8KG2: P97-N/D1 hexamer

Crystal structure of p97-N/D1 hexamer in complex with FAF1-UBX domain. Determined by X-ray diffraction at 3.1 Å resolution. Released 29 May 2024.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 24
Atoms: 48,735
Mol. weight: 699.48 kDa
Ligands: ADP
Released: 29 May 2024

Explore 8KG2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8KG2 contains 376 α-helices and 365 β-strands across 24 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.

Chains A, C, E, F, G and L: 29 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	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	81-84	4	1
α-helix	86-91	6
β-strand	99-104	6	1
β-strand	110	1	2
β-strand	113-118	6	3
β-strand	119	1	4
α-helix	120-123	4
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	2
β-strand	151-156	6	3
β-strand	159-168	10	3
β-strand	173-176	4	2
β-strand	181-183	3	3
α-helix	188	1
β-strand	189	1	4
α-helix	190-192	3
α-helix	195-197	3
α-helix	203-205	3
α-helix	210-220	11
α-helix	221-225	5
α-helix	229-232	4
α-helix	235-238	4
β-strand	240-244	5	5
α-helix	251-262	12
β-strand	265-270	6	5
α-helix	271-276	6
α-helix	280-295	16
β-strand	299-304	6	5
α-helix	306-309	4
β-strand	311	1	6
α-helix	319-333	15
α-helix	337-339	3
β-strand	341-347	7	5
α-helix	350-352	3
β-strand	353	1	6
α-helix	355-358	4
β-strand	365-368	4	5
α-helix	371-373	3
α-helix	374-384	11
β-strand	390	1	7
α-helix	396-402	7
α-helix	408-429	22
α-helix	439-444	6
β-strand	447	1	7
α-helix	449-456	8

Chains B and I: 29 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	8
β-strand	38-41	4	8
α-helix	43-48	6
β-strand	56-60	5	8
α-helix	62-64	3
β-strand	66-73	8	8
β-strand	81-84	4	8
α-helix	86-91	6
β-strand	99-104	6	8
β-strand	110	1	9
β-strand	113-118	6	10
β-strand	119	1	11
α-helix	120-123	4
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	9
β-strand	151-156	6	10
β-strand	159-168	10	10
β-strand	173-176	4	9
β-strand	181-183	3	10
α-helix	188	1
β-strand	189	1	11
α-helix	190-192	3
α-helix	195-197	3
α-helix	203-205	3
α-helix	210-220	11
α-helix	221-225	5
α-helix	229-232	4
α-helix	235-238	4
β-strand	240-244	5	12
α-helix	251-262	12
β-strand	265-270	6	12
α-helix	271-276	6
α-helix	280-295	16
β-strand	299-304	6	12
α-helix	306-309	4
β-strand	311	1	13
α-helix	319-334	16
α-helix	337-339	3
β-strand	341-347	7	12
α-helix	350-352	3
β-strand	353	1	13
α-helix	355-358	4
β-strand	365-368	4	12
α-helix	371-373	3
α-helix	374-384	11
β-strand	390	1	14
α-helix	396-402	7
α-helix	408-429	22
α-helix	439-444	6
β-strand	447	1	14
α-helix	449-456	8

Chain D: 29 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	22
β-strand	38-41	4	22
α-helix	43-48	6
β-strand	56-60	5	22
α-helix	62-64	3
β-strand	66-73	8	22
β-strand	81-84	4	22
α-helix	86-91	6
β-strand	99-104	6	22
β-strand	110	1	23
β-strand	113-118	6	24
β-strand	119	1	25
α-helix	120-123	4
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	23
β-strand	151-156	6	24
β-strand	159-168	10	24
β-strand	173-176	4	23
β-strand	181-183	3	24
α-helix	188	1
β-strand	189	1	25
α-helix	190-192	3
α-helix	195-197	3
α-helix	203-205	3
α-helix	210-220	11
α-helix	221-225	5
α-helix	229-232	4
α-helix	235-238	4
β-strand	240-244	5	26
α-helix	251-262	12
β-strand	265-270	6	26
α-helix	271-276	6
α-helix	280-295	16
β-strand	299-304	6	26
α-helix	306-309	4
β-strand	311	1	27
α-helix	319-333	15
α-helix	337-339	3
β-strand	341-347	7	26
α-helix	350-352	3
β-strand	353	1	27
α-helix	355-358	4
β-strand	365-368	4	26
α-helix	371-373	3
α-helix	374-383	10
β-strand	390	1	28
α-helix	396-402	7
α-helix	408-429	22
α-helix	439-444	6
β-strand	447	1	28
α-helix	449-456	8

