6TSA | pdb_00006tsa

Crystal structure of human L ferritin (HuLf) Fe(III)-loaded for 30 minutes

PDB DOI: https://doi.org/10.2210/pdb6TSA/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-12-20 Released: 2020-02-19
Deposition Author(s): Pozzi, C., Ciambellotti, S., Turano, P., Mangani, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.258 (Depositor), 0.258 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Iron Biomineral Growth from the Initial Nucleation Seed in L-Ferritin.

Ciambellotti, S., Pozzi, C., Mangani, S., Turano, P.

(2020) Chemistry 26: 5770-5773

PubMed: 32027764 Search on PubMed
DOI: https://doi.org/10.1002/chem.202000064
Primary Citation Related Structures:
6TR9, 6TRZ, 6TS0, 6TS1, 6TSA, 6TSF, 6TSJ, 6TSS, 6TSX

PubMed Abstract:
X-ray structures of homopolymeric human L-ferritin and horse spleen ferritin were solved by freezing protein crystals at different time intervals after exposure to a ferric salt and revealed the growth of an octa-nuclear iron cluster on the inner surface of the protein cage with a key role played by some glutamate residues. An atomic resolution view of how the cluster formation develops starting from a (μ ³ -oxo)tris[(μ ² -glutamato-κO:κO')](glutamato-κO)(diaquo)triiron(III) seed is provided. The results support the idea that iron biomineralization in ferritin is a process initiating at the level of the protein surface, capable of contributing coordination bonds and electrostatic guidance.

Organizational Affiliation

Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, 50019, Italy.

Macromolecule Content

Total Structure Weight: 21.06 kDa
Atom Count: 1,566
Modeled Residue Count: 172
Deposited Residue Count: 175
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin light chain	A [auth AAA]	175	Homo sapiens	Mutation(s): 0 Gene Names: FTL
UniProt & NIH Common Fund Data Resources
Find proteins for P02792 (Homo sapiens) Explore P02792 Go to UniProtKB: P02792
PHAROS: P02792 GTEx: ENSG00000087086
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02792
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain Q [auth AAA] MOL2 format, chain Q [auth AAA] mmCIF format, chain Q [auth AAA]	Q [auth AAA]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain Q [auth AAA] Interactions & Density Focus chain Q [auth AAA]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain B [auth AAA] SDF format, chain C [auth AAA] SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] SDF format, chain J [auth AAA] SDF format, chain K [auth AAA] SDF format, chain L [auth AAA] SDF format, chain M [auth AAA] SDF format, chain N [auth AAA] SDF format, chain O [auth AAA] SDF format, chain P [auth AAA] MOL2 format, chain B [auth AAA] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain N [auth AAA] MOL2 format, chain O [auth AAA] MOL2 format, chain P [auth AAA] mmCIF format, chain B [auth AAA] mmCIF format, chain C [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain M [auth AAA] mmCIF format, chain N [auth AAA] mmCIF format, chain O [auth AAA] mmCIF format, chain P [auth AAA]	B [auth AAA] C [auth AAA] D [auth AAA] E [auth AAA] F [auth AAA] B [auth AAA], C [auth AAA], D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], L [auth AAA], M [auth AAA], N [auth AAA], O [auth AAA], P [auth AAA]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Interactions & Density Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA]
O Query on O Download:Ideal Coordinates CCD File SDF format, chain R [auth AAA] SDF format, chain S [auth AAA] SDF format, chain T [auth AAA] SDF format, chain U [auth AAA] MOL2 format, chain R [auth AAA] MOL2 format, chain S [auth AAA] MOL2 format, chain T [auth AAA] MOL2 format, chain U [auth AAA] mmCIF format, chain R [auth AAA] mmCIF format, chain S [auth AAA] mmCIF format, chain T [auth AAA] mmCIF format, chain U [auth AAA]	R [auth AAA], S [auth AAA], T [auth AAA], U [auth AAA]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain R [auth AAA] Focus chain S [auth AAA] Focus chain T [auth AAA] Focus chain U [auth AAA] Interactions & Density Focus chain R [auth AAA] Focus chain S [auth AAA] Focus chain T [auth AAA] Focus chain U [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.258 (Depositor), 0.258 (DCC)
R-Value Work: 0.202 (Depositor), 0.202 (DCC)

Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.69	α = 90
b = 152.69	β = 90
c = 152.69	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-02-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-02-19
Type: Initial release
Version 1.1: 2020-05-20
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description