1E9J

SOLUTION STRUCTURE OF THE A-SUBUNIT OF HUMAN CHORIONIC GONADOTROPIN [INCLUDING A SINGLE GLCNAC RESIDUE AT ASN52 AND ASN78]


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 26 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Effects of the N-linked glycans on the 3D structure of the free alpha-subunit of human chorionic gonadotropin.

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

(2000) Biochemistry 39: 6012-6021

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHORIONIC GONADOTROPINA92Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 26 
  • OLDERADO: 1E9J Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-25
    Type: Initial release
  • Version 1.1: 2011-10-19
    Changes: Non-polymer description, Other, Version format compliance
  • Version 1.2: 2017-07-12
    Changes: Advisory
  • Version 1.3: 2018-01-17
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary