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- PDB-1qfw: TERNARY COMPLEX OF HUMAN CHORIONIC GONADOTROPIN WITH FV ANTI ALPH... -

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Basic information

Entry
Database: PDB / ID: 1qfw
TitleTERNARY COMPLEX OF HUMAN CHORIONIC GONADOTROPIN WITH FV ANTI ALPHA SUBUNIT AND FV ANTI BETA SUBUNIT
Components
  • (ANTIBODY (ANTI ALPHA SUBUNIT) ...) x 2
  • (ANTIBODY (ANTI BETA SUBUNIT) ...) x 2
  • GONADOTROPHIN BETA SUBUNIT
  • GONADOTROPIN ALPHA SUBUNIT
KeywordsIMMUNE 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 / Thyroxine biosynthesis / Mineralocorticoid biosynthesis / Hormone ligand-binding receptors / Glycoprotein hormones ...follicle-stimulating hormone activity / follicle-stimulating hormone complex / pituitary gonadotropin complex / luteinizing hormone secretion / follicle-stimulating hormone secretion / positive regulation of steroid biosynthetic process / 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 / organ growth / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / immunoglobulin complex / thyroid gland development / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / hormone-mediated signaling pathway / 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
Gonadotropin, beta subunit, conserved site / Glycoprotein hormones beta chain signature 1. / Glycoprotein hormones beta chain signature 2. / Glycoprotein hormone beta chain homologues. / Glycoprotein hormone alpha chain / Glycoprotein hormone / Glycoprotein hormones alpha chain signature 1. / Glycoprotein hormones alpha chain signature 2. / Glycoprotein hormones alpha chain family profile. / Glycoprotein hormone alpha chain homologues. ...Gonadotropin, beta subunit, conserved site / Glycoprotein hormones beta chain signature 1. / Glycoprotein hormones beta chain signature 2. / Glycoprotein hormone beta chain homologues. / Glycoprotein hormone alpha chain / Glycoprotein hormone / Glycoprotein hormones alpha chain signature 1. / Glycoprotein hormones alpha chain signature 2. / Glycoprotein hormones alpha chain family profile. / Glycoprotein hormone alpha chain homologues. / Gonadotropin, beta subunit / Glycoprotein hormone subunit beta / Cystine-knot domain / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ribbon / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Glycoprotein hormones alpha chain / Choriogonadotropin subunit beta 7 / Ig kappa chain V-III region PC 3741/TEPC 111 / Ig heavy chain V region 102 / Choriogonadotropin subunit beta 3 / Ig heavy chain V region 345
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTegoni, 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
DepositionApr 15, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 27, 2019Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GONADOTROPIN ALPHA SUBUNIT
B: GONADOTROPHIN BETA SUBUNIT
L: ANTIBODY (ANTI ALPHA SUBUNIT) (LIGHT CHAIN)
H: ANTIBODY (ANTI ALPHA SUBUNIT) (HEAVY CHAIN)
M: ANTIBODY (ANTI BETA SUBUNIT) (LIGHT CHAIN)
I: ANTIBODY (ANTI BETA SUBUNIT) (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1538
Polymers76,7106
Non-polymers4422
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-49 kcal/mol
Surface area30300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.900, 104.900, 150.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein GONADOTROPIN ALPHA SUBUNIT / HCG


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
#2: Protein GONADOTROPHIN BETA SUBUNIT / HCG


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

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Antibody , 4 types, 4 molecules LHMI

#3: Antibody ANTIBODY (ANTI ALPHA SUBUNIT) (LIGHT CHAIN) / FV


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
#4: Antibody ANTIBODY (ANTI ALPHA SUBUNIT) (HEAVY CHAIN) / FV


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 ANTIBODY (ANTI BETA SUBUNIT) (LIGHT CHAIN) / FV


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 ANTIBODY (ANTI BETA SUBUNIT) (HEAVY CHAIN) / FV


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

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Sugars , 1 types, 2 molecules

#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.3 Å3/Da / Density % sol: 54 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDDetails
13 mg/mlprotein1drop
21.8 Mammonium sulfate1reservoir
3100 mMTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HRP, 1IGC, 2IMN

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
RfactorNum. reflection% reflectionSelection details
Rfree0.31 890 6 %RANDOM
Rwork0.26 ---
obs0.26 9772 79 %-
Displacement parametersBiso mean: 25 Å2
Refinement stepCycle: LAST / Resolution: 3.5→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4910 0 28 0 4938
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.14
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.29
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.5→3.65 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.37 116 10 %
Rwork0.36 1261 -
obs--80 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.14
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.29
LS refinement shell
*PLUS
Highest resolution: 3.5 Å / Rfactor Rfree: 0.37 / Rfactor Rwork: 0.36

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