7Y53: Human ERAD retro-translocation complex

The cryo-EM structure of human ERAD retro-translocation complex. Determined by electron microscopy at 3.61 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 3.61 Å
Organism: Homo sapiens
Chains: 10
Atoms: 42,966
Mol. weight: 636.32 kDa
Ligands: ADP
Released: 18 Oct 2023

Explore 7Y53 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y53 contains 291 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: 42 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	26-29	4	5
β-strand	38-40	3	5
α-helix	43-48	6
β-strand	56-60	5	5
α-helix	62-64	3
β-strand	66-72	7	5
β-strand	81-83	3	5
α-helix	86-92	7
β-strand	99-103	5	5
β-strand	110	1	6
β-strand	113-118	6	2
β-strand	119	1	7
α-helix	120-122	3
α-helix	131-135	5
α-helix	136-138	3
β-strand	145-147	3	6
β-strand	151-155	5	2
β-strand	160-167	8	2
β-strand	173-175	3	6
β-strand	181-183	3	2
α-helix	187-188	2
β-strand	189	1	7
α-helix	190-191	2
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
β-strand	241-244	4	8
α-helix	252-262	11
β-strand	267-270	4	8
α-helix	271-275	5
α-helix	281-294	14
β-strand	300-304	5	8
α-helix	306-308	3
α-helix	320-333	14
β-strand	342-347	6	8
α-helix	355-358	4
β-strand	360	1	9
β-strand	362	1	9
β-strand	365-368	4	8
α-helix	370-372	3
α-helix	374-384	11
α-helix	396-402	7
α-helix	408-424	17
α-helix	440-443	4
α-helix	449-457	9
β-strand	470	1	10
α-helix	476-478	3
α-helix	483-489	7
α-helix	490-494	5
α-helix	495-498	4
α-helix	500-504	5
β-strand	513-517	5	10
α-helix	524-535	12
β-strand	538-542	5	10
α-helix	544-549	6
α-helix	558-568	11
β-strand	572-576	5	10
α-helix	581-586	6
α-helix	594-609	16
β-strand	617-623	7	10
α-helix	626-628	3
β-strand	641-644	4	10
α-helix	646-648	3
α-helix	650-652	3
α-helix	653-661	9
α-helix	672-678	7
α-helix	684-712	29
α-helix	727-728	2
α-helix	733-741	9
α-helix	749-764	16

Chain B: 39 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	11
β-strand	39-41	3	11
α-helix	43-49	7
β-strand	56-60	5	11
α-helix	62-64	3
β-strand	66-73	8	11
β-strand	81-83	3	11
α-helix	86-91	6
β-strand	99-104	6	11
β-strand	110	1	12
β-strand	113-118	6	4
β-strand	119	1	13
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-146	2	12
β-strand	151-155	5	4
β-strand	160-169	10	4
β-strand	174-175	2	12
β-strand	181-183	3	4
α-helix	187-188	2
β-strand	189	1	13
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	14
α-helix	252-262	11
β-strand	267-269	3	14
α-helix	271-275	5
α-helix	282-294	13
β-strand	299-303	5	14
α-helix	306-308	3
α-helix	320-333	14
β-strand	341-347	7	14
α-helix	355-358	4
β-strand	360	1	15
β-strand	362	1	15
β-strand	365-368	4	14
α-helix	370-372	3
α-helix	374-384	11
β-strand	390	1	16
α-helix	396-401	6
α-helix	408-425	18
α-helix	440-444	5
β-strand	447	1	16
α-helix	449-457	9
β-strand	470	1	17
α-helix	476-478	3
α-helix	483-498	16
α-helix	500-506	7
β-strand	513-517	5	17
α-helix	524-535	12
β-strand	538-542	5	17
α-helix	544-549	6
α-helix	556-568	13
β-strand	572-576	5	17
α-helix	581-586	6
α-helix	594-609	16
β-strand	617-623	7	17
β-strand	641-644	4	17
α-helix	646-648	3
α-helix	651-660	10
β-strand	666	1	18
α-helix	672-678	7
α-helix	684-713	30
α-helix	727-729	3
β-strand	731	1	18
α-helix	733-741	9
α-helix	749-764	16

