5UP9

Crystal Structure of Zn-bound Human Heavy-Chain ferritin variant 122H-delta C-star with para-xylenedihydroxamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Synthetic Modularity of Protein-Metal-Organic Frameworks.

Bailey, J.B.Zhang, L.Chiong, J.A.Ahn, S.Tezcan, F.A.

(2017) J Am Chem Soc 139: 8160-8166

  • DOI: https://doi.org/10.1021/jacs.7b01202
  • Primary Citation of Related Structures:  
    5UP7, 5UP8, 5UP9, 5VTD

  • PubMed Abstract: 

    Previously, we adopted the construction principles of metal-organic frameworks (MOFs) to design a 3D crystalline protein lattice in which pseudospherical ferritin nodes decorated on their C 3 symmetric vertices with Zn coordination sites were connected via a ditopic benzene-dihydroxamate linker. In this work, we have systematically varied both the metal ions presented at the vertices of the ferritin nodes (Zn(II), Ni(II), and Co(II)) and the synthetic dihydroxamate linkers, which yielded an expanded library of 15 ferritin-MOFs with the expected body-centered (cubic or tetragonal) lattice arrangements. Crystallographic and small-angle X-ray scattering (SAXS) analyses indicate that lattice symmetries and dimensions of ferritin-MOFs can be dictated by both the metal and linker components. SAXS measurements on bulk crystalline samples reveal that some ferritin-MOFs can adopt multiple lattice conformations, suggesting dynamic behavior. This work establishes that the self-assembly of ferritin-MOFs is highly robust and that the synthetic modularity that underlies the structural diversity of conventional MOFs can also be applied to the self-assembly of protein-based crystalline materials.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin heavy chain
A, B, C, D, E
A, B, C, D, E, F
182Homo sapiensMutation(s): 5 
Gene Names: FTH1FTHFTHL6OK/SW-cl.84PIG15
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02794
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BYX
Query on BYX

Download Ideal Coordinates CCD File 
W [auth B]2,2'-(1,4-phenylene)bis(N-hydroxyacetamide)
C10 H12 N2 O4
BKDWYNGFJRBIJD-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
MA [auth D]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
GA [auth C]
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
HA [auth C],
M [auth A],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
Q [auth B],
RA [auth E],
SA [auth E],
V [auth B],
VA [auth F],
WA [auth F],
XA [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
G [auth A]
H [auth A]
I [auth A]
AA [auth C],
BA [auth C],
G [auth A],
H [auth A],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
PA [auth E],
QA [auth E],
R [auth B],
S [auth B],
T [auth B],
TA [auth F],
U [auth B],
UA [auth F],
X [auth C],
Y [auth C],
Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.883α = 90
b = 149.883β = 90
c = 162.228γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description