8DNU | pdb_00008dnu

Human Brain Glutamine Synthetase

PDB DOI: https://doi.org/10.2210/pdb8DNU/pdb
EM Map EMD-27580: EMDB EMDataResource

Classification: LIGASE
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 Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.73 Å
Aggregation State: TISSUE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 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: 421.73 kDa
Atom Count: 29,320
Modeled Residue Count: 3,700
Deposited Residue Count: 3,730
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine synthetase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	373	Homo sapiens	Mutation(s): 0 EC: 6.3.1.2 (PDB Primary Data), 2.3.1.225 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P15104 (Homo sapiens) Explore P15104 Go to UniProtKB: P15104
PHAROS: P15104 GTEx: ENSG00000135821
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15104
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain T [auth J] SDF format, chain S [auth I] SDF format, chain R [auth H] SDF format, chain Q [auth G] SDF format, chain P [auth F] SDF format, chain O [auth E] SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth A] MOL2 format, chain T [auth J] MOL2 format, chain S [auth I] MOL2 format, chain R [auth H] MOL2 format, chain Q [auth G] MOL2 format, chain P [auth F] MOL2 format, chain O [auth E] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth A] mmCIF format, chain T [auth J] mmCIF format, chain S [auth I] mmCIF format, chain R [auth H] mmCIF format, chain Q [auth G] mmCIF format, chain P [auth F] mmCIF format, chain O [auth E] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth A]	K [auth A] L [auth B] M [auth C] N [auth D] O [auth E] K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth H], S [auth I], T [auth J]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth I] Focus chain T [auth J] Interactions & Density Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth I] Focus chain T [auth J]