Macromolecule Content

Total Structure Weight: 486.14 kDa
Atom Count: 35,855
Modelled Residue Count: 4,152
Deposited Residue Count: 4,152
Unique protein chains: 1

8CPV

Human apoferritin

PDB DOI: 10.2210/pdb8CPV/pdb
EM Map EMD-16787: EMDB EMDataResource

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-03-03 Released: 2023-03-15
Deposition Author(s): Last, M.G.F., Noteborn, W.E.M., Sharp, T.H.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.76 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Super-resolution fluorescence imaging of cryosamples does not damage protein structure

Last, M.G.F., Noteborn, W.E.M., Voortman, L.M., Sharp, T.H.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin heavy chain, N-terminally processed	A [auth 1], B [auth 2], C [auth 4], D [auth 6], E [auth A], A [auth 1], B [auth 2], C [auth 4], D [auth 6], E [auth A], F [auth B], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth K], M, N [auth O], O [auth P], P [auth Q], Q [auth S], R [auth U], S [auth W], T [auth X], U [auth Y], V [auth a], W [auth e], X [auth r]	173	Homo sapiens	Mutation(s): 1 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02794
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth 1] SDF format, chain CA [auth 2] SDF format, chain DA [auth 2] SDF format, chain FA [auth 4] SDF format, chain HA [auth 6] SDF format, chain IA [auth 6] SDF format, chain KA [auth A] SDF format, chain MA [auth B] SDF format, chain QA [auth G] SDF format, chain SA [auth H] SDF format, chain TA [auth H] SDF format, chain XA [auth M] SDF format, chain Z [auth 1] SDF format, chain ZA [auth O] MOL2 format, chain AA [auth 1] MOL2 format, chain CA [auth 2] MOL2 format, chain DA [auth 2] MOL2 format, chain FA [auth 4] MOL2 format, chain HA [auth 6] MOL2 format, chain IA [auth 6] MOL2 format, chain KA [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain SA [auth H] MOL2 format, chain TA [auth H] MOL2 format, chain XA [auth M] MOL2 format, chain Z [auth 1] MOL2 format, chain ZA [auth O]	AA [auth 1], CA [auth 2], DA [auth 2], FA [auth 4], HA [auth 6], AA [auth 1], CA [auth 2], DA [auth 2], FA [auth 4], HA [auth 6], IA [auth 6], KA [auth A], MA [auth B], QA [auth G], SA [auth H], TA [auth H], XA [auth M], Z [auth 1], ZA [auth O]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AB [auth P] SDF format, chain BA [auth 2] SDF format, chain BB [auth Q] SDF format, chain CB [auth S] SDF format, chain DB [auth U] SDF format, chain EA [auth 4] SDF format, chain EB [auth W] SDF format, chain FB [auth X] SDF format, chain GA [auth 6] SDF format, chain GB [auth Y] SDF format, chain HB [auth a] SDF format, chain IB [auth e] SDF format, chain JA [auth A] SDF format, chain JB [auth r] SDF format, chain LA [auth B] SDF format, chain NA [auth E] SDF format, chain OA [auth F] SDF format, chain PA [auth G] SDF format, chain RA [auth H] SDF format, chain UA [auth I] SDF format, chain VA [auth K] SDF format, chain WA [auth M] SDF format, chain Y [auth 1] SDF format, chain YA [auth O] MOL2 format, chain AB [auth P] MOL2 format, chain BA [auth 2] MOL2 format, chain BB [auth Q] MOL2 format, chain CB [auth S] MOL2 format, chain DB [auth U] MOL2 format, chain EA [auth 4] MOL2 format, chain EB [auth W] MOL2 format, chain FB [auth X] MOL2 format, chain GA [auth 6] MOL2 format, chain GB [auth Y] MOL2 format, chain HB [auth a] MOL2 format, chain IB [auth e] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth r] MOL2 format, chain LA [auth B] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth G] MOL2 format, chain RA [auth H] MOL2 format, chain UA [auth I] MOL2 format, chain VA [auth K] MOL2 format, chain WA [auth M] MOL2 format, chain Y [auth 1] MOL2 format, chain YA [auth O]	AB [auth P], BA [auth 2], BB [auth Q], CB [auth S], DB [auth U], AB [auth P], BA [auth 2], BB [auth Q], CB [auth S], DB [auth U], EA [auth 4], EB [auth W], FB [auth X], GA [auth 6], GB [auth Y], HB [auth a], IB [auth e], JA [auth A], JB [auth r], LA [auth B], NA [auth E], OA [auth F], PA [auth G], RA [auth H], UA [auth I], VA [auth K], WA [auth M], Y [auth 1], YA [auth O]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX Query on CSX	A [auth 1], B [auth 2], C [auth 4], D [auth 6], E [auth A], A [auth 1], B [auth 2], C [auth 4], D [auth 6], E [auth A], F [auth B], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth K], M, N [auth O], O [auth P], P [auth Q], Q [auth S], R [auth U], S [auth W], T [auth X], U [auth Y], V [auth a], W [auth e], X [auth r]	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 1.76 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-15

Deposition Author(s):

Noteborn, W.E.M.

Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	VI.Vidi.193.014

Revision History (Full details and data files)

Version 1.0: 2023-03-15
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.