9LLK: Heterododecameric human Derlin-1/p97 complex

The cryo-EM structure of the heterododecameric human Derlin-1/p97 complex. Determined by electron microscopy at 3.55 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 3.55 Å
Organism: Homo sapiens
Chains: 12
Atoms: 46,434
Mol. weight: 689.28 kDa
Ligands: ADP
Released: 29 Oct 2025

Explore 9LLK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9LLK contains 336 α-helices and 182 β-strands across 12 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: 41 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	25
β-strand	27-30	4	26
β-strand	38-41	4	26
α-helix	43-48	6
β-strand	57-60	4	27
α-helix	62-64	3
β-strand	66-69	4	27
β-strand	70-73	4	26
β-strand	81-84	4	26
α-helix	86-92	7
β-strand	100	1	25
β-strand	101-104	4	27
β-strand	109-110	2	28
β-strand	113-118	6	29
β-strand	119	1	30
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-138	3
β-strand	147	1	31
β-strand	151-155	5	29
β-strand	160-169	10	29
β-strand	173	1	31
β-strand	174-175	2	28
β-strand	181	1	32
β-strand	182-183	2	29
α-helix	187-188	2
β-strand	189	1	30
α-helix	190	1
α-helix	212-225	14
α-helix	229-233	5
α-helix	235-238	4
β-strand	241-244	4	33
α-helix	254-262	9
β-strand	267-269	3	33
α-helix	271-275	5
α-helix	279-282	4
α-helix	283-287	5
α-helix	289-292	4
β-strand	300-303	4	33
α-helix	306-308	3
α-helix	313-315	3
α-helix	323-332	10
β-strand	342-347	6	33
β-strand	365-368	4	33
α-helix	370-372	3
α-helix	376-384	9
β-strand	390	1	34
α-helix	396-402	7
α-helix	410-424	15
α-helix	439-443	5
β-strand	447	1	34
α-helix	449-457	9
β-strand	470	1	35
α-helix	476-478	3
α-helix	483-493	11
α-helix	495-498	4
α-helix	500-504	5
β-strand	513-517	5	35
α-helix	524-535	12
β-strand	538-542	5	35
α-helix	544-547	4
α-helix	557-568	12
β-strand	572-577	6	35
α-helix	581-586	6
α-helix	594-609	16
β-strand	617-623	7	35
β-strand	636	1	36
β-strand	638	1	36
β-strand	641-644	4	35
α-helix	646-648	3
α-helix	650-660	11
α-helix	672-678	7
α-helix	684-712	29
α-helix	734-741	8
α-helix	749-763	15

Chain B: 40 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	1
β-strand	38-41	4	1
α-helix	43-48	6
β-strand	56-60	5	1
α-helix	62-64	3
β-strand	66-73	8	1
β-strand	81-83	3	1
α-helix	86-92	7
β-strand	101-104	4	1
β-strand	110	1	2
β-strand	113-118	6	3
β-strand	119	1	4
α-helix	120-122	3
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-147	3	2
β-strand	151-155	5	3
β-strand	160-167	8	3
β-strand	173-175	3	2
β-strand	181-183	3	3
α-helix	187-188	2
β-strand	189	1	4
α-helix	190-192	3
α-helix	203-205	3
α-helix	211-225	15
α-helix	227-233	7
α-helix	236-238	3
β-strand	240-244	5	5
α-helix	252-262	11
β-strand	266-269	4	5
α-helix	272-275	4
α-helix	281-294	14
β-strand	299-303	5	5
α-helix	306-308	3
α-helix	313-315	3
α-helix	320-332	13
β-strand	341-347	7	5
α-helix	355-358	4
β-strand	365-368	4	5
α-helix	374-384	11
β-strand	390	1	6
α-helix	396-401	6
α-helix	408-424	17
α-helix	427-430	4
α-helix	439-442	4
β-strand	447	1	6
α-helix	449-457	9
β-strand	470	1	7
α-helix	476-478	3
α-helix	483-493	11
α-helix	495-498	4
α-helix	500-504	5
β-strand	513-517	5	7
α-helix	524-535	12
β-strand	538-542	5	7
α-helix	544-549	6
α-helix	557-568	12
β-strand	572-576	5	7
α-helix	581-586	6
α-helix	594-608	15
β-strand	617-623	7	7
β-strand	641-644	4	7
α-helix	645-648	4
α-helix	651-660	10
α-helix	672-677	6
α-helix	684-712	29
α-helix	733-741	9
α-helix	749-763	15

