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- PDB-1hcn: STRUCTURE OF HUMAN CHORIONIC GONADOTROPIN AT 2.6 ANGSTROMS RESOLU... -

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Basic information

Entry
Database: PDB / ID: 1hcn
TitleSTRUCTURE OF HUMAN CHORIONIC GONADOTROPIN AT 2.6 ANGSTROMS RESOLUTION FROM MAD ANALYSIS OF THE SELENOMETHIONYL PROTEIN
Components(HUMAN CHORIONIC GONADOTROPIN) x 2
KeywordsHORMONE
Function / homology
Function and homology information


positive regulation of steroid biosynthetic process / follicle-stimulating hormone activity / follicle-stimulating hormone complex / pituitary gonadotropin complex / luteinizing hormone secretion / follicle-stimulating hormone secretion / Thyroxine biosynthesis / Mineralocorticoid biosynthesis / Glycoprotein hormones / Reactions specific to the complex N-glycan synthesis pathway ...positive regulation of steroid biosynthetic process / follicle-stimulating hormone activity / follicle-stimulating hormone complex / pituitary gonadotropin complex / luteinizing hormone secretion / follicle-stimulating hormone secretion / Thyroxine biosynthesis / Mineralocorticoid biosynthesis / Glycoprotein hormones / Reactions specific to the complex N-glycan synthesis pathway / Hormone ligand-binding receptors / Androgen biosynthesis / follicle-stimulating hormone signaling pathway / female gamete generation / negative regulation of organ growth / regulation of signaling receptor activity / thyroid hormone generation / organ growth / thyroid gland development / hormone-mediated signaling pathway / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / hormone activity / Golgi lumen / cell-cell signaling / G alpha (s) signalling events / positive regulation of cell migration / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / apoptotic process / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Glycoprotein hormones alpha chain / Choriogonadotropin subunit beta 7 / Choriogonadotropin subunit beta 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsWu, H. / Lustbader, J.W. / Liu, Y. / Canfield, R.E. / Hendrickson, W.A.
Citation
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.
#1: Journal: To be Published
Title: The Expression, Characterization and Crystallization of Wild-Type and Selenomethionyl Hcg
Authors: Lustbader, J.W. / Wu, H. / Birken, S. / Pollak, S. / Kolks, M.A.G. / Pound, A.M. / Austin, D. / Hendrickson, W.A. / Canfield, R.E.
History
DepositionJul 1, 1994Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / software / struct_conn
Item: _pdbx_database_status.process_site / _software.classification / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Jul 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 1.6Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
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: HUMAN CHORIONIC GONADOTROPIN
B: HUMAN CHORIONIC GONADOTROPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2094
Polymers25,7672
Non-polymers4422
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-11 kcal/mol
Surface area11090 Å2
MethodPISA
2
A: HUMAN CHORIONIC GONADOTROPIN
B: HUMAN CHORIONIC GONADOTROPIN
hetero molecules

A: HUMAN CHORIONIC GONADOTROPIN
B: HUMAN CHORIONIC GONADOTROPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4188
Polymers51,5334
Non-polymers8854
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area11330 Å2
ΔGint-45 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.100, 85.100, 177.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Atom site foot note1: CIS PROLINE - PRO B 50

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Components

#1: Protein HUMAN CHORIONIC GONADOTROPIN


Mass: 10217.769 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01215
#2: Protein HUMAN CHORIONIC GONADOTROPIN


Mass: 15548.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P01233, UniProt: P0DN86*PLUS
#3: 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


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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.84 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→5 Å / σ(F): 3
Details: HOH 301 MIGHT BE SO4, BUT NO ATTEMPT WAS MADE TO MODEL IT AS S04.
RfactorNum. reflection
Rwork0.199 -
obs0.199 8876
Refinement stepCycle: LAST / Resolution: 2.6→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 28 63 1553
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
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_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.4981
X-RAY DIFFRACTIONx_mcangle_it6.8321.5
X-RAY DIFFRACTIONx_scbond_it5.1241.5
X-RAY DIFFRACTIONx_scangle_it7.7132
Refinement
*PLUS
Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.030.052
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_planar_d0.050.066
X-RAY DIFFRACTIONx_plane_restr0.020.026
X-RAY DIFFRACTIONx_chiral_restr0.150.158

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