8CVZ: Glycogenin-1

Human glycogenin-1 and glycogen synthase-1 complex in the apo ordered state. Determined by electron microscopy at 3.52 Å resolution. Released 13 Jul 2022.

Method: Electron microscopy
Resolution: 3.52 Å
Organism: Homo sapiens
Chains: 10
Atoms: 24,517
Mol. weight: 527.9 kDa
Released: 13 Jul 2022

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

Secondary structure: helices and β-sheets

8CVZ contains 154 α-helices and 111 β-strands across 10 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: 27 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	29-32	4	22
α-helix	43-58	16
α-helix	59-61	3
β-strand	62-67	6	22
α-helix	70-76	7
β-strand	77-79	3	22
α-helix	85-96	12
β-strand	102-106	5	22
β-strand	113-117	5	22
α-helix	125-129	5
α-helix	130-137	8
α-helix	147-168	22
α-helix	171	1
β-strand	176-179	4	22
α-helix	185-193	9
β-strand	199-204	6	22
α-helix	208-216	9
α-helix	229-235	7
α-helix	239-251	13
β-strand	254-257	4	22
α-helix	260-269	10
β-strand	276-277	2	22
β-strand	282	1	23
α-helix	295-311	17
β-strand	324-329	6	24
α-helix	339-355	17
β-strand	362-367	6	24
β-strand	372-375	4	25
α-helix	377-410	34
α-helix	416-419	4
α-helix	422-434	13
α-helix	440-442	3
β-strand	444	1	24
β-strand	446-448	3	25
α-helix	455-463	9
β-strand	473-477	5	24
α-helix	493-499	7
β-strand	502-504	3	24
α-helix	514-522	9
β-strand	526-527	2	24
β-strand	528-529	2	26
α-helix	533-541	9
β-strand	552-553	2	26
α-helix	560-575	16
α-helix	579-589	11
α-helix	593-596	4
β-strand	597	1	23
α-helix	598-615	18

Chain B: 27 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	29-32	4	4
α-helix	43-58	16
α-helix	59-61	3
β-strand	62-67	6	4
α-helix	70-76	7
β-strand	77-79	3	4
α-helix	85-96	12
β-strand	102-106	5	4
β-strand	113-117	5	4
α-helix	125-129	5
α-helix	130-137	8
α-helix	146-168	23
α-helix	171	1
β-strand	176-179	4	4
α-helix	185-193	9
β-strand	199-204	6	4
α-helix	208-216	9
α-helix	229-235	7
α-helix	239-251	13
β-strand	254-257	4	4
α-helix	260-269	10
β-strand	276-277	2	4
α-helix	295-311	17
β-strand	324-328	5	5
α-helix	339-355	17
β-strand	362-366	5	5
β-strand	374-375	2	6
α-helix	377-410	34
α-helix	416-419	4
α-helix	422-435	14
α-helix	440-442	3
β-strand	444	1	5
β-strand	446-447	2	6
α-helix	455-463	9
β-strand	473-477	5	5
α-helix	493-499	7
β-strand	502-504	3	5
α-helix	514-522	9
β-strand	526-527	2	5
β-strand	528-529	2	7
α-helix	533-541	9
β-strand	552-553	2	7
α-helix	560-575	16
α-helix	579-589	11
α-helix	593-596	4
α-helix	598-615	18

