Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.23 kDa 
• Atom Count: 1883 
• Modelled Residue Count: 184 
• Deposited Residue Count: 187 
• Unique protein chains: 1

4M6J

Crystal structure of human dihydrofolate reductase (DHFR) bound to NADPH

• PDB DOI: 10.2210/pdb4M6J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-09 Released: 2013-09-25 
• Deposition Author(s): Bhabha, G., Ekiert, D.C., Wright, P.E., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.184 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Literature

Divergent evolution of protein conformational dynamics in dihydrofolate reductase.

Bhabha, G., Ekiert, D.C., Jennewein, M., Zmasek, C.M., Tuttle, L.M., Kroon, G., Dyson, H.J., Godzik, A., Wilson, I.A., Wright, P.E.

(2013) Nat Struct Mol Biol 20: 1243-1249

• PubMed: 24077226 
• DOI: 10.1038/nsmb.2676
• Primary Citation of Related Structures:  
  4M6J, 4M6K, 4M6L


• PubMed Abstract: 
  

Molecular evolution is driven by mutations, which may affect the fitness of an organism and are then subject to natural selection or genetic drift. Analysis of primary protein sequences and tertiary structures has yielded valuable insights into the evolution of protein function, but little is known about the evolution of functional mechanisms, protein dynamics and conformational plasticity essential for activity. We characterized the atomic-level motions across divergent members of the dihydrofolate reductase (DHFR) family. Despite structural similarity, Escherichia coli and human DHFRs use different dynamic mechanisms to perform the same function, and human DHFR cannot complement DHFR-deficient E. coli cells. Identification of the primary-sequence determinants of flexibility in DHFRs from several species allowed us to propose a likely scenario for the evolution of functionally important DHFR dynamics following a pattern of divergent evolution that is tuned by cellular environment.

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Organizational Affiliation: 

1] Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California, USA. [2] Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, California, USA. [3].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	187	Homo sapiens	Mutation(s): 0  Gene Names: DHFR EC: 1.5.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P00374 (Homo sapiens) Explore P00374  Go to UniProtKB:  P00374
PHAROS:  P00374 GTEx:  ENSG00000228716

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.184 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.958	α = 90
b = 65.525	β = 90
c = 152.251	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-09 
• Released Date: 2013-09-25 
Deposition Author(s): Bhabha, G., Ekiert, D.C., Wright, P.E., Wilson, I.A.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2013-10-16
  Changes: Database references
• Version 1.2: 2013-11-20
  Changes: Database references