7Y59: Human ERAD retro-translocation complex

The cryo-EM structure of human ERAD retro-translocation complex. Determined by electron microscopy at 4.51 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 4.51 Å
Organism: Homo sapiens
Chains: 10
Atoms: 41,564
Mol. weight: 653.31 kDa
Ligands: ADP, ATP
Released: 18 Oct 2023

Explore 7Y59 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y59 contains 301 α-helices and 178 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: 40 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	6
β-strand	38-41	4	6
α-helix	43-48	6
β-strand	56-60	5	6
α-helix	62-64	3
β-strand	66-73	8	6
β-strand	81-83	3	6
α-helix	86-91	6
β-strand	99-104	6	6
β-strand	110	1	7
β-strand	113-117	5	1
β-strand	119	1	8
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-138	3
β-strand	145-146	2	7
β-strand	151-155	5	1
β-strand	160-167	8	1
β-strand	174-175	2	7
β-strand	181-183	3	1
α-helix	187-188	2
β-strand	189	1	8
α-helix	190-192	3
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
β-strand	241-244	4	9
α-helix	251-262	12
β-strand	267-269	3	9
α-helix	272-275	4
α-helix	280-294	15
β-strand	299-303	5	9
α-helix	306-309	4
α-helix	320-334	15
β-strand	341-347	7	9
α-helix	355-358	4
β-strand	365-368	4	9
α-helix	370-372	3
α-helix	374-384	11
α-helix	396-402	7
α-helix	408-424	17
α-helix	439-443	5
α-helix	449-457	9
β-strand	470	1	10
α-helix	476-478	3
α-helix	483-498	16
α-helix	500-506	7
α-helix	508-511	4
β-strand	513-517	5	10
α-helix	524-535	12
β-strand	538-542	5	10
α-helix	544-551	8
α-helix	557-568	12
β-strand	572-576	5	10
α-helix	581-586	6
α-helix	594-610	17
β-strand	617-623	7	10
β-strand	641-644	4	10
α-helix	646-648	3
α-helix	651-659	9
α-helix	672-678	7
α-helix	684-715	32
α-helix	725-728	4
α-helix	733-741	9
α-helix	749-765	17

Chain B: 44 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	11
β-strand	38-41	4	11
α-helix	43-49	7
β-strand	57-60	4	11
α-helix	62-64	3
β-strand	68	1	11
β-strand	70-73	4	11
β-strand	81-83	3	11
α-helix	86-92	7
β-strand	99-104	6	11
β-strand	110	1	12
β-strand	113-118	6	3
β-strand	119	1	13
α-helix	120-123	4
α-helix	130	1
α-helix	131-135	5
α-helix	136-138	3
β-strand	145-147	3	12
β-strand	151-155	5	3
β-strand	160-167	8	3
β-strand	173-175	3	12
β-strand	181-183	3	3
α-helix	187-188	2
β-strand	189	1	13
α-helix	190-191	2
α-helix	203-205	3
α-helix	210-218	9
α-helix	221-225	5
α-helix	227-233	7
α-helix	236-238	3
β-strand	240-244	5	14
α-helix	251-262	12
β-strand	267-269	3	14
α-helix	271-275	5
α-helix	282-294	13
β-strand	300-304	5	14
α-helix	306-309	4
α-helix	320-333	14
β-strand	342-347	6	14
α-helix	350-352	3
α-helix	355-358	4
β-strand	365-368	4	14
α-helix	370-372	3
α-helix	374-384	11
β-strand	390	1	15
α-helix	396-402	7
α-helix	408-424	17
α-helix	437-438	2
α-helix	439-444	6
β-strand	447	1	15
α-helix	449-457	9
β-strand	470	1	16
α-helix	483-498	16
α-helix	500-506	7
α-helix	509-511	3
β-strand	513-517	5	16
α-helix	524-535	12
β-strand	538-542	5	16
α-helix	544-551	8
α-helix	556-568	13
β-strand	572-576	5	16
α-helix	581-586	6
α-helix	594-608	15
β-strand	617-623	7	16
α-helix	626-628	3
β-strand	639-644	6	16
α-helix	646-648	3
α-helix	651-661	11
α-helix	672-678	7
α-helix	684-715	32
α-helix	725-728	4
α-helix	733-741	9
α-helix	749-765	17

