: 2.2→2.257 Å / Num. unique all: 1934 / % possible all: 90.78

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.37 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.886 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1421 5.1 %RANDOM
Rwork0.199 ---
obs0.202 26600 89.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.24 Å2 / Biso mean: 26.389 Å2 / Biso min: 5.54 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å20 Å2
2---1.29 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3732 0 16 194 3942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223902
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9555308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1175506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86724.151159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97715633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7331521
X-RAY DIFFRACTIONr_chiral_restr0.1110.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022950
X-RAY DIFFRACTIONr_nbd_refined0.2190.21761
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22651
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.214
X-RAY DIFFRACTIONr_mcbond_it0.9581.52532
X-RAY DIFFRACTIONr_mcangle_it1.65524014
X-RAY DIFFRACTIONr_scbond_it2.43331565
X-RAY DIFFRACTIONr_scangle_it3.4614.51287
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 104 -
Rwork0.234 1934 -
all-2038 -
obs--90.78 %

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