Chain C: 28 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	8
α-helix	43-58	16
α-helix	59-61	3
β-strand	62	1	8
β-strand	63-67	5	9
α-helix	70-75	6
β-strand	77-79	3	9
α-helix	85-96	12
β-strand	101-106	6	9
β-strand	113-117	5	9
α-helix	122-124	3
α-helix	125-129	5
α-helix	130-137	8
α-helix	146-167	22
α-helix	172-174	3
β-strand	175-178	4	8
α-helix	182-193	12
β-strand	198-201	4	8
β-strand	204	1	10
α-helix	208-216	9
α-helix	229-235	7
α-helix	239-251	13
β-strand	256-257	2	10
α-helix	260-268	9
β-strand	276-277	2	10
β-strand	282	1	11
α-helix	296-312	17
β-strand	323-327	5	12
α-helix	339-355	17
β-strand	361-364	4	12
β-strand	367	1	13
β-strand	372-375	4	14
α-helix	377-410	34
α-helix	422-434	13
α-helix	440-442	3
β-strand	444	1	15
β-strand	446-448	3	14
α-helix	455-463	9
β-strand	473-475	3	12
β-strand	477	1	15
β-strand	478	1	13
α-helix	481-482	2
α-helix	493-499	7
β-strand	502-504	3	12
α-helix	514-521	8
β-strand	526-527	2	12
β-strand	529	1	16
α-helix	533-541	9
β-strand	553	1	16
α-helix	560-575	16
α-helix	579-589	11
α-helix	594-596	3
β-strand	597	1	11
α-helix	598-616	19

Chain D: 29 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	17
α-helix	43-58	16
α-helix	59-61	3
β-strand	62-63	2	17
β-strand	66-67	2	17
α-helix	70-76	7
β-strand	77	1	18
α-helix	85-96	12
β-strand	101-105	5	17
β-strand	106	1	18
β-strand	113-117	5	17
α-helix	121-125	5
α-helix	126-137	12
α-helix	146-168	23
β-strand	174-178	5	17
α-helix	182-184	3
α-helix	185-194	10
β-strand	198-204	7	17
α-helix	208-216	9
α-helix	229-235	7
α-helix	239-251	13
β-strand	254-257	4	17
α-helix	260-268	9
β-strand	276-277	2	17
α-helix	294-312	19
β-strand	324-329	6	19
α-helix	339-355	17
β-strand	362-367	6	19
β-strand	372-375	4	20
α-helix	377-410	34
α-helix	412-414	3
α-helix	416-419	4
α-helix	424-435	12
α-helix	440-442	3
β-strand	444	1	19
β-strand	446-448	3	20
α-helix	455-463	9
β-strand	473-478	6	19
β-strand	483	1	21
β-strand	490	1	21
α-helix	493-497	5
β-strand	502-505	4	19
α-helix	514-521	8
β-strand	526-529	4	19
α-helix	533-541	9
α-helix	546-548	3
β-strand	552-553	2	19
α-helix	560-575	16
α-helix	579-591	13
α-helix	593-596	4
α-helix	598-615	18

Chains E, F and G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	319-326	8
α-helix	338-346	9

Chain H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	319-326	8
α-helix	338-347	10

Chain I: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	1-10	10	27
α-helix	14-28	15
β-strand	33-39	7	27
α-helix	47-54	8
β-strand	59-60	2	27
α-helix	71-76	6
α-helix	78-80	3
α-helix	81-87	7
α-helix	88-91	4
β-strand	97-101	5	27
β-strand	105-107	3	28
α-helix	112-116	5
β-strand	121-124	4	27
α-helix	125	1
β-strand	132-139	8	27
α-helix	143-155	13
α-helix	163-170	8
α-helix	173-175	3
α-helix	183-184	2
α-helix	185-187	3
β-strand	189-190	2	28
α-helix	191-196	6
α-helix	198-204	7
β-strand	210-212	3	28
α-helix	219-221	3
β-strand	224-225	2	29
β-strand	230-231	2	29
α-helix	239-241	3
α-helix	247-256	10
α-helix	258-263	6

Chain J: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
α-helix	14-28	15
β-strand	34-39	6	1
α-helix	45-52	8
β-strand	57-60	4	1
α-helix	71-76	6
α-helix	78-80	3
α-helix	81-86	6
α-helix	87-91	5
β-strand	97-101	5	1
β-strand	105-107	3	2
α-helix	112-116	5
β-strand	121-124	4	1
α-helix	125	1
β-strand	132-139	8	1
α-helix	143-155	13
α-helix	163-170	8
α-helix	172-175	4
β-strand	182	1	1
α-helix	185-188	4
β-strand	189-190	2	2
α-helix	191-196	6
α-helix	198-204	7
β-strand	210-212	3	2
β-strand	224-225	2	3
β-strand	230-231	2	3
α-helix	244-256	13
α-helix	258-262	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycogenin-1	E, F, G, H, I, J	protein	352	Homo sapiens	P46976 (AlphaFold model)
Glycogen [starch] synthase, muscle	A, B, C, D	protein	634	Homo sapiens	P13807 (AlphaFold model)