Chain C: 39 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	24-29	6	19
β-strand	38-42	5	19
α-helix	43-49	7
β-strand	56-60	5	19
α-helix	62-64	3
β-strand	66-74	9	19
β-strand	81-83	3	19
α-helix	86-92	7
β-strand	99-104	6	19
β-strand	110-118	9	20
α-helix	120-123	4
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-147	3	20
β-strand	151-155	5	20
β-strand	160-169	10	20
β-strand	173-183	11	20
α-helix	195-200	6
α-helix	210-225	16
α-helix	227-233	7
α-helix	236-238	3
β-strand	241-244	4	21
α-helix	251-262	12
β-strand	267-270	4	21
α-helix	271-275	5
α-helix	279-281	3
α-helix	282-294	13
β-strand	299-304	6	21
α-helix	306-308	3
α-helix	320-334	15
β-strand	341-347	7	21
α-helix	350-352	3
α-helix	355-358	4
β-strand	360	1	22
β-strand	362	1	22
β-strand	365-368	4	21
α-helix	370-372	3
α-helix	374-384	11
α-helix	396-402	7
α-helix	408-424	17
α-helix	436-437	2
α-helix	441-444	4
α-helix	449-457	9
α-helix	483-498	16
α-helix	500-506	7
α-helix	509-511	3
β-strand	514-517	4	23
α-helix	524-534	11
β-strand	540-542	3	23
α-helix	544-552	9
α-helix	559-568	10
β-strand	573-576	4	23
α-helix	581-585	5
α-helix	596-609	14
β-strand	618-623	6	23
β-strand	636	1	24
β-strand	638	1	24
β-strand	642-644	3	23
α-helix	646-648	3
α-helix	651-660	10
α-helix	684-715	32
α-helix	733-740	8
α-helix	749-762	14

Chain D: 38 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	25
β-strand	38-41	4	25
α-helix	43-49	7
β-strand	56-60	5	25
β-strand	66-73	8	25
β-strand	81-84	4	25
α-helix	86-92	7
β-strand	99-104	6	25
β-strand	113-118	6	26
β-strand	119	1	27
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-146	2	28
β-strand	151-155	5	26
β-strand	160-169	10	26
β-strand	174-175	2	28
β-strand	181-183	3	26
β-strand	189	1	27
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
α-helix	236-238	3
β-strand	241-244	4	29
α-helix	251-262	12
β-strand	267-269	3	29
α-helix	271-275	5
α-helix	282-295	14
β-strand	299-303	5	29
α-helix	306-308	3
α-helix	320-333	14
β-strand	341-347	7	29
α-helix	350-352	3
α-helix	355-358	4
β-strand	360	1	30
β-strand	362	1	30
β-strand	365-368	4	29
α-helix	374-384	11
α-helix	396-401	6
α-helix	408-426	19
α-helix	439-442	4
α-helix	449-457	9
β-strand	470	1	31
α-helix	483-498	16
α-helix	500-506	7
α-helix	509-511	3
β-strand	513-517	5	31
α-helix	524-535	12
β-strand	538-542	5	31
α-helix	544-549	6
α-helix	557-568	12
β-strand	572-577	6	31
α-helix	581-586	6
α-helix	594-609	16
β-strand	617-623	7	31
α-helix	626-628	3
β-strand	641-644	4	31
α-helix	646-648	3
α-helix	651-660	10
α-helix	673-678	6
α-helix	684-715	32
α-helix	724-727	4
α-helix	733-739	7
α-helix	750-762	13

Chain E: 42 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	32
β-strand	38-41	4	32
α-helix	43-48	6
β-strand	56-60	5	32
α-helix	62-64	3
β-strand	66-73	8	32
β-strand	81-83	3	32
α-helix	86-92	7
β-strand	99-104	6	32
β-strand	117-118	2	33
β-strand	119	1	34
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-138	3
β-strand	145-146	2	35
β-strand	151-155	5	33
β-strand	160-164	5	33
β-strand	174-175	2	35
α-helix	187-188	2
β-strand	189	1	34
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	36
α-helix	251-262	12
β-strand	267-269	3	36
α-helix	271-275	5
α-helix	282-294	13
β-strand	300-303	4	36
α-helix	306-309	4
α-helix	320-333	14
β-strand	342-347	6	36
α-helix	355-358	4
β-strand	365-368	4	36
α-helix	370-372	3
α-helix	374-384	11
β-strand	390	1	37
α-helix	396-402	7
α-helix	408-425	18
α-helix	441-443	3
β-strand	447	1	37
α-helix	449-457	9
β-strand	470	1	38
α-helix	476-478	3
α-helix	483-489	7
α-helix	490-494	5
α-helix	495-498	4
α-helix	500-505	6
β-strand	513-517	5	38
α-helix	524-535	12
β-strand	538-542	5	38
α-helix	544-551	8
α-helix	557-559	3
α-helix	561-568	8
β-strand	572-576	5	38
α-helix	581-586	6
α-helix	594-609	16
β-strand	617-623	7	38
α-helix	626-628	3
β-strand	641-644	4	38
α-helix	646-648	3
α-helix	653-661	9
α-helix	674-678	5
α-helix	684-713	30
α-helix	733-737	5
α-helix	749-765	17

