6KTR | pdb_00006ktr

Crystal structure of fibroblast growth factor 19 in complex with Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.253 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Novel Abs targeting the N-terminus of fibroblast growth factor 19 inhibit hepatocellular carcinoma growth without bile-acid-related side-effects.

Liu, H.Zheng, S.Hou, X.Liu, X.Du, K.Lv, X.Li, Y.Yang, F.Li, W.Sui, J.

(2020) Cancer Sci 111: 1750-1760

  • DOI: https://doi.org/10.1111/cas.14353
  • Primary Citation Related Structures: 
    6KTR

  • PubMed Abstract: 

    Hepatocellular carcinoma (HCC) is a common and particularly fatal form of cancer for which very few drugs are effective. The fibroblast growth factor 19 (FGF19) has been viewed as a driver of HCC development and a potential Ab target for developing novel HCC therapy. However, a previously developed anti-FGF19 Ab disrupted FGF19's normal regulatory function and caused severe bile-acid-related side-effects despite of having potent antitumor effects in preclinical models. Here, we developed novel human Abs (G1A8 and HS29) that specifically target the N-terminus of FGF19. Both Abs inhibited FGF19-induced HCC cell proliferation in vitro and significantly suppressed HCC tumor growth in mouse models. Importantly, no bile-acid-related side effects were observed in preclinical cynomolgus monkeys. Fundamentally, our study demonstrates that it is possible to target FGF19 for anti-HCC therapies without adversely affecting its normal bile acid regulatory function, and highlights the exciting promise of G1A8 or HS29 as potential therapy for HCC.


  • Organizational Affiliation
    • National Institute of Biological Sciences (NIBS), Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 145.33 kDa 
  • Atom Count: 8,740 
  • Modeled Residue Count: 1,118 
  • Deposited Residue Count: 1,334 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
G1A8-Fab-HCA,
E [auth F]
233Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
G1A8-Fab-LCB,
F [auth G]
216Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fibroblast growth factor 19
C, D
218Homo sapiensMutation(s): 0 
Gene Names: FGF19UNQ334/PRO533
UniProt & NIH Common Fund Data Resources
Find proteins for O95750 (Homo sapiens)
Explore O95750 
Go to UniProtKB:  O95750
PHAROS:  O95750
GTEx:  ENSG00000162344 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95750
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
(Subject of Investigation/LOI)

Query on SO4



Download:Ideal Coordinates CCD File
G [auth B]
H [auth C]
I [auth C]
J [auth C]
K [auth C]
G [auth B],
H [auth C],
I [auth C],
J [auth C],
K [auth C],
L [auth D],
M [auth D],
N [auth D],
O [auth D],
R [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NA
(Subject of Investigation/LOI)

Query on NA



Download:Ideal Coordinates CCD File
P [auth F],
Q [auth F],
S [auth G]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.253 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.968α = 90
b = 104.125β = 90
c = 165.365γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary