8W4J: KLHL22 E3 ligase

Cryo-EM structure of the KLHL22 E3 ligase bound to human glutamate dehydrogenase I. Determined by electron microscopy at 3.06 Å resolution. Released 1 Nov 2023.

Method: Electron microscopy
Resolution: 3.06 Å
Organism: Homo sapiens
Chains: 8
Atoms: 27,165
Mol. weight: 512.37 kDa
Released: 1 Nov 2023

Explore 8W4J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8W4J contains 187 α-helices and 155 β-strands across 8 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: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	68-87	20
α-helix	100-103	4
α-helix	104-109	6
β-strand	114-123	10	1
β-strand	129-138	10	1
β-strand	146-147	2	2
β-strand	150-152	3	1
α-helix	158-174	17
β-strand	180-181	2	2
β-strand	182-186	5	1
α-helix	190-192	3
α-helix	195-211	17
β-strand	220-221	2	2
α-helix	230-243	14
α-helix	245-247	3
α-helix	251-254	4
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	378-381	4	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	456-477	22
α-helix	489-490	2
α-helix	491-498	8
α-helix	502-527	26
β-strand	533	1	3
α-helix	534-551	18

Chain B: 19 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	66-85	20
α-helix	104-109	6
β-strand	114-123	10	5
β-strand	129-138	10	5
β-strand	147-149	3	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	195-210	16
β-strand	221-223	3	6
α-helix	230-243	14
α-helix	245-247	3
α-helix	251-254	4
α-helix	271-284	14
α-helix	287-293	7
β-strand	303-307	5	7
α-helix	311-321	11
β-strand	326-331	6	7
β-strand	336-338	3	7
α-helix	345-354	10
β-strand	365-367	3	7
β-strand	378-380	3	7
β-strand	400-402	3	7
α-helix	411-419	9
β-strand	423-425	3	7
α-helix	427-430	4
α-helix	433-447	15
α-helix	456-474	19
α-helix	491-498	8
α-helix	502-525	24
α-helix	534-553	20

Chain C: 26 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	66-86	21
α-helix	99-102	4
α-helix	103-105	3
α-helix	106-109	4
β-strand	114-123	10	8
β-strand	129-138	10	8
β-strand	146-147	2	9
β-strand	150-153	4	8
α-helix	158-174	17
β-strand	182-187	6	8
α-helix	190-192	3
α-helix	195-211	17
β-strand	220-221	2	9
β-strand	224	1	8
α-helix	231-239	9
α-helix	240-244	5
α-helix	245-247	3
α-helix	251-254	4
α-helix	260-262	3
α-helix	271-284	14
α-helix	287-293	7
β-strand	303-306	4	10
α-helix	311-321	11
β-strand	326-330	5	10
β-strand	337-338	2	10
α-helix	345-354	10
β-strand	365-366	2	10
α-helix	371-373	3
β-strand	380	1	10
β-strand	388	1	11
α-helix	393-395	3
β-strand	400-402	3	12
β-strand	409	1	11
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	534-551	18

Chain D: 23 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	66-88	23
α-helix	101-103	3
α-helix	104-109	6
β-strand	114-122	9	5
β-strand	130-138	9	5
β-strand	146-147	2	13
β-strand	148-153	6	5
α-helix	158-174	17
β-strand	182-187	6	5
α-helix	190-192	3
α-helix	195-212	18
β-strand	220-221	2	13
β-strand	224	1	5
α-helix	230-240	11
α-helix	251-253	3
α-helix	260-262	3
α-helix	271-284	14
α-helix	287-290	4
β-strand	303-307	5	14
α-helix	311-322	12
β-strand	326-331	6	14
β-strand	337-338	2	14
α-helix	345-354	10
β-strand	365	1	14
α-helix	371-373	3
β-strand	378-381	4	14
β-strand	388	1	15
α-helix	393-395	3
β-strand	400-402	3	14
β-strand	409	1	15
α-helix	411-419	9
β-strand	423-425	3	14
α-helix	427-430	4
α-helix	433-447	15
α-helix	456-477	22
α-helix	488-490	3
α-helix	491-498	8
α-helix	502-527	26
α-helix	534-551	18

