4KN2

Human folate receptor beta (FOLR2) in complex with antifolate pemetrexed


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of human folate receptors reveal biological trafficking states and diversity in folate and antifolate recognition.

Wibowo, A.S.Singh, M.Reeder, K.M.Carter, J.J.Kovach, A.R.Meng, W.Ratnam, M.Zhang, F.Dann, C.E.

(2013) Proc.Natl.Acad.Sci.USA 110: 15180-15188

  • DOI: 10.1073/pnas.1308827110
  • Primary Citation of Related Structures:  
  • Also Cited By: 5EJN

  • PubMed Abstract: 
  • Antifolates, folate analogs that inhibit vitamin B9 (folic acid)-using cellular enzymes, have been used over several decades for the treatment of cancer and inflammatory diseases. Cellular uptake of the antifolates in clinical use occurs primarily vi ...

    Antifolates, folate analogs that inhibit vitamin B9 (folic acid)-using cellular enzymes, have been used over several decades for the treatment of cancer and inflammatory diseases. Cellular uptake of the antifolates in clinical use occurs primarily via widely expressed facilitative membrane transporters. More recently, human folate receptors (FRs), high affinity receptors that transport folate via endocytosis, have been proposed as targets for the specific delivery of new classes of antifolates or folate conjugates to tumors or sites of inflammation. The development of specific, FR-targeted antifolates would be accelerated if additional biophysical data, particularly structural models of the receptors, were available. Here we describe six distinct crystallographic models that provide insight into biological trafficking of FRs and distinct binding modes of folate and antifolates to these receptors. From comparison of the structures, we delineate discrete structural conformations representative of key stages in the endocytic trafficking of FRs and propose models for pH-dependent conformational changes. Additionally, we describe the molecular details of human FR in complex with three clinically prevalent antifolates, pemetrexed (also Alimta), aminopterin, and methotrexate. On the whole, our data form the basis for rapid design and implementation of unique, FR-targeted, folate-based drugs for the treatment of cancer and inflammatory diseases.


    Organizational Affiliation

    Department of Chemistry, Indiana University, Bloomington, IN 47405.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Folate receptor beta
A, B, C
207Homo sapiensMutation(s): 0 
Gene Names: FOLR2
Find proteins for P14207 (Homo sapiens)
Go to Gene View: FOLR2
Go to UniProtKB:  P14207
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A, B, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
LYA
Query on LYA

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Download CCD File 
A, B, C
2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID
LY231514
C20 H21 N5 O6
WBXPDJSOTKVWSJ-ZDUSSCGKSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LYAIC50: 60 - 254 nM (100) BINDINGDB
LYAKd: 54 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 97.443α = 90.00
b = 97.443β = 90.00
c = 348.105γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2013-10-02
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description