Chain C: 45 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	26-29	4	17
β-strand	38-42	5	17
α-helix	43-48	6
β-strand	56-60	5	17
α-helix	62-64	3
β-strand	66-74	9	17
β-strand	81-83	3	17
α-helix	86-92	7
β-strand	99-104	6	17
α-helix	108-109	2
β-strand	110	1	18
α-helix	111	1
β-strand	113-118	6	4
α-helix	121-123	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-138	3
β-strand	145-147	3	18
β-strand	151-154	4	4
β-strand	161-169	9	4
β-strand	173-175	3	18
α-helix	180	1
β-strand	181-183	3	4
α-helix	193-200	8
α-helix	203-205	3
α-helix	210-218	9
α-helix	221-225	5
α-helix	227-233	7
α-helix	236-238	3
β-strand	241-244	4	19
α-helix	251-262	12
β-strand	267-270	4	19
α-helix	271-275	5
α-helix	282-293	12
β-strand	299-304	6	19
α-helix	306-308	3
α-helix	320-334	15
β-strand	341-347	7	19
α-helix	350-352	3
α-helix	355-358	4
β-strand	360	1	20
β-strand	362	1	20
β-strand	365-368	4	19
α-helix	374-384	11
α-helix	396-402	7
α-helix	408-424	17
α-helix	441-444	4
α-helix	449-457	9
β-strand	470	1	21
α-helix	476-478	3
α-helix	483-493	11
α-helix	495-498	4
α-helix	500-505	6
β-strand	514-517	4	21
α-helix	525-535	11
β-strand	538-542	5	21
α-helix	544-549	6
α-helix	559-568	10
β-strand	572-576	5	21
α-helix	580-586	7
α-helix	596-609	14
β-strand	618-623	6	21
α-helix	626-628	3
β-strand	636	1	22
β-strand	638	1	22
β-strand	641-644	4	21
α-helix	646-648	3
α-helix	651-660	10
α-helix	674-677	4
α-helix	684-715	32
α-helix	724-726	3
α-helix	733-741	9
α-helix	749-761	13

Chain D: 42 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	23
β-strand	38-41	4	23
α-helix	43-49	7
β-strand	56-60	5	23
β-strand	66-73	8	23
β-strand	81-83	3	23
α-helix	86-92	7
β-strand	99-101	3	23
β-strand	104	1	23
β-strand	113-118	6	5
β-strand	119	1	24
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-146	2	25
β-strand	151-155	5	5
β-strand	160-169	10	5
β-strand	174-175	2	25
β-strand	181-183	3	5
α-helix	187-188	2
β-strand	189	1	24
α-helix	190-191	2
α-helix	193-199	7
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
α-helix	236-238	3
β-strand	240-244	5	26
α-helix	251-262	12
β-strand	267-269	3	26
α-helix	272-275	4
α-helix	282-295	14
β-strand	300-303	4	26
α-helix	306-309	4
α-helix	313-315	3
α-helix	320-333	14
β-strand	342-347	6	26
α-helix	355-358	4
β-strand	360	1	27
β-strand	362	1	27
β-strand	365-368	4	26
α-helix	370-372	3
α-helix	374-384	11
α-helix	396-402	7
α-helix	408-426	19
α-helix	438-442	5
α-helix	449-457	9
β-strand	470	1	28
α-helix	476-479	4
α-helix	483-498	16
α-helix	500-506	7
α-helix	509-511	3
β-strand	513-517	5	28
α-helix	524-535	12
β-strand	538-540	3	28
α-helix	544-551	8
α-helix	556-568	13
β-strand	572-575	4	28
α-helix	581-586	6
α-helix	594-609	16
β-strand	618-622	5	28
α-helix	626-628	3
β-strand	641-644	4	28
α-helix	646-648	3
α-helix	651-660	10
α-helix	672-678	7
α-helix	684-715	32
α-helix	727-728	2
α-helix	733-740	8
α-helix	750-762	13

Chain E: 41 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	29
β-strand	38-40	3	30
α-helix	43-48	6
β-strand	56-60	5	30
α-helix	62-64	3
β-strand	66-72	7	30
β-strand	81-83	3	29
α-helix	86-91	6
β-strand	99	1	29
β-strand	101-103	3	30
α-helix	108-109	2
β-strand	110	1	31
α-helix	111	1
β-strand	113-118	6	32
β-strand	119	1	33
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-138	3
β-strand	145-147	3	31
β-strand	151-155	5	32
β-strand	160-169	10	32
β-strand	173-175	3	31
β-strand	182	1	32
α-helix	188	1
β-strand	189	1	33
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
α-helix	236-238	3
β-strand	240-244	5	34
α-helix	251-262	12
β-strand	267-270	4	34
α-helix	271-275	5
α-helix	281-294	14
β-strand	300-304	5	34
α-helix	306-308	3
α-helix	320-333	14
β-strand	342-347	6	34
α-helix	355-358	4
β-strand	363-368	6	34
α-helix	370-372	3
α-helix	374-384	11
β-strand	390	1	35
α-helix	396-402	7
α-helix	408-424	17
α-helix	439-444	6
β-strand	447	1	35
α-helix	449-457	9
β-strand	470	1	36
α-helix	476-478	3
α-helix	483-498	16
α-helix	500-506	7
α-helix	509-511	3
β-strand	513-517	5	36
α-helix	524-535	12
β-strand	538-540	3	36
α-helix	544-551	8
α-helix	556-568	13
β-strand	572-576	5	36
α-helix	581-586	6
α-helix	594-610	17
β-strand	617-623	7	36
β-strand	641-644	4	36
α-helix	646-648	3
α-helix	653-661	9
α-helix	672-678	7
α-helix	684-713	30
α-helix	733-741	9
α-helix	749-766	18
β-strand	768	1	37

