8B5R: P97-p37-SPI substrate complex

p97-p37-SPI substrate complex. Determined by electron microscopy at 6.1 Å resolution. Released 7 Jun 2023.

Method: Electron microscopy
Resolution: 6.1 Å
Organism: Homo sapiens
Chains: 11
Atoms: 25,660
Mol. weight: 633.01 kDa
Released: 7 Jun 2023

Explore 8B5R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8B5R contains 230 α-helices and 168 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: 37 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	1
β-strand	30	1	2
β-strand	37	1	2
α-helix	43-48	6
β-strand	52	1	3
β-strand	56	1	3
β-strand	57-58	2	4
β-strand	83	1	1
α-helix	86-92	7
β-strand	103-104	2	4
β-strand	116	1	5
α-helix	117-119	3
α-helix	120-123	4
α-helix	130-138	9
β-strand	165	1	5
α-helix	191-198	8
α-helix	203-206	4
α-helix	210-225	16
α-helix	227-233	7
β-strand	240	1	6
α-helix	252-260	9
β-strand	267-268	2	7
α-helix	282-296	15
β-strand	301-302	2	7
α-helix	306-309	4
α-helix	319-333	15
α-helix	350-352	3
α-helix	355-358	4
β-strand	360	1	8
β-strand	363	1	8
β-strand	366	1	6
α-helix	374-387	14
α-helix	396-402	7
α-helix	410-430	21
α-helix	439-443	5
α-helix	449-458	10
α-helix	462-467	6
α-helix	483-494	12
α-helix	500-506	7
α-helix	508-511	4
β-strand	516-517	2	9
α-helix	524-535	12
β-strand	538-540	3	10
α-helix	544-546	3
α-helix	554-568	15
β-strand	572-574	3	10
α-helix	579-583	5
α-helix	596-609	14
β-strand	617-619	3	10
β-strand	622-623	2	9
α-helix	626-628	3
α-helix	651-662	12
α-helix	672-678	7
α-helix	679-681	3
α-helix	684-715	32
α-helix	731-732	2
α-helix	733-742	10
β-strand	744	1	11
α-helix	749-760	12

Chain B: 35 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	12
β-strand	38-41	4	12
α-helix	43-48	6
β-strand	56-61	6	12
β-strand	65-73	9	12
β-strand	81-84	4	12
α-helix	86-92	7
β-strand	98-104	7	12
β-strand	110	1	13
β-strand	113-118	6	14
β-strand	119	1	15
β-strand	144-146	3	13
β-strand	151-154	4	14
β-strand	161-165	5	14
β-strand	174-176	3	13
β-strand	181-184	4	14
α-helix	188	1
β-strand	189	1	15
α-helix	190	1
α-helix	191-198	8
α-helix	210-225	16
α-helix	227-233	7
β-strand	240-244	5	16
α-helix	251-261	11
β-strand	266	1	16
β-strand	269	1	16
α-helix	271-273	3
α-helix	281-296	16
β-strand	300-303	4	16
α-helix	319-332	14
β-strand	342-346	5	16
α-helix	350-352	3
α-helix	355-358	4
β-strand	365-368	4	16
α-helix	369-373	5
α-helix	374-385	12
α-helix	396-402	7
α-helix	410-429	20
α-helix	439-442	4
α-helix	449-457	9
α-helix	483-498	16
α-helix	500-506	7
β-strand	513-517	5	17
α-helix	524-533	10
β-strand	540-542	3	17
α-helix	554-568	15
β-strand	572-576	5	17
α-helix	579-582	4
α-helix	596-608	13
β-strand	617-620	4	17
β-strand	623	1	17
α-helix	626-628	3
α-helix	631-634	4
β-strand	636	1	18
β-strand	639	1	18
β-strand	641-644	4	17
α-helix	647-649	3
α-helix	650-660	11
α-helix	665-666	2
α-helix	672-678	7
α-helix	684-715	32
α-helix	723-725	3
α-helix	733-742	10
α-helix	749-765	17
β-strand	766	1	11