Chain E: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	66-85	20
α-helix	104-109	6
β-strand	114-123	10	1
β-strand	129-138	10	1
β-strand	146-149	4	16
β-strand	150-152	3	1
α-helix	158-175	18
β-strand	180-181	2	16
β-strand	182-186	5	1
α-helix	190-192	3
α-helix	195-210	16
β-strand	221-223	3	16
α-helix	230-243	14
α-helix	251-254	4
α-helix	271-284	14
α-helix	287-293	7
β-strand	303-307	5	17
α-helix	311-322	12
β-strand	326-331	6	17
β-strand	337-338	2	17
α-helix	345-354	10
β-strand	365	1	17
α-helix	371-373	3
β-strand	378-381	4	17
β-strand	388	1	18
α-helix	393-395	3
β-strand	400-402	3	17
β-strand	409	1	18
α-helix	411-419	9
β-strand	423-425	3	17
α-helix	427-430	4
α-helix	433-447	15
α-helix	456-477	22
α-helix	488-490	3
α-helix	491-498	8
α-helix	502-527	26
α-helix	534-553	20

Chain F: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	66-88	23
α-helix	100-103	4
α-helix	104-109	6
β-strand	114-123	10	8
β-strand	129-138	10	8
β-strand	146-149	4	8
β-strand	152-153	2	8
α-helix	158-174	17
β-strand	182-187	6	8
α-helix	190-192	3
α-helix	195-211	17
β-strand	220-223	4	8
α-helix	230-239	10
α-helix	240-244	5
α-helix	251-254	4
α-helix	260-262	3
α-helix	271-284	14
α-helix	287-293	7
β-strand	303-307	5	19
α-helix	311-322	12
β-strand	326-330	5	19
β-strand	337-338	2	19
α-helix	345-354	10
β-strand	361	1	20
β-strand	364	1	20
β-strand	365	1	19
α-helix	366-368	3
β-strand	378-381	4	19
β-strand	388	1	21
β-strand	400-402	3	19
β-strand	409	1	21
α-helix	411-419	9
β-strand	423-425	3	19
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 I: 26 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	32-46	15
β-strand	56	1	22
β-strand	59	1	22
α-helix	65-71	7
α-helix	74-79	6
α-helix	85-87	3
α-helix	98-110	13
α-helix	121-128	8
α-helix	133-145	13
α-helix	149-151	3
α-helix	152-162	11
α-helix	168-177	10
α-helix	179-182	4
α-helix	187-190	4
α-helix	194-201	8
α-helix	212-221	10
α-helix	224-227	4
α-helix	239-242	4
α-helix	251-260	10
α-helix	267-275	9
α-helix	276-278	3
α-helix	292-294	3
β-strand	322	1	23
β-strand	327	1	23
β-strand	347	1	24
β-strand	350	1	24
α-helix	382-385	4
β-strand	417-418	2	25
β-strand	427-428	2	25
α-helix	430-432	3
β-strand	442-444	3	26
β-strand	447-449	3	26
β-strand	455	1	27
β-strand	458	1	27
β-strand	467	1	28
β-strand	472	1	28
β-strand	488-491	4	29
β-strand	494-497	4	29
β-strand	498	1	30
β-strand	514	1	30
α-helix	528-530	3
β-strand	533	1	31
α-helix	537-539	3
β-strand	552-553	2	31
β-strand	558-559	2	31
β-strand	565-567	3	32
β-strand	572-574	3	32
α-helix	592-594	3
α-helix	595-599	5