Chain F: 40 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	38
β-strand	39-41	3	38
α-helix	43-49	7
β-strand	56-60	5	38
α-helix	62-64	3
β-strand	66-73	8	38
β-strand	81-84	4	38
α-helix	86-91	6
β-strand	99-104	6	38
β-strand	110	1	39
β-strand	113-118	6	40
β-strand	119	1	41
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-147	3	39
β-strand	151-155	5	40
β-strand	160-168	9	40
β-strand	173-175	3	39
β-strand	181-183	3	40
α-helix	188	1
β-strand	189	1	41
α-helix	190-191	2
α-helix	203-205	3
α-helix	210-225	16
α-helix	229-233	5
α-helix	236-238	3
β-strand	240-244	5	42
α-helix	251-258	8
α-helix	259-263	5
β-strand	267-270	4	42
α-helix	271-276	6
α-helix	280-294	15
β-strand	300-304	5	42
β-strand	311	1	43
α-helix	320-334	15
β-strand	342-347	6	42
β-strand	353	1	43
β-strand	363-368	6	42
α-helix	370-372	3
α-helix	375-384	10
β-strand	390	1	44
α-helix	396-402	7
α-helix	408-424	17
α-helix	439-443	5
β-strand	447	1	44
α-helix	449-457	9
β-strand	470	1	45
α-helix	476-478	3
α-helix	483-498	16
α-helix	500-506	7
α-helix	508-511	4
β-strand	513-517	5	45
α-helix	524-535	12
β-strand	538-542	5	45
α-helix	544-551	8
α-helix	557-568	12
β-strand	572-577	6	45
α-helix	580-586	7
α-helix	594-610	17
β-strand	617-622	6	45
α-helix	631-633	3
β-strand	639-644	6	45
α-helix	646-648	3
α-helix	651-661	11
α-helix	672-678	7
α-helix	684-715	32
α-helix	733-741	9
β-strand	743	1	37
α-helix	749-765	17

Chain W: 11 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	3-9	7
α-helix	13-31	19
α-helix	36-38	3
α-helix	43-47	5
α-helix	69-87	19
α-helix	95-115	21
α-helix	123-136	14
α-helix	155-165	11
α-helix	171-193	23
α-helix	201-203	3
α-helix	205-209	5
β-strand	247	1	1

Chain X: 12 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-9	7
α-helix	13-31	19
α-helix	36-38	3
α-helix	43-48	6
α-helix	69-88	20
α-helix	95-115	21
α-helix	123-136	14
β-strand	141	1	2
β-strand	151	1	2
α-helix	155-165	11
α-helix	171-184	14
α-helix	185-189	5
α-helix	190-193	4
α-helix	204-209	6
β-strand	246-247	2	3

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Derlin-1	W, X, Y, Z	protein	267	Homo sapiens	Q9BUN8 (AlphaFold model)
Transitional endoplasmic reticulum ATPase	A, B, C, D, E, F	protein	787	Homo sapiens	P55072 (AlphaFold model)

Sequence of entity 1 (W, X, Y, Z), FASTA

>7Y59_1 Derlin-1 (chains W, X, Y, Z)
MSDIGDWFRSIPAITRYWFAATVAVPLVGKLGLISPAYLFLWPEAFLYRFQIWRPITATF
YFPVGPGTGFLYLVNLYFLYQYSTRLETGAFDGRPADYLFMLLFNWICIVITGLAMDMQL
LMIPLIMSVLYVWAQLNRDMIVSFWFGTRFKACYLPWVILGFNYIIGGSVINELIGNLVG
HLYFFLMFRYPMDLGGRNFLSTPQFLYRWLPSRRHNWGQGFRLGDQAAALEVLFQGPSAW
SHPQFEKGGGSGGGSGGSAWSHPQFEK

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

>7Y59_2 Transitional endoplasmic reticulum ATPase (chains A, B, C, D, E, F)
MNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSD
EKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYF
LEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLN
EVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVA
NETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGE
VERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLE
ILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDA
EVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEH
PDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANV
REIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFI
IGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMT
NGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEA
MRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYTED
NDDDLYG

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	6
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	6

Primary citation

The cryo-EM structure of the human ERAD retrotranslocation complex. Rao, B., Wang, Q., Yao, D. et al. Sci Adv (2023) 9:eadi5656-eadi5656. DOI 10.1126/sciadv.adi5656 · PubMed

Other PDB entries of the same protein (UniProt Q9BUN8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GLF 2.25 Å, Structural insights into the interaction of p97 N-terminal domain and SHP motif in…
9LLK 3.55 Å, The cryo-EM structure of the heterododecameric human Derlin-1/p97 complex
7Y53 3.61 Å, The cryo-EM structure of human ERAD retro-translocation complex
7Y4W 3.67 Å, The cryo-EM structure of human ERAD retro-translocation complex
7CZB 3.8 Å, The cryo-EM structure of the ERAD retrotranslocation channel formed by human Derlin-1

Browse structure collections

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