Chain C: 37 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	29-30	2	19
β-strand	40	1	20
α-helix	43-48	6
β-strand	58	1	21
β-strand	59	1	22
β-strand	67	1	22
β-strand	73	1	20
β-strand	83-84	2	19
α-helix	86-91	6
β-strand	103	1	21
β-strand	116	1	23
β-strand	119	1	24
α-helix	120-123	4
α-helix	130-139	10
β-strand	155	1	25
β-strand	160	1	25
β-strand	184	1	23
α-helix	188	1
β-strand	189	1	24
α-helix	190	1
α-helix	191-198	8
α-helix	203-206	4
α-helix	212-225	14
α-helix	227-232	6
α-helix	236-238	3
α-helix	242-244	3
β-strand	245	1	26
α-helix	252-261	10
β-strand	267-268	2	27
α-helix	272-274	3
α-helix	281-296	16
β-strand	301-302	2	27
α-helix	319-332	14
β-strand	343	1	27
α-helix	355-358	4
β-strand	360	1	28
β-strand	363	1	28
β-strand	369	1	26
α-helix	374-387	14
α-helix	396-402	7
α-helix	411-429	19
α-helix	439-443	5
α-helix	449-458	10
α-helix	462-467	6
α-helix	483-498	16
α-helix	500-506	7
β-strand	516	1	29
α-helix	524-534	11
β-strand	538-540	3	30
α-helix	555-568	14
β-strand	572-574	3	30
α-helix	579-581	3
α-helix	596-608	13
β-strand	622	1	29
α-helix	626-628	3
α-helix	631-634	4
β-strand	644	1	29
α-helix	650-662	13
α-helix	672-679	8
α-helix	684-712	29
α-helix	722-725	4
α-helix	733-741	9
β-strand	744	1	31
α-helix	749-764	16

Chain D: 30 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	39	1	32
β-strand	40	1	33
α-helix	43-48	6
α-helix	57	1
β-strand	58-59	2	34
β-strand	71	1	32
β-strand	83	1	33
α-helix	86-91	6
β-strand	102-103	2	34
β-strand	115	1	35
β-strand	116	1	36
β-strand	119	1	37
α-helix	120-123	4
α-helix	130-138	9
β-strand	165	1	36
β-strand	183	1	35
β-strand	189	1	37
α-helix	191-198	8
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
β-strand	242-244	3	38
α-helix	251-261	11
β-strand	265-266	2	38
α-helix	281-296	16
β-strand	299-304	6	38
α-helix	319-332	14
β-strand	341-347	7	38
β-strand	360	1	39
β-strand	363	1	39
β-strand	366-368	3	38
α-helix	374-386	13
β-strand	393	1	40
α-helix	396-402	7
α-helix	409-429	21
α-helix	439-445	7
β-strand	448	1	40
α-helix	449-458	10
α-helix	462-465	4
α-helix	483-505	23
α-helix	509-511	3
β-strand	514-516	3	41
α-helix	525-534	10
β-strand	538-541	4	41
β-strand	551	1	42
α-helix	554-568	15
β-strand	572-576	5	41
α-helix	579-583	5
α-helix	592-608	17
β-strand	619-621	3	41
α-helix	631-634	4
β-strand	636	1	43
β-strand	639	1	43
β-strand	641-643	3	41
α-helix	650-661	12
α-helix	672-679	8
α-helix	684-711	28
α-helix	733-741	9
α-helix	749-764	16
β-strand	766	1	31

Chain E: 38 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
β-strand	58-60	3	44
β-strand	66-68	3	44
α-helix	74-76	3
α-helix	88-92	5
β-strand	101-102	2	44
α-helix	116-118	3
α-helix	120-123	4
α-helix	130-138	9
α-helix	193-199	7
α-helix	203-205	3
α-helix	209-225	17
α-helix	227-229	3
α-helix	236-238	3
β-strand	242	1	45
α-helix	251-261	11
β-strand	266-268	3	45
α-helix	272-274	3
α-helix	281-296	16
β-strand	300-303	4	45
α-helix	319-331	13
β-strand	342-345	4	45
α-helix	355-358	4
α-helix	376-387	12
α-helix	396-404	9
α-helix	409-429	21
α-helix	439-442	4
α-helix	449-459	11
α-helix	463-467	5
α-helix	483-494	12
α-helix	500-506	7
α-helix	509-511	3
β-strand	513-514	2	46
α-helix	524-534	11
β-strand	540-542	3	46
α-helix	544-547	4
α-helix	554-568	15
β-strand	573-576	4	46
α-helix	579-583	5
α-helix	591-607	17
β-strand	618-621	4	46
α-helix	626-628	3
α-helix	631-634	4
β-strand	641	1	46
α-helix	650-663	14
α-helix	672-679	8
α-helix	684-700	17
α-helix	703-711	9
α-helix	733-742	10
α-helix	749-766	18

