8SK8: Glutamate dehydrogenase 1, mitochondrial

human liver mitochondrial Glutamate dehydrogenase 1. Determined by electron microscopy at 2.31 Å resolution. Released 21 Feb 2024.

Method: Electron microscopy
Resolution: 2.31 Å
Organism: Homo sapiens
Chains: 6
Atoms: 22,920
Mol. weight: 368.88 kDa
Released: 21 Feb 2024

Explore 8SK8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SK8 contains 142 α-helices and 84 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, C, E and F: 24 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	65-69	5
α-helix	70-87	18
α-helix	95-109	15
β-strand	114-123	10	1
β-strand	129-139	11	1
β-strand	146-152	7	1
α-helix	158-174	17
β-strand	180-186	7	1
α-helix	190-192	3
α-helix	195-211	17
β-strand	220-223	4	1
α-helix	230-240	11
α-helix	241-245	5
α-helix	249-254	6
α-helix	260-262	3
α-helix	271-284	14
α-helix	287-293	7
β-strand	303-307	5	2
α-helix	311-322	12
β-strand	326-331	6	2
β-strand	336-338	3	2
α-helix	345-355	11
β-strand	365-366	2	2
α-helix	367	1
α-helix	371-373	3
β-strand	378-381	4	2
β-strand	388	1	3
α-helix	393-395	3
β-strand	400-402	3	2
β-strand	409	1	3
α-helix	411-419	9
β-strand	423-425	3	2
α-helix	427-430	4
α-helix	433-447	15
α-helix	456-478	23
α-helix	491-498	8
α-helix	502-527	26
α-helix	534-551	18

Chains B and D: 23 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	65-69	5
α-helix	70-87	18
α-helix	95-109	15
β-strand	114-123	10	4
β-strand	129-139	11	4
β-strand	146-152	7	4
α-helix	158-174	17
β-strand	180-186	7	4
α-helix	190-192	3
α-helix	195-211	17
β-strand	220-223	4	4
α-helix	230-240	11
α-helix	241-245	5
α-helix	249-254	6
α-helix	260-262	3
α-helix	271-284	14
α-helix	287-293	7
β-strand	303-307	5	5
α-helix	311-322	12
β-strand	326-331	6	5
β-strand	336-338	3	5
α-helix	345-355	11
β-strand	365-366	2	5
α-helix	367	1
α-helix	371-373	3
β-strand	378-381	4	5
β-strand	388	1	6
β-strand	400-402	3	5
β-strand	409	1	6
α-helix	411-419	9
β-strand	423-425	3	5
α-helix	427-430	4
α-helix	433-447	15
α-helix	456-478	23
α-helix	491-498	8
α-helix	502-527	26
α-helix	534-551	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate dehydrogenase 1, mitochondrial	A, B, C, D, E, F	protein	558	Homo sapiens	P00367 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>8SK8_1 Glutamate dehydrogenase 1, mitochondrial (chains A, B, C, D, E, F)
MYRYLGEALLLSRAGPAALGSASADSAALLGWARGQPAAAPQPGLALAARRHYSEAVADR
EDDPNFFKMVEGFFDRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSF
PIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFG
GAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGIDVPAPDMSTGEREMSWIADTY
ASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFG
DKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELEDFKLQHGSILG
FPKAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLER
NIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGK
HGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYV
NAIEKVFKVYNEAGVTFT

Primary citation

High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology. Zhang, Z., Tringides, M.L., Morgan, C.E. et al. Mol Cell Proteomics (2023) 22:100666-100666. DOI 10.1016/j.mcpro.2023.100666 · PubMed

Other PDB entries of the same protein (UniProt P00367 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8KGY 2.59 Å, Human glutamate dehydrogenase I
1L1F 2.7 Å, Structure of human glutamate dehydrogenase-apo form
6DQG 2.7 Å, Human glutamate dehydrogenase, H454Y mutant
8W4J 3.06 Å, Cryo-EM structure of the KLHL22 E3 ligase bound to human glutamate dehydrogenase I
7UZM 3.24 Å, Glutamate dehydrogenase 1 from human liver
1NR1 3.3 Å, Crystal structure of the R463A mutant of human Glutamate dehydrogenase

Browse structure collections

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