8KGY: Human glutamate dehydrogenase I

Human glutamate dehydrogenase I. Determined by electron microscopy at 2.59 Å resolution. Released 25 Oct 2023.

Method: Electron microscopy
Resolution: 2.59 Å
Organism: Homo sapiens
Chains: 6
Atoms: 21,846
Mol. weight: 368.88 kDa
Released: 25 Oct 2023

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

Secondary structure: helices and β-sheets

8KGY contains 132 α-helices and 90 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.

Chain A: 21 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	66-87	22
α-helix	99-102	4
α-helix	104-109	6
β-strand	114-123	10	1
β-strand	129-138	10	1
β-strand	146-149	4	2
β-strand	150-152	3	1
α-helix	158-174	17
β-strand	182-186	5	1
α-helix	190-192	3
α-helix	195-211	17
β-strand	220-223	4	2
α-helix	230-243	14
α-helix	251-253	3
α-helix	260-262	3
α-helix	271-284	14
α-helix	287-293	7
β-strand	303-307	5	3
α-helix	311-322	12
β-strand	326-331	6	3
β-strand	337-338	2	3
α-helix	345-354	10
β-strand	365	1	3
α-helix	371-373	3
β-strand	378-380	3	3
β-strand	388	1	4
β-strand	400-402	3	3
β-strand	409	1	4
α-helix	411-419	9
β-strand	423-425	3	3
α-helix	427-430	4
α-helix	433-447	15
α-helix	456-475	20
α-helix	491-498	8
α-helix	502-527	26
α-helix	534-551	18

Chain B: 22 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	66-87	22
α-helix	98-100	3
α-helix	104-109	6
β-strand	114-123	10	5
β-strand	129-138	10	5
β-strand	146-149	4	6
β-strand	150-152	3	5
α-helix	158-174	17
β-strand	182-186	5	5
α-helix	190-192	3
α-helix	195-211	17
β-strand	220-223	4	6
α-helix	230-243	14
α-helix	251-253	3
α-helix	260-262	3
α-helix	271-284	14
α-helix	287-293	7
β-strand	302-307	6	7
α-helix	311-322	12
β-strand	325-331	7	7
β-strand	338	1	8
α-helix	345-354	10
β-strand	365	1	8
α-helix	371-373	3
β-strand	378-381	4	7
β-strand	388	1	9
α-helix	393-395	3
β-strand	400-402	3	7
β-strand	409	1	9
α-helix	411-419	9
β-strand	423-425	3	7
α-helix	427-430	4
α-helix	433-447	15
α-helix	456-475	20
α-helix	491-498	8
α-helix	502-527	26
α-helix	534-552	19

Chain C: 22 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	66-86	21
α-helix	104-109	6
β-strand	114-123	10	10
β-strand	129-138	10	10
β-strand	146-149	4	11
β-strand	150-152	3	10
α-helix	158-174	17
β-strand	182-186	5	10
α-helix	190-192	3
α-helix	195-211	17
β-strand	220-223	4	11
α-helix	230-243	14
α-helix	251-253	3
α-helix	260-262	3
α-helix	271-284	14
α-helix	287-293	7
β-strand	303-306	4	12
α-helix	311-322	12
β-strand	326-330	5	12
β-strand	337-338	2	12
α-helix	345-354	10
β-strand	365	1	12
α-helix	371-373	3
β-strand	378-380	3	12
β-strand	388	1	13
α-helix	393-395	3
β-strand	400-402	3	12
β-strand	409	1	13
α-helix	411-419	9
β-strand	423-425	3	12
α-helix	427-430	4
α-helix	433-447	15
α-helix	456-478	23
α-helix	488-490	3
α-helix	491-498	8
α-helix	502-527	26
α-helix	534-553	20

