5CMQ

Crystal Structure of Zn-bound Human H-Ferritin variant 122H-delta C-star

• PDB DOI: https://doi.org/10.2210/pdb5CMQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-07-17 Released: 2015-09-09 
• Deposition Author(s): Sontz, P.A., Bailey, J.B., Ahn, S., Tezcan, F.A.
• Funding Organization(s): Department of Energy (DOE, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.180 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 

Literature

A Metal Organic Framework with Spherical Protein Nodes: Rational Chemical Design of 3D Protein Crystals.

Sontz, P.A., Bailey, J.B., Ahn, S., Tezcan, F.A.

(2015) J Am Chem Soc 137: 11598-11601

• PubMed: 26305584 
• DOI: https://doi.org/10.1021/jacs.5b07463
• Primary Citation of Related Structures:  
  5CMQ, 5CMR


• PubMed Abstract: 
  

  We describe here the construction of a three-dimensional, porous, crystalline framework formed by spherical protein nodes that assemble into a prescribed lattice arrangement through metal-organic linker-directed interactions. The octahedral iron storage enzyme, ferritin, was engineered in its C3 symmetric pores with tripodal Zn coordination sites. Dynamic light scattering and crystallographic studies established that this Zn-ferritin construct could robustly self-assemble into the desired bcc-type crystals upon coordination of a ditopic linker bearing hydroxamic acid functional groups. This system represents the first example of a ternary protein-metal-organic crystalline framework whose formation is fully dependent on each of its three components.

---

Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

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

Macromolecule Content

• Total Structure Weight: 21.71 kDa 
• Atom Count: 1,676 
• Modelled Residue Count: 172 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin heavy chain	A	182	Homo sapiens	Mutation(s): 5  Gene Names: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P02794 (Homo sapiens) Explore P02794  Go to UniProtKB:  P02794
PHAROS:  P02794 GTEx:  ENSG00000167996

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.180 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.21	α = 90
b = 180.21	β = 90
c = 180.21	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
REFMAC	refinement
Coot	model building
MOLREP	phasing
SCALA	data scaling
MOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Sontz, P.A., Bailey, J.B., Ahn, S., Tezcan, F.A.

---

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-FG02-10ER46677

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2015-09-30
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Advisory, Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description