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Yorodumi- PDB-1qfw: TERNARY COMPLEX OF HUMAN CHORIONIC GONADOTROPIN WITH FV ANTI ALPH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qfw | ||||||
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Title | TERNARY COMPLEX OF HUMAN CHORIONIC GONADOTROPIN WITH FV ANTI ALPHA SUBUNIT AND FV ANTI BETA SUBUNIT | ||||||
Components |
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Keywords | IMMUNE SYSTEM / GLYCOPROTEIN HORMONE / STIMULATION OF PRODUCTION OF PROGESTERONE / FVS SPECIFICALLY DIRECTED AGAINST ALPHA AND BETA SUBUNIT | ||||||
Function / homology | Function and homology information follicle-stimulating hormone activity / follicle-stimulating hormone complex / pituitary gonadotropin complex / luteinizing hormone secretion / follicle-stimulating hormone secretion / positive regulation of steroid biosynthetic process / ovulation / Thyroxine biosynthesis / Mineralocorticoid biosynthesis / Hormone ligand-binding receptors ...follicle-stimulating hormone activity / follicle-stimulating hormone complex / pituitary gonadotropin complex / luteinizing hormone secretion / follicle-stimulating hormone secretion / positive regulation of steroid biosynthetic process / ovulation / Thyroxine biosynthesis / Mineralocorticoid biosynthesis / Hormone ligand-binding receptors / Glycoprotein hormones / Reactions specific to the complex N-glycan synthesis pathway / Androgen biosynthesis / follicle-stimulating hormone signaling pathway / female gamete generation / negative regulation of organ growth / positive regulation of B cell activation / phagocytosis, recognition / thyroid hormone generation / regulation of signaling receptor activity / immunoglobulin complex / phagocytosis, engulfment / organ growth / thyroid gland development / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / hormone-mediated signaling pathway / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / hormone activity / Golgi lumen / cell-cell signaling / G alpha (s) signalling events / adaptive immune response / positive regulation of cell migration / defense response to bacterium / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / innate immune response / apoptotic process / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Tegoni, M. / Spinelli, S. / Cambillau, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structure of a ternary complex between human chorionic gonadotropin (hCG) and two Fv fragments specific for the alpha and beta-subunits. Authors: Tegoni, M. / Spinelli, S. / Verhoeyen, M. / Davis, P. / Cambillau, C. #1: Journal: Eur.J.Biochem. / Year: 1998 Title: Partially deglycosylated human choriogonadotropin, stabilized by intersubunit disulfide bonds, shows full bioactivity. Authors: Heikoop, J.C. / van den Boogaart, P. / de Leeuw, R. / Rose, U.M. / Mulders, J.W. / Grootenhuis, P.D. #2: Journal: Nature / Year: 1994 Title: Crystal structure of human chorionic gonadotropin. Authors: Lapthorn, A.J. / Harris, D.C. / Littlejohn, A. / Lustbader, J.W. / Canfield, R.E. / Machin, K.J. / Morgan, F.J. / Isaacs, N.W. #3: Journal: Structure / Year: 1994 Title: Structure of human chorionic gonadotropin at 2.6 A resolution from MAD analysis of the selenomethionyl protein. Authors: Wu, H. / Lustbader, J.W. / Liu, Y. / Canfield, R.E. / Hendrickson, W.A. #4: Journal: Biochemistry / Year: 1989 Title: Crystallization and characterization of human chorionic gonadotropin in chemically deglycosylated and enzymatically desialylated states. Authors: Lustbader, J.W. / Birken, S. / Pileggi, N.F. / Kolks, M.A. / Pollak, S. / Cuff, M.E. / Yang, W. / Hendrickson, W.A. / Canfield, R.E. #5: Journal: J.Biol.Chem. / Year: 1989 Title: Site specificity of the chorionic gonadotropin N-linked oligosaccharides in signal transduction. Authors: Matzuk, M.M. / Keene, J.L. / Boime, I. #6: Journal: J.Biol.Chem. / Year: 1975 Title: Role of carbohydrate of human chorionic gonadotropin in the mechanism of hormone action. Authors: Moyle, W.R. / Bahl, O.P. / Marz, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qfw.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qfw.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 1qfw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/1qfw ftp://data.pdbj.org/pub/pdb/validation_reports/qf/1qfw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 10219.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SUGAR RESIDUES LINKED TO ASN52 AND ASN78 / Source: (natural) Homo sapiens (human) / Secretion: HUMAN PREGNANCY URINE / References: UniProt: P01215 |
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#2: Protein | Mass: 15548.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Secretion: HUMAN PREGNANCY URINE / References: UniProt: P01233, UniProt: P0DN86*PLUS |
-Antibody , 4 types, 4 molecules LHMI
#3: Antibody | Mass: 12687.999 Da / Num. of mol.: 1 / Fragment: FV Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01660*PLUS |
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#4: Antibody | Mass: 12896.261 Da / Num. of mol.: 1 / Fragment: FV Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01750*PLUS |
#5: Antibody | Mass: 11896.147 Da / Num. of mol.: 1 / Fragment: FV Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01660*PLUS |
#6: Antibody | Mass: 13460.987 Da / Num. of mol.: 1 / Fragment: FV Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P18526*PLUS |
-Sugars , 1 types, 2 molecules
#7: Sugar |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: 1.8 M ammonium Sulfate, 100 mM tris/HCl pH 8.0, protein concentration 3 mg/ml | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→20 Å / Num. obs: 12096 / % possible obs: 96.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.166 / Net I/σ(I): 9 |
Reflection shell | Resolution: 3.5→3.6 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.46 / % possible all: 97 |
Reflection | *PLUS Highest resolution: 3.5 Å / Lowest resolution: 22 Å / Redundancy: 4 % / Rmerge(I) obs: 0.166 / Biso Wilson estimate: 30 Å2 |
Reflection shell | *PLUS Highest resolution: 3.5 Å / Lowest resolution: 3.56 Å / % possible obs: 97 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HRP, 1IGC, 2IMN Resolution: 3.5→9 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 250 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.65 Å / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.5 Å / Num. reflection Rfree: 898 / Rfactor obs: 0.268 / Rfactor Rfree: 0.316 / Rfactor Rwork: 0.268 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3.5 Å / Rfactor Rfree: 0.37 / Rfactor Rwork: 0.36 |