Chain D: 22 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	66-88	23
α-helix	99-102	4
α-helix	104-109	6
β-strand	114-122	9	5
β-strand	130-138	9	5
β-strand	146-149	4	14
β-strand	150-152	3	5
α-helix	158-174	17
β-strand	182-186	5	5
α-helix	190-192	3
α-helix	195-211	17
β-strand	220-223	4	14
α-helix	230-243	14
α-helix	251-253	3
α-helix	260-262	3
α-helix	271-284	14
α-helix	287-293	7
β-strand	303-307	5	15
α-helix	311-322	12
β-strand	326-331	6	15
β-strand	337-338	2	15
α-helix	345-354	10
β-strand	365	1	15
α-helix	371-373	3
β-strand	378-380	3	15
β-strand	388	1	16
α-helix	393-395	3
β-strand	400-402	3	15
β-strand	409	1	16
α-helix	411-419	9
β-strand	423-425	3	15
α-helix	427-430	4
α-helix	433-447	15
α-helix	456-475	20
α-helix	491-498	8
α-helix	503-527	25
α-helix	534-553	20

Chain E: 22 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	66-88	23
α-helix	99-102	4
α-helix	104-109	6
β-strand	114-123	10	1
β-strand	129-138	10	1
β-strand	146-149	4	17
β-strand	150-152	3	1
α-helix	158-174	17
β-strand	182-186	5	1
α-helix	190-192	3
α-helix	195-211	17
β-strand	220-223	4	17
α-helix	230-243	14
α-helix	251-253	3
α-helix	260-262	3
α-helix	271-284	14
α-helix	287-293	7
β-strand	303-307	5	18
α-helix	311-322	12
β-strand	326-331	6	18
β-strand	337-338	2	18
α-helix	345-354	10
β-strand	365	1	18
α-helix	371-373	3
β-strand	378-381	4	18
β-strand	388	1	19
β-strand	400-402	3	18
β-strand	409	1	19
α-helix	411-419	9
β-strand	423-425	3	18
α-helix	427-430	4
α-helix	433-447	15
α-helix	456-475	20
α-helix	488-490	3
α-helix	491-498	8
α-helix	502-527	26
α-helix	534-553	20

Chain F: 23 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	66-87	22
α-helix	98-103	6
α-helix	104-109	6
β-strand	114-123	10	10
β-strand	129-138	10	10
β-strand	146-149	4	20
β-strand	150-152	3	10
α-helix	158-174	17
β-strand	182-186	5	10
α-helix	190-192	3
α-helix	195-211	17
β-strand	220-223	4	20
α-helix	230-243	14
α-helix	251-253	3
α-helix	260-262	3
α-helix	271-284	14
α-helix	287-293	7
β-strand	303-307	5	21
α-helix	311-322	12
β-strand	326-331	6	21
β-strand	337-338	2	21
α-helix	345-354	10
β-strand	365	1	21
α-helix	371-373	3
β-strand	378-381	4	21
β-strand	388	1	22
α-helix	393-395	3
β-strand	400-402	3	21
β-strand	409	1	22
α-helix	411-419	9
β-strand	423-425	3	21
α-helix	427-430	4
α-helix	433-447	15
α-helix	456-475	20
α-helix	488-490	3
α-helix	491-498	8
α-helix	502-527	26
α-helix	534-552	19

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

>8KGY_1 Glutamate dehydrogenase 1, mitochondrial (chains A, B, C, D, E, F)
MYRYLGEALLLSRAGPAALGSASADSAALLGWARGQPAAAPQPGLALAARRHYSEAVADR
EDDPNFFKMVEGFFDRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSF
PIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFG
GAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGIDVPAPDMSTGEREMSWIADTY
ASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFG
DKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELEDFKLQHGSILG
FPKAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLER
NIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGK
HGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYV
NAIEKVFKVYNEAGVTFT

Primary citation

Cryo-EM structure of the KLHL22 E3 ligase bound to an oligomeric metabolic enzyme. Teng, F., Wang, Y., Liu, M. et al. Structure (2023) 31:1431. DOI 10.1016/j.str.2023.09.002 · PubMed

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

8SK8 2.31 Å, human liver mitochondrial Glutamate dehydrogenase 1
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

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