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- PDB-1dz7: Solution structure of the a-subunit of human chorionic gonadotrop... -

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Basic information

Entry
Database: PDB / ID: 1dz7
TitleSolution structure of the a-subunit of human chorionic gonadotropin [modeled without carbohydrate residues]
ComponentsCHORIONIC GONADOTROPIN
KeywordsGLYCOPROTEIN / CHORIONIC GONADOTROPIN / CHORIONIC GONADOTROPIN FREE A SUBUNIT / GLYCOPROTEIN STRUCTURE / CYSTINE KNOT / XPLOR
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 / Glycoprotein hormones / 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 / Thyroxine biosynthesis / Mineralocorticoid biosynthesis / Glycoprotein hormones / Hormone ligand-binding receptors / Reactions specific to the complex N-glycan synthesis pathway / Androgen biosynthesis / follicle-stimulating hormone signaling pathway / negative regulation of organ growth / regulation of signaling receptor activity / thyroid hormone generation / organ growth / thyroid gland development / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / hormone-mediated signaling pathway / hormone activity / Golgi lumen / G alpha (s) signalling events / positive regulation of cell migration / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
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. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Glycoprotein hormones alpha chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / DG, SA
AuthorsErbel, P.J.A. / Karimi-Nejad, Y. / De Beer, T. / Boelens, R. / Kamerling, J.P. / Vliegenthart, J.F.G.
CitationJournal: Eur.J.Biochem. / Year: 1999
Title: Solution structure of the alpha-subunit of human chorionic gonadotropin.
Authors: Erbel, P.J. / Karimi-Nejad, Y. / De Beer, T. / Boelens, R. / Kamerling, J.P. / Vliegenthart, J.F.
History
DepositionFeb 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 29, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.4Oct 9, 2019Group: Data collection / Database references / Category: citation / pdbx_nmr_software
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _pdbx_nmr_software.name
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHORIONIC GONADOTROPIN


Theoretical massNumber of molelcules
Total (without water)10,2181
Polymers10,2181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)27 / 100
Representative

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Components

#1: Protein CHORIONIC GONADOTROPIN


Mass: 10217.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM URINE OF PREGNANT WOMEN / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P01215
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: STRUCTURAL STATISTICS FOR THE FAMILY OF 27 AHCG CONFORMERS EXCLUDE THE FLEXIBLE LOOP AND ENDS, SEGMENTS 1-10, 29-58 AND 85-92 (SEE REFERENCE)

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 100 mM / pH: 5.1 / Temperature: 328 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX6002
Varian UNITYPLUSVarianUNITYPLUS7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DG, SA / Software ordinal: 1
Details: SPECIAL REFINEMENT PROCEDURE TO OPTIMIZE CONVERGENCE RATE OF THE CYSTINE KNOT FORMATION
NMR ensembleConformers calculated total number: 100 / Conformers submitted total number: 27

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