Chain C: 42 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	8
β-strand	27-29	3	9
β-strand	38-41	4	9
α-helix	43-49	7
β-strand	57-60	4	8
α-helix	62-64	3
β-strand	66-69	4	8
β-strand	70-73	4	9
β-strand	81-83	3	9
α-helix	86-92	7
β-strand	100-103	4	8
β-strand	109-110	2	10
β-strand	113-118	6	11
β-strand	119	1	12
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-138	3
β-strand	145-146	2	10
β-strand	151-155	5	11
β-strand	160-168	9	11
β-strand	174-175	2	10
β-strand	181-183	3	11
α-helix	187-188	2
β-strand	189	1	12
α-helix	190	1
α-helix	203-205	3
α-helix	210-220	11
α-helix	222-225	4
α-helix	227-233	7
α-helix	235-238	4
β-strand	241-244	4	13
α-helix	252-262	11
β-strand	267-269	3	13
α-helix	271-275	5
α-helix	282-293	12
β-strand	299-303	5	13
α-helix	306-309	4
α-helix	313-315	3
α-helix	320-332	13
β-strand	341-347	7	13
α-helix	355-358	4
β-strand	365-368	4	13
α-helix	370-372	3
α-helix	374-384	11
β-strand	390	1	14
α-helix	396-402	7
α-helix	408-425	18
α-helix	439-443	5
β-strand	447	1	14
α-helix	449-457	9
α-helix	483-493	11
α-helix	495-498	4
α-helix	501-504	4
α-helix	508-511	4
β-strand	514-517	4	15
α-helix	524-535	12
β-strand	538-542	5	16
α-helix	544-549	6
α-helix	557-568	12
β-strand	572-576	5	16
α-helix	581-586	6
α-helix	594-609	16
β-strand	617-618	2	16
β-strand	621-623	3	15
β-strand	636	1	17
β-strand	638	1	17
β-strand	641-644	4	15
α-helix	652-660	9
α-helix	672-678	7
α-helix	684-712	29
α-helix	713-715	3
α-helix	734-741	8
α-helix	749-763	15

Chain D: 38 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	37
β-strand	38-41	4	37
α-helix	43-48	6
β-strand	56-60	5	37
α-helix	62-64	3
β-strand	66-73	8	37
β-strand	81-83	3	37
α-helix	86-92	7
β-strand	99	1	37
β-strand	101-104	4	37
β-strand	113-118	6	38
β-strand	119	1	39
α-helix	120-122	3
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-147	3	40
β-strand	151-155	5	38
β-strand	160-169	10	38
β-strand	173-175	3	40
β-strand	181-182	2	38
α-helix	187-188	2
β-strand	189	1	39
α-helix	190-191	2
α-helix	212-225	14
α-helix	227-233	7
α-helix	236-238	3
β-strand	240-244	5	41
α-helix	254-262	9
β-strand	267-269	3	41
α-helix	272-275	4
α-helix	283-287	5
α-helix	289-292	4
β-strand	299-303	5	41
α-helix	306-308	3
α-helix	313-315	3
α-helix	320-332	13
β-strand	341-347	7	41
β-strand	365-368	4	41
α-helix	377-384	8
β-strand	390	1	42
α-helix	396-401	6
α-helix	408-424	17
α-helix	427-430	4
α-helix	439-442	4
β-strand	447	1	42
α-helix	449-457	9
β-strand	470	1	43
α-helix	476-478	3
α-helix	483-498	16
α-helix	501-504	4
β-strand	513-517	5	43
α-helix	524-535	12
β-strand	538-542	5	43
α-helix	544-547	4
α-helix	558-568	11
β-strand	572-576	5	43
α-helix	581-586	6
α-helix	594-606	13
β-strand	617-623	7	43
β-strand	641-644	4	43
α-helix	646-648	3
α-helix	651-658	8
α-helix	672-677	6
α-helix	685-712	28
α-helix	733-740	8
α-helix	749-763	15

