Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.86 kDa 
• Atom Count: 817 
• Modelled Residue Count: 92 
• Deposited Residue Count: 92 
• Unique protein chains: 1

1HD4

SOLUTION STRUCTURE OF THE A-SUBUNIT OF HUMAN CHORIONIC GONADOTROPIN [MODELED WITH DIANTENNARY GLYCAN AT ASN78]

• PDB DOI: 10.2210/pdb1HD4/pdb

• Classification: GLYCOPROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2000-11-07 Released: 2000-12-07 
• Deposition Author(s): Erbel, P.J.A., Karimi-Nejad, Y., van Kuik, J.A., Boelens, R., Kamerling, J.P., Vliegenthart, J.F.G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 150 
• Conformers Submitted: 26 

Literature

Effects of the N-Linked Glycans on the 3D Structure of the Free A-Subunit of Human Chorionic Gonadotropin

Erbel, P.J.A., Karimi-Nejad, Y., van Kuik, J.A., Boelens, R., Kamerling, J.P., Vliegenthart, J.F.G.

(2000) Biochemistry 39: 6012-6021

• PubMed: 10821673 
• DOI: 10.1021/bi992786n
• Primary Citation of Related Structures:  
  1E9J, 1HD4


• PubMed Abstract: 
  

To gain insight into intramolecular carbohydrate-protein interactions at the molecular level, the solution structure of differently deglycosylated variants of the alpha-subunit of human chorionic gonadotropin have been studied by NMR spectroscopy. Significant differences in chemical shifts and NOE intensities were observed for amino acid residues close to the carbohydrate chain at Asn78 upon deglycosylation beyond Asn78-bound GlcNAc. As no straightforward strategy is available for the calculation of the NMR structure of intact glycoproteins, a suitable computational protocol had to be developed. To this end, the X-PLOR carbohydrate force field designed for structure refinement was extended and modified. Furthermore, a computational strategy was devised to facilitate successful protein folding in the presence of extended glycans during the simulation. The values for phi and psi dihedral angles of the glycosidic linkages of the oligosaccharide core fragments GlcNAc2(beta1-4)GlcNAc1 and Man3(beta1-4)GlcNAc2 are restricted to a limited range of the broad conformational energy minima accessible for free glycans. This demonstrates that the protein core affects the dynamic behavior of the glycan at Asn78 by steric hindrance. Reciprocally, the NMR structures indicate that the glycan at Asn78 affects the stability of the protein core. The backbone angular order parameters and displacement data of the generated conformers display especially for the beta-turn 20-23 a decreased structural order upon splitting off the glycan beyond the Asn78-bound GlcNAc. In particular, the Asn-bound GlcNAc shields the protein surface from the hydrophilic environment through interaction with predominantly hydrophobic amino acid residues located in both twisted beta-hairpins consisting of residues 10-28 and 59-84.

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Organizational Affiliation: 

Department of Bio-Organic Chemistry, Bijvoet Center, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHORIONIC GONADOTROPIN	A	92	Homo sapiens	Mutation(s): 0  Gene Names: CGA
UniProt & NIH Common Fund Data Resources
Find proteins for P01215 (Homo sapiens) Explore P01215  Go to UniProtKB:  P01215
PHAROS:  P01215 GTEx:  ENSG00000135346

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G36191CD GlyCosmos:  G36191CD GlyGen:  G36191CD

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 150 
• Conformers Submitted: 26 
• OLDERADO: 1HD4 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-11-07 
• Released Date: 2000-12-07 
Deposition Author(s): Erbel, P.J.A., Karimi-Nejad, Y., van Kuik, J.A., Boelens, R., Kamerling, J.P., Vliegenthart, J.F.G.

Revision History  

• Version 1.0: 2000-12-07
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Database references, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary