6QIO

Ternary complex of FcRn ectodomain, FcRn binding optimised human serum albumin and the human growth hormone derivative somapacitan

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


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Literature

Identification of Binding Sites on Human Serum Albumin for Somapacitan, a Long-Acting Growth Hormone Derivative.

Johansson, E., Nielsen, A.D., Demuth, H., Wiberg, C., Schjodt, C.B., Huang, T., Chen, J., Jensen, S., Petersen, J., Thygesen, P.

(2020) Biochemistry 59: 1410-1419

  • DOI: 10.1021/acs.biochem.0c00019
  • Primary Citation of Related Structures:  
    6QIO, 6QIP

  • PubMed Abstract: 

    • Somapacitan, a human growth hormone derivative that binds reversibly to albumin, was investigated for human serum albumin (HSA) and HSA domain binding. Isothermal titration calorimetry (ITC) binding profiles showed high-affinity binding (∼100-1000 nM ...

    Somapacitan, a human growth hormone derivative that binds reversibly to albumin, was investigated for human serum albumin (HSA) and HSA domain binding. Isothermal titration calorimetry (ITC) binding profiles showed high-affinity binding (∼100-1000 nM) of one somapacitan molecule and low-affinity binding (∼1000-10000 nM) of one to two somapacitan molecules to HSA. The high-affinity site was identified in HSA domain III using size exclusion chromatography (SEC) and ITC. SEC studies showed that the neonatal Fc receptor shields one binding site for somapacitan, indicating its position in domain III. A crystal structure of somapacitan in complex with HSA optimized for neonatal Fc receptor binding, having four amino acid residue replacements, identified a low-affinity site in fatty acid-binding site 6 (domain II). Surface plasmon resonance (SPR) showed these replacements affect the kinetics of the high-affinity binding site. Furthermore, small-angle X-ray scattering and SPR brace two somapacitan-binding sites on HSA.

    Organizational Affiliation: 

    Novo Nordisk A/S, Novo Nordisk Park 1, DK-2760 Måløv, Denmark.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serum albuminA585Homo sapiensMutation(s): 4 
Gene Names: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Find proteins for P02768 (Homo sapiens)
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Go to UniProtKB:  P02768
NIH Common Fund Data Resources
PHAROS  P02768
GTEx  ENSG00000163631
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IgG receptor FcRn large subunit p51B274Homo sapiensMutation(s): 0 
Gene Names: FCGRT, FCRN
Find proteins for P55899 (Homo sapiens)
Explore P55899 
Go to UniProtKB:  P55899
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PHAROS  P55899
GTEx  ENSG00000104870
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinC105Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
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PHAROS  P61769
GTEx  ENSG00000166710
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
SomatotropinD191Homo sapiensMutation(s): 1 
Gene Names: GH1
Find proteins for P01241 (Homo sapiens)
Explore P01241 
Go to UniProtKB:  P01241
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PHAROS  P01241
GTEx  ENSG00000259384
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JG5
Query on JG5
Download Ideal Coordinates CCD File 
D
(2S)-6-acetamido-2-[[2-[2-[2-[[4-carboxy-4-[[(4S)-4-carboxy-4-[[2-[2-[2-[4-[16-(1H-tetrazol-5-yl)hexadecanoylsulfamoyl]butanoylamino]ethoxy]ethoxy]acetyl]amino]butanoyl]amino]butanoyl]amino]ethoxy]ethoxy]acetyl]amino]hexanoic acid
C51 H89 N11 O19 S
FKEQBELVDINLPJ-HMVVSKLPSA-N		 Ligand Interaction
MES
Query on MES
Download Ideal Coordinates CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
CYS
Query on CYS
Download Ideal Coordinates CCD File 
B
CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.29α = 90
b = 108.12β = 90
c = 159.53γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2019-01-21 
  • Released Date: 2020-02-05 
    • Deposition Author(s): Johansson, E.

Revision History 

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references