8DNP | pdb_00008dnp

Human Brain Ferritin Heavy Chain

PDB DOI: https://doi.org/10.2210/pdb8DNP/pdb
EM Map EMD-27576: EMDB EMDataResource

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2022-07-11 Released: 2022-11-16
Deposition Author(s): Tringides, M.L.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.69 Å
Aggregation State: TISSUE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

A cryo-electron microscopic approach to elucidate protein structures from human brain microsomes.

Tringides, M.L., Zhang, Z., Morgan, C.E., Su, C.C., Yu, E.W.

(2023) Life Sci Alliance 6

PubMed: 36450447 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.26508/lsa.202201724
Primary Citation Related Structures:
8DNM, 8DNO, 8DNP, 8DNS, 8DNU

PubMed Abstract:
We recently developed a "Build and Retrieve" cryo-electron microscopy (cryo-EM) methodology, which is capable of simultaneously producing near-atomic resolution cryo-EM maps for several individual proteins from a heterogeneous, multiprotein sample. Here we report the use of "Build and Retrieve" to define the composition of a raw human brain microsomal lysate. From this sample, we simultaneously identify and solve cryo-EM structures of five different brain enzymes whose functions affect neurotransmitter recycling, iron metabolism, glycolysis, axonal development, energy homeostasis, and retinoic acid biosynthesis. Interestingly, malfunction of these important proteins has been directly linked to several neurodegenerative disorders, such as Alzheimer's, Huntington's, and Parkinson's diseases. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.

Organizational Affiliation

Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA.

Macromolecule Content

Total Structure Weight: 511.48 kDa
Atom Count: 33,936
Modeled Residue Count: 4,128
Deposited Residue Count: 4,392
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin heavy chain	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	183	Homo sapiens	Mutation(s): 0 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02794
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth A] SDF format, chain VA [auth X] SDF format, chain UA [auth W] SDF format, chain TA [auth V] SDF format, chain SA [auth U] SDF format, chain RA [auth T] SDF format, chain QA [auth S] SDF format, chain PA [auth R] SDF format, chain OA [auth Q] SDF format, chain NA [auth P] SDF format, chain MA [auth O] SDF format, chain LA [auth N] SDF format, chain KA [auth M] SDF format, chain JA [auth L] SDF format, chain IA [auth K] SDF format, chain HA [auth J] SDF format, chain GA [auth I] SDF format, chain FA [auth H] SDF format, chain EA [auth G] SDF format, chain DA [auth F] SDF format, chain CA [auth E] SDF format, chain BA [auth D] SDF format, chain AA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain VA [auth X] MOL2 format, chain UA [auth W] MOL2 format, chain TA [auth V] MOL2 format, chain SA [auth U] MOL2 format, chain RA [auth T] MOL2 format, chain QA [auth S] MOL2 format, chain PA [auth R] MOL2 format, chain OA [auth Q] MOL2 format, chain NA [auth P] MOL2 format, chain MA [auth O] MOL2 format, chain LA [auth N] MOL2 format, chain KA [auth M] MOL2 format, chain JA [auth L] MOL2 format, chain IA [auth K] MOL2 format, chain HA [auth J] MOL2 format, chain GA [auth I] MOL2 format, chain FA [auth H] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain VA [auth X] mmCIF format, chain UA [auth W] mmCIF format, chain TA [auth V] mmCIF format, chain SA [auth U] mmCIF format, chain RA [auth T] mmCIF format, chain QA [auth S] mmCIF format, chain PA [auth R] mmCIF format, chain OA [auth Q] mmCIF format, chain NA [auth P] mmCIF format, chain MA [auth O] mmCIF format, chain LA [auth N] mmCIF format, chain KA [auth M] mmCIF format, chain JA [auth L] mmCIF format, chain IA [auth K] mmCIF format, chain HA [auth J] mmCIF format, chain GA [auth I] mmCIF format, chain FA [auth H] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth D] CA [auth E] DA [auth F] EA [auth G] AA [auth C], BA [auth D], CA [auth E], DA [auth F], EA [auth G], FA [auth H], GA [auth I], HA [auth J], IA [auth K], JA [auth L], KA [auth M], LA [auth N], MA [auth O], NA [auth P], OA [auth Q], PA [auth R], QA [auth S], RA [auth T], SA [auth U], TA [auth V], UA [auth W], VA [auth X], Y [auth A], Z [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain KA [auth M] Focus chain LA [auth N] Focus chain MA [auth O] Focus chain NA [auth P] Focus chain OA [auth Q] Focus chain PA [auth R] Focus chain QA [auth S] Focus chain RA [auth T] Focus chain SA [auth U] Focus chain TA [auth V] Focus chain UA [auth W] Focus chain VA [auth X] Focus chain Y [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain KA [auth M] Focus chain LA [auth N] Focus chain MA [auth O] Focus chain NA [auth P] Focus chain OA [auth Q] Focus chain PA [auth R] Focus chain QA [auth S] Focus chain RA [auth T] Focus chain SA [auth U] Focus chain TA [auth V] Focus chain UA [auth W] Focus chain VA [auth X] Focus chain Y [auth A] Focus chain Z [auth B]