Chain J: 28 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	32-45	14
β-strand	55-56	2	33
β-strand	59-60	2	33
α-helix	65-69	5
α-helix	73-79	7
α-helix	84-87	4
α-helix	98-110	13
α-helix	120-129	10
α-helix	133-145	13
α-helix	149-151	3
α-helix	153-162	10
α-helix	167-184	18
α-helix	187-190	4
α-helix	193-201	9
α-helix	210-221	12
α-helix	224-227	4
α-helix	239-243	5
α-helix	251-259	9
α-helix	265-278	14
α-helix	280-282	3
α-helix	284-286	3
β-strand	303	1	34
β-strand	306-307	2	35
β-strand	313-314	2	35
β-strand	319-322	4	36
β-strand	327-330	4	36
β-strand	343-347	5	37
β-strand	350-354	5	37
β-strand	370-373	4	37
β-strand	378-380	3	37
β-strand	394-397	4	38
β-strand	400-403	4	38
β-strand	407	1	39
β-strand	412	1	39
β-strand	420	1	40
β-strand	425	1	40
α-helix	430-432	3
β-strand	442-443	2	41
β-strand	448-449	2	41
β-strand	450	1	42
β-strand	454-455	2	43
β-strand	458-459	2	43
α-helix	460	1
β-strand	464	1	42
β-strand	467	1	44
β-strand	472	1	44
β-strand	475	1	42
α-helix	477-479	3
β-strand	491	1	45
β-strand	494	1	45
α-helix	503-505	3
β-strand	518	1	46
β-strand	523	1	46
α-helix	528-530	3
α-helix	537	1
β-strand	538-542	5	47
β-strand	545-549	5	47
β-strand	552-553	2	48
β-strand	558-559	2	48
β-strand	564-566	3	47
α-helix	575-579	5
β-strand	583-584	2	35
β-strand	587	1	34
α-helix	592-594	3
α-helix	595-598	4

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)
Kelch-like protein 22	I, J	protein	634	Homo sapiens	Q53GT1 (AlphaFold model)

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

>8W4J_1 Glutamate dehydrogenase 1, mitochondrial (chains A, B, C, D, E, F)
MYRYLGEALLLSRAGPAALGSASADSAALLGWARGQPAAAPQPGLALAARRHYSEAVADR
EDDPNFFKMVEGFFDRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSF
PIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFG
GAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGIDVPAPDMSTGEREMSWIADTY
ASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFG
DKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELEDFKLQHGSILG
FPKAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLER
NIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGK
HGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYV
NAIEKVFKVYNEAGVTFT

Sequence of entity 2 (I, J), FASTA

>8W4J_2 Kelch-like protein 22 (chains I, J)
MAEEQEFTQLCKLPAQPSHPHCVNNTYRSAQHSQALLRGLLALRDSGILFDVVLVVEGRH
IEAHRILLAASCDYFRGMFAGGLKEMEQEEVLIHGVSYNAMCQILHFIYTSELELSLSNV
QETLVAACQLQIPEIIHFCCDFLMSWVDEENILDVYRLAELFDLSRLTEQLDTYILKNFV
AFSRTDKYRQLPLEKVYSLLSSNRLEVSCETEVYEGALLYHYSLEQVQADQISLHEPPKL
LETVRFPLMEAEVLQRLHDKLDPSPLRDTVASALMYHRNESLQPSLQSPQTELRSDFQCV
VGFGGIHSTPSTVLSDQAKYLNPLLGEWKHFTASLAPRMSNQGIAVLNNFVYLIGGDNNV
QGFRAESRCWRYDPRHNRWFQIQSLQQEHADLSVCVVGRYIYAVAGRDYHNDLNAVERYD
PATNSWAYVAPLKREVYAHAGATLEGKMYITCGRRGEDYLKETHCYDPGSNTWHTLADGP
VRRAWHGMATLLNKLYVIGGSNNDAGYRRDVHQVACYSCTSGQWSSVCPLPAGHGEPGIA
VLDNRIYVLGGRSHNRGSRTGYVHIYDVEKDCWEEGPQLDNSISGLAACVLTLPRSLLLE
PPRGTPDRSQADPDFASEVMSVSDWEEFDNSSED

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
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
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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