8PP5 | pdb_00008pp5

Unitary crystal structure of positively supercharged ferritin variant Ftn(pos)-m1 (Mg Formate condition)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.193 (Depositor), 0.159 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.160 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8PP5

This is version 1.1 of the entry. See complete history

Literature

Assembly Requirements for the Construction of Large-Scale Binary Protein Structures.

Lang, L.Bohler, H.Wagler, H.Beck, T.

(2024) Biomacromolecules 25: 177-187

  • DOI: https://doi.org/10.1021/acs.biomac.3c00891
  • Primary Citation Related Structures: 
    8PP2, 8PP3, 8PP4, 8PP5

  • PubMed Abstract: 

    The precise assembly of multiple biomacromolecules into well-defined structures and materials is of great importance for various biomedical and nanobiotechnological applications. In this study, we investigate the assembly requirements for two-component materials using charged protein nanocages as building blocks. To achieve this, we designed several variants of ferritin nanocages to determine the surface characteristics necessary for the formation of large-scale binary three-dimensional (3D) assemblies. These nanocage variants were employed in protein crystallization experiments and macromolecular crystallography analyses, complemented by computational methods. Through the screening of nanocage variant combinations at various ionic strengths, we identified three essential features for successful assembly: (1) the presence of a favored crystal contact region, (2) the presence of a charged patch not involved in crystal contacts, and (3) sufficient distinctiveness between the nanocages. Surprisingly, the absence of noncrystal contact mediating patches had a detrimental effect on the assemblies, highlighting their unexpected importance. Intriguingly, we observed the formation of not only binary structures but also both negatively and positively charged unitary structures under previously exclusively binary conditions. Overall, our findings will inform future design strategies by providing some design rules, showcasing the utility of supercharging symmetric building blocks in facilitating the assembly of biomacromolecules into large-scale binary 3D assemblies.


  • Organizational Affiliation
    • Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 122.24 kDa 
  • Atom Count: 9,503 
  • Modeled Residue Count: 1,032 
  • Deposited Residue Count: 1,032 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferritin heavy chain, N-terminally processed
A, B, C, D, E
A, B, C, D, E, F
172Homo sapiensMutation(s): 9 
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE

Query on FE



Download:Ideal Coordinates CCD File
G [auth A]
I [auth B]
K [auth C]
N [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
N [auth D],
O [auth E],
P [auth F]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A],
J [auth B],
L [auth C],
M [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.193 (Depositor), 0.159 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.898α = 90
b = 126.898β = 90
c = 187.468γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata scaling
xia2data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany2056

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Database references