Chain F: 36 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	39
β-strand	39-41	3	39
α-helix	43-49	7
β-strand	56-60	5	39
α-helix	62-64	3
β-strand	66-73	8	39
β-strand	81-84	4	39
α-helix	86-91	6
β-strand	99-104	6	39
β-strand	110	1	40
β-strand	113-118	6	41
β-strand	119	1	42
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-138	3
β-strand	145-147	3	40
β-strand	151-155	5	41
β-strand	160-169	10	41
β-strand	173-175	3	40
β-strand	181-183	3	41
α-helix	187-188	2
β-strand	189	1	42
α-helix	190-191	2
α-helix	210-225	16
α-helix	229-233	5
β-strand	241-244	4	43
α-helix	251-262	12
β-strand	267-269	3	43
α-helix	271-276	6
α-helix	281-293	13
β-strand	300-303	4	43
α-helix	306-308	3
β-strand	311	1	44
α-helix	320-334	15
β-strand	342-347	6	43
β-strand	353	1	44
β-strand	360	1	45
β-strand	362	1	45
β-strand	365-368	4	43
α-helix	370-372	3
α-helix	375-384	10
β-strand	390	1	46
α-helix	396-402	7
α-helix	408-424	17
α-helix	436-438	3
α-helix	439-442	4
β-strand	447	1	46
α-helix	449-457	9
β-strand	470	1	47
α-helix	483-498	16
α-helix	500-506	7
α-helix	508-511	4
β-strand	513-517	5	47
α-helix	524-535	12
β-strand	538-542	5	47
α-helix	544-552	9
α-helix	556-568	13
β-strand	572-577	6	47
α-helix	581-586	6
α-helix	594-609	16
β-strand	617-623	7	47
β-strand	639-644	6	47
α-helix	651-660	10
β-strand	668	1	48
β-strand	670	1	48
α-helix	672-678	7
α-helix	684-715	32
α-helix	733-741	9
α-helix	749-764	16

Chain W: 14 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	57-59	3
α-helix	69-88	20
α-helix	95-115	21
α-helix	123-136	14
β-strand	141	1	1
β-strand	151	1	1
α-helix	155-165	11
α-helix	170-184	15
α-helix	185-189	5
α-helix	190-193	4
α-helix	204-209	6
α-helix	211-213	3
β-strand	246-247	2	2

Chain X: 14 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
α-helix	13-31	19
α-helix	36-38	3
α-helix	43-48	6
α-helix	57-60	4
α-helix	69-88	20
α-helix	95-115	21
α-helix	123-136	14
β-strand	141-142	2	3
β-strand	150-151	2	3
α-helix	155-165	11
α-helix	170-184	15
α-helix	185-189	5
α-helix	190-193	4
α-helix	204-209	6
α-helix	211-213	3
β-strand	246-247	2	4

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	226	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

>7Y53_1 Derlin-1 (chains W, X, Y, Z)
MSDIGDWFRSIPAITRYWFAATVAVPLVGKLGLISPAYLFLWPEAFLYRFQIWRPITATF
YFPVGPGTGFLYLVNLYFLYQYSTRLETGAFDGRPADYLFMLLFNWICIVITGLAMDMQL
LMIPLIMSVLYVWAQLNRDMIVSFWFGTRFKACYLPWVILGFNYIIGGSVINELIGNLVG
HLYFFLMFRYPMDLGGRNFLSTPQFLYRWLPSRRHNWGQGFRLGDQ

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

>7Y53_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	12

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
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
7Y59 4.51 Å, The cryo-EM structure of human ERAD retro-translocation complex

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