Chain E: 45 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	44
β-strand	27-30	4	45
β-strand	38-41	4	45
α-helix	43-47	5
β-strand	56-60	5	45
α-helix	62-64	3
β-strand	66-73	8	45
β-strand	81-84	4	45
α-helix	86-92	7
β-strand	100	1	44
β-strand	101-104	4	45
α-helix	108-109	2
β-strand	110	1	46
α-helix	111	1
β-strand	113-118	6	47
β-strand	119	1	48
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-138	3
β-strand	151-155	5	47
β-strand	160-169	10	47
β-strand	175	1	46
β-strand	181-183	3	47
α-helix	187-188	2
β-strand	189	1	48
α-helix	190	1
α-helix	196-197	2
α-helix	203-205	3
α-helix	212-225	14
α-helix	227-233	7
α-helix	236-238	3
β-strand	241-244	4	49
α-helix	254-262	9
β-strand	267-269	3	49
α-helix	271-275	5
α-helix	283-287	5
α-helix	290-295	6
β-strand	300-303	4	49
α-helix	306-308	3
α-helix	320-332	13
β-strand	342-347	6	49
α-helix	355-358	4
β-strand	365-368	4	49
α-helix	370-372	3
α-helix	377-384	8
β-strand	390	1	50
α-helix	396-401	6
α-helix	410-424	15
α-helix	437-438	2
α-helix	439-443	5
β-strand	447	1	50
α-helix	449-457	9
β-strand	470	1	51
α-helix	476-478	3
α-helix	483-493	11
α-helix	495-498	4
α-helix	500-504	5
β-strand	513-517	5	51
α-helix	524-535	12
β-strand	538-542	5	51
α-helix	544-547	4
α-helix	558-568	11
β-strand	572-577	6	51
α-helix	581-586	6
α-helix	594-606	13
β-strand	617-623	7	51
β-strand	641-644	4	51
α-helix	648-649	2
α-helix	650-660	11
α-helix	673-678	6
α-helix	684-712	29
α-helix	734-740	7
α-helix	749-763	15

Chain F: 44 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	18
β-strand	38-41	4	18
α-helix	43-48	6
β-strand	56-60	5	18
α-helix	62-64	3
β-strand	66-73	8	18
β-strand	81-83	3	18
α-helix	86-92	7
β-strand	101	1	18
β-strand	104	1	18
α-helix	109-111	3
β-strand	113-118	6	19
β-strand	119	1	20
α-helix	120-122	3
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-147	3	21
β-strand	151-155	5	19
β-strand	160-169	10	19
β-strand	173-175	3	21
β-strand	182	1	19
α-helix	187-188	2
β-strand	189	1	20
α-helix	190-191	2
α-helix	203-205	3
α-helix	212-214	3
α-helix	221-225	5
α-helix	228-233	6
α-helix	236-238	3
β-strand	241-244	4	22
α-helix	252-262	11
β-strand	267-269	3	22
α-helix	272-275	4
α-helix	283-287	5
α-helix	289-292	4
β-strand	299-304	6	22
α-helix	306-308	3
α-helix	313-315	3
α-helix	320-332	13
β-strand	341-347	7	22
β-strand	365-368	4	22
α-helix	377-384	8
β-strand	390	1	23
α-helix	396-401	6
α-helix	411-424	14
α-helix	427-430	4
α-helix	439-442	4
β-strand	447	1	23
α-helix	449-457	9
β-strand	470	1	24
α-helix	476-478	3
α-helix	483-491	9
α-helix	494-498	5
α-helix	500-504	5
β-strand	513-517	5	24
α-helix	524-535	12
β-strand	538-542	5	24
α-helix	544-547	4
α-helix	558-568	11
β-strand	572-576	5	24
α-helix	581-586	6
α-helix	594-606	13
β-strand	617-623	7	24
β-strand	641-644	4	24
α-helix	645-648	4
α-helix	650-652	3
α-helix	653-656	4
α-helix	658-660	3
α-helix	672-678	7
α-helix	684-712	29
α-helix	733-740	8
α-helix	749-763	15