Chain F: 33 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	43-48	6
α-helix	58	1
β-strand	59-61	3	47
β-strand	65-67	3	47
α-helix	86-92	7
α-helix	117-119	3
α-helix	120-123	4
α-helix	130-139	10
α-helix	210-225	16
α-helix	227-233	7
α-helix	259-262	4
α-helix	281-293	13
α-helix	301-303	3
α-helix	306-309	4
α-helix	320-332	13
α-helix	369-371	3
α-helix	374-387	14
α-helix	396-402	7
α-helix	409-430	22
α-helix	439-444	6
α-helix	449-458	10
α-helix	483-494	12
α-helix	500-506	7
α-helix	509-511	3
β-strand	514-516	3	48
α-helix	524-534	11
α-helix	555-568	14
α-helix	579-583	5
α-helix	592-608	17
β-strand	620-622	3	48
α-helix	631-634	4
α-helix	652-663	12
β-strand	667	1	49
α-helix	672-676	5
α-helix	686-715	30
β-strand	730	1	49
α-helix	733-742	10
α-helix	749-761	13

Chain I: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	42
α-helix	5-8	4

Chain P: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
α-helix	33-48	16
β-strand	52-55	4	50
β-strand	59-62	4	51
α-helix	69-75	7
α-helix	76-80	5
β-strand	87-88	2	52
α-helix	100-113	14
α-helix	115-117	3
β-strand	118-119	2	52
α-helix	134-143	10
α-helix	146-157	12
β-strand	162-165	4	50
β-strand	169-170	2	50
α-helix	184-188	5
α-helix	201-205	5
α-helix	229-239	11
β-strand	243-245	3	50
β-strand	255-258	4	50
β-strand	263-266	4	50
β-strand	272	1	53
β-strand	276	1	53
α-helix	278-279	2
β-strand	280-285	6	51
β-strand	291-296	6	51

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
Transitional endoplasmic reticulum ATPase	A, B, C, D, E, F	protein	812	Homo sapiens	P55072 (AlphaFold model)
I3 sequence being threaded through the p97 channel	I	protein	22	Homo sapiens
Serine/threonine-protein phosphatase PP1-gamma catalytic subunit	P	protein	323	Homo sapiens	P36873 (AlphaFold model)
Protein phosphatase 1 regulatory subunit 7	S	protein	360	Homo sapiens	Q15435 (AlphaFold model)
UBX domain-containing protein 2B	X	protein	11	Homo sapiens	Q14CS0 (AlphaFold model)
UBX domain-containing protein 2B	Y	protein	86	Homo sapiens	Q14CS0 (AlphaFold model)

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

>8B5R_1 Transitional endoplasmic reticulum ATPase (chains A, B, C, D, E, F)
MHHHHHHASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRG
DTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRI
HVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYC
IVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIG
VKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAE
KNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSID
PALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAAL
CSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQV
TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE
CQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGG
GAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRV
AILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQ
TNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFP
SGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG

Sequence of entity 2 (I), FASTA

>8B5R_2 I3 sequence being threaded through the p97 channel (chains I)
XXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 3 (P), FASTA

>8B5R_3 Serine/threonine-protein phosphatase PP1-gamma catalytic subunit (chains P)
MADLDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLK
ICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFL
LRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDL
QSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDRGVSFTFGAEVVAKFLHKHD
LDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAE
KKKPNATRPVTPPRGMITKQAKK

Sequence of entity 4 (S), FASTA

>8B5R_4 Protein phosphatase 1 regulatory subunit 7 (chains S)
MAAERGAGQQQSQEMMEVDRRVESEESGDEEGKKHSSGIVADLSEQSLKDGEERGEEDPE
EEHELPVDMETINLDRDAEDVDLNHYRIGKIEGFEVLKKVKTLCLRQNLIKCIENLEELQ
SLRELDLYDNQIKKIENLEALTELEILDISFNLLRNIEGVDKLTRLKKLFLVNNKISKIE
NLSNLHQLQMLELGSNRIRAIENIDTLTNLESLFLGKNKITKLQNLDALTNLTVLSMQSN
RLTKIEGLQNLVNLRELYLSHNGIEVIEGLENNNKLTMLDIASNRIKKIENISHLTELQE
FWMNDNLLESWSDLDELKGARSLETVYLERNPLQKDPQYRRKVMLALPSVRQIDATFVRF

Sequence of entity 5 (X), FASTA

>8B5R_5 UBX domain-containing protein 2B (chains X)
FSGEGQKLGSL

Sequence of entity 6 (Y), FASTA

>8B5R_6 UBX domain-containing protein 2B (chains Y)
AVVLIDDSVPTTKIQIRLADGSRLIQRFNSTHRILDVRNFIVQSRPEFAALDFILVTSFP
NKELTDESLTLLEADILNTVLLQQLK

Primary citation

Structural basis of ubiquitin-independent PP1 complex disassembly by p97. van den Boom, J., Marini, G., Meyer, H. et al. EMBO J (2023) 42:e113110-e113110. DOI 10.15252/embj.2022113110 · 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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