Sequence of entity 1 (E, F, G, H, I, J), FASTA

>8CVZ_1 Glycogenin-1 (chains E, F, G, H, I, J)
GPMTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRRLVVLATPQVSDSMRKVLETVFDEV
IMVDVLDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFDRE
ELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHLASEQGSFDGGDQGILNTFFSSWATTD
IRKHLPFIYNLSSISIFSYLPAFKVFGASAKVVHFLGRVKPWNYTYDPKTKSVKSEAHDP
NMTHPEFLILWWNIFTTNVLPLLQQFGLVKDTCSYVNVLSDLVYTLAFSCGFCRKEDVSG
AISHLSLGEIPAMAQPFVSSEERKERWEQGQADYMGADSFDNIKRKLDTYLQ

Sequence of entity 2 (A, B, C, D), FASTA

>8CVZ_2 Glycogen [starch] synthase, muscle (chains A, B, C, D)
MPLNRTLEMSELPGLEDWEDEFDLENAVLFEVAWEVANKVGGIYTVLQTKAKVTGDEWGD
NYFLVGPYTEQGVRTQVELLEAPTPALKRTLDSMNSKGCKVYFGRWLIEGGPLVVLLDVG
ASAWALERWKGELWDTCNIGVPWYDREANDAVLFGFLTTWFLGEFLAQSEEKPHVVAHFH
EWLAGVGLCLCRARRLPVATIFTTHATLLGRYLCAGAVDFYNNLENFNVDKEAGERQIYH
RYCMERAAAHCAHVFTTVSQITAIEAQHLLKRKPDIVTPNGLNVKKFSAMHEFQNLHAQS
KARIQEFVRGHFYGHLDFNLDKTLYFFIAGRYEFSNKGADVFLEALARLNYLLRVNGSEQ
TVVAFFIMPARTNNFNVETLKGQAVRKQLWDTANTVKEKFGRKLYESLLVGSLPDMNKML
DKEDFTMMKRAIFATQRQSFPPVCTHNMLDDSSDPILTTIRRIGLFNSSADRVKVIFHPE
FLSSTSPLLPVDYEEFVRGCHLGVFPSYYEPWGYTPAECTVMGIPSISTNLSGFGCFMEE
HIADPSAYGIYILDRRFRSLDDSCSQLTSFLYSFCQQSRRQRIIQRNRTERLSDLLDWKY
LGRYYMSARHMALSKAFPEHFTYEPNEADAAQGY

Primary citation

The structural mechanism of human glycogen synthesis by the GYS1-GYG1 complex. Fastman, N.M., Liu, Y., Ramanan, V. et al. Cell Rep (2022) 40:111041-111041. DOI 10.1016/j.celrep.2022.111041 · PubMed

Other PDB entries of the same protein (UniProt P46976 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3U2U 1.45 Å, Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP and…
3U2V 1.5 Å, Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP and…
3U2W 1.68 Å, Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and glucose or a…
7OVX 1.7 Å, E3 RING ligase binding domain
3U2X 1.77 Å, Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP and…
3T7M 1.8 Å, Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and UDP, in a…
3RMV 1.82 Å, Crystal Structure of Human Glycogenin-1 (GYG1) T83M mutant complexed with manganese and…
3T7O 1.85 Å, Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP-Glucose and…
3RMW 1.93 Å, Crystal Structure of Human Glycogenin-1 (GYG1) T83M mutant complexed with manganese and…
3Q4S 1.98 Å, Crystal Structure of Human Glycogenin-1 (GYG1), apo form
3T7N 1.98 Å, Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and UDP, in a…
3U2T 2.05 Å, Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese

Browse structure collections

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