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- PDB-1hrp: CRYSTAL STRUCTURE OF HUMAN CHORIONIC GONADOTROPIN -

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Basic information

Entry
Database: PDB / ID: 1hrp
TitleCRYSTAL STRUCTURE OF HUMAN CHORIONIC GONADOTROPIN
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 / 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 / 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: 3 Å
AuthorsLapthorn, A.J. / Harris, D.C. / Isaacs, N.W.
Citation
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Preliminary X-Ray Diffraction Analysis of Human Chorionic Gonadotropin
Authors: Harris, D.C. / Machin, K.J. / Evin, G.M. / Morgan, F.J. / Isaacs, N.W.
History
DepositionAug 15, 1994Processing site: BNL
Revision 1.0Nov 1, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: 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
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)27,0606
Polymers25,7692
Non-polymers1,2914
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint1 kcal/mol
Surface area11460 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)54,12012
Polymers51,5374
Non-polymers2,5828
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area13780 Å2
ΔGint-19 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.680, 88.680, 177.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein HUMAN CHORIONIC GONADOTROPIN


Mass: 10219.741 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: placenta / 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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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
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: 3.9 Å3/Da / Density % sol: 68.46 %
Crystal
*PLUS
Density % sol: 62 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: taken from Harris, D.C., (1989) J. Biol. Chem., 264, 6705.
PH range low: 4.5 / PH range high: 4.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130-40 mg/mlprotein1drop
230 mMsodium acetate1drop
330-36 %satammonium sulfate1reservoir
4sodium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 8365 / % possible obs: 94.9 % / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 3 Å / Rmerge(I) obs: 0.111

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→10 Å / σ(F): 2
Details: IN FINAL CYCLES OF REFINEMENT, 1/2 THE STANDARD X-PLOR WEIGHT WAS APPLIED.
RfactorNum. reflection% reflection
Rfree0.314 --
Rwork0.218 --
obs0.218 7877 92.4 %
Displacement parametersBiso mean: 26.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 84 0 1550
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg2.28
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.218 / Rfactor Rfree: 0.314
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.28

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