Chains U and Y: 14 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-10	7
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
α-helix	155-165	11
α-helix	170-183	14
α-helix	184-189	6
α-helix	190-193	4
α-helix	201-203	3
α-helix	204-209	6
β-strand	247	1	32

Chain V: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	4-10	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
α-helix	155-165	11
α-helix	170-183	14
α-helix	184-189	6
α-helix	190-193	4
α-helix	201-203	3
α-helix	204-209	6

3 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
Transitional endoplasmic reticulum ATPase	A, B, C, D, E, F	protein	787	Homo sapiens	P55072 (AlphaFold model)
Derlin-1	U, V, W, X, Y, Z	protein	226	Homo sapiens	Q9BUN8 (AlphaFold model)

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

>9LLK_1 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

Sequence of entity 2 (U, V, W, X, Y, Z), FASTA

>9LLK_2 Derlin-1 (chains U, V, W, X, Y, Z)
MSDIGDWFRSIPAITRYWFAATVAVPLVGKLGLISPAYLFLWPEAFLYRFQIWRPITATF
YFPVGPGTGFLYLVNLYFLYQYSTRLETGAFDGRPADYLFMLLFNWICIVITGLAMDMQL
LMIPLIMSVLYVWAQLNRDMIVSFWFGTRFKACYLPWVILGFNYIIGGSVINELIGNLVG
HLYFFLMFRYPMDLGGRNFLSTPQFLYRWLPSRRHNWGQGFRLGDQ

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	12

Primary citation

Cryo-EM structure of the human Derlin-1/p97 complex reveals a hexameric channel in ERAD. Wang, Q., Yao, D., Rao, B. et al. Commun Biol (2025) 8:1481-1481. DOI 10.1038/s42003-025-08880-5 · PubMed

Other PDB entries of the same protein (UniProt P55072 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5B6C 1.55 Å, Structural Details of Ufd1 binding to p97
7PUX 1.73 Å, Structure of p97 N-D1(L198W) in complex with Fragment TROLL2
3TIW 1.8 Å, Crystal structure of p97N in complex with the C-terminus of gp78
4KDL 1.81 Å, Crystal structure of p97/VCP N in complex with OTU1 UBXL
4KDI 1.86 Å, Crystal structure of p97/VCP N in complex with OTU1 UBXL
5EPP 1.88 Å, Structural Insights into the Interaction of p97 N-terminus Domain and VBM Motif in…
3EBB 1.9 Å, PLAP/P97 complex
6G2V 1.9 Å, Crystal structure of the p97 D2 domain in a helical split-washer conformation
6G2Z 1.92 Å, Crystal structure of the p97 D2 domain in a helical split-washer conformation
4KO8 1.98 Å, Structure of p97 N-D1 R155H mutant in complex with ATPgS
3QQ8 2.0 Å, Crystal structure of p97-N in complex with FAF1-UBX
3QWZ 2.0 Å, Crystal structure of FAF1 UBX-p97N-domain complex

Browse structure collections

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