Chains H and J: 29 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	61
β-strand	38-41	4	61
α-helix	43-48	6
β-strand	56-60	5	61
α-helix	62-64	3
β-strand	66-73	8	61
β-strand	81-84	4	61
α-helix	86-91	6
β-strand	99-104	6	61
β-strand	113-118	6	62
β-strand	119	1	63
α-helix	120-123	4
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	64
β-strand	151-156	6	62
β-strand	159-168	10	62
β-strand	173-176	4	64
β-strand	181-183	3	62
α-helix	188	1
β-strand	189	1	63
α-helix	190-192	3
α-helix	195-197	3
α-helix	203-205	3
α-helix	210-220	11
α-helix	221-225	5
α-helix	229-232	4
α-helix	235-238	4
β-strand	240-244	5	65
α-helix	251-262	12
β-strand	265-270	6	65
α-helix	271-276	6
α-helix	280-295	16
β-strand	299-304	6	65
α-helix	306-309	4
β-strand	311	1	66
α-helix	319-333	15
α-helix	337-339	3
β-strand	341-347	7	65
α-helix	350-352	3
β-strand	353	1	66
α-helix	355-358	4
β-strand	365-368	4	65
α-helix	371-373	3
α-helix	374-384	11
β-strand	390	1	67
α-helix	396-402	7
α-helix	408-429	22
α-helix	439-444	6
β-strand	447	1	67
α-helix	449-456	8

Chain K: 29 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	82
β-strand	38-41	4	82
α-helix	43-48	6
β-strand	56-60	5	82
α-helix	62-64	3
β-strand	66-73	8	82
β-strand	81-84	4	82
α-helix	86-91	6
β-strand	99-104	6	82
β-strand	110	1	83
β-strand	113-118	6	84
β-strand	119	1	85
α-helix	120-123	4
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	83
β-strand	151-156	6	84
β-strand	159-168	10	84
β-strand	173-176	4	83
β-strand	181-183	3	84
α-helix	188	1
β-strand	189	1	85
α-helix	190-192	3
α-helix	195-197	3
α-helix	203-205	3
α-helix	210-220	11
α-helix	221-225	5
α-helix	229-232	4
α-helix	235-238	4
β-strand	240-244	5	86
α-helix	251-262	12
β-strand	265-270	6	86
α-helix	271-276	6
α-helix	280-295	16
β-strand	299-304	6	86
α-helix	306-309	4
β-strand	311	1	87
α-helix	319-334	16
α-helix	337-339	3
β-strand	341-347	7	86
α-helix	350-352	3
β-strand	353	1	87
α-helix	355-358	4
β-strand	365-368	4	86
α-helix	371-373	3
α-helix	374-383	10
β-strand	390	1	88
α-helix	396-402	7
α-helix	408-429	22
α-helix	439-444	6
β-strand	447	1	88
α-helix	449-456	8

Chains M, R, T, V and X: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	576-579	4	43
β-strand	585-588	4	43
β-strand	595	1	44
α-helix	596-605	10
β-strand	613-617	5	43
β-strand	622-623	2	43
α-helix	624-626	3
β-strand	632	1	44
β-strand	642-648	7	43

Chain N: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	578-579	2	45
β-strand	585-586	2	45
α-helix	598-605	8
β-strand	613-617	5	45
β-strand	622-623	2	45
α-helix	624-626	3
β-strand	644-648	5	45

Chains O, P, Q, S and U: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	576-579	4	46
α-helix	580	1
β-strand	585-588	4	46
β-strand	595	1	47
α-helix	596-605	10
β-strand	613-617	5	46
β-strand	622-623	2	46
α-helix	624-626	3
β-strand	632	1	47
β-strand	642-648	7	46

1 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, G, H, I, J, K, L	protein	438	Homo sapiens	P55072 (AlphaFold model)
FAS-associated factor 1	M, N, O, P, Q, R, S, T, U, V, W, X	protein	76	Homo sapiens	Q9UNN5 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA

>8KG2_1 Transitional endoplasmic reticulum ATPase (chains A, B, C, D, E, F, G, H, I, J, K, L)
NRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDE
KIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFL
EAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKRAAAEESLNE
VGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN
ETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEV
ERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEI
LQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAE
VMNSLAVTMDDFRWALSQ

Sequence of entity 2 (M, N, O, P, Q, R, S, T, U, V, W, X), FASTA

>8KG2_2 FAS-associated factor 1 (chains M, N, O, P, Q, R, S, T, U, V, W, X)
KLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLL
EVKLFPQETLFLEAKE

Ligands and cofactors

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

Primary citation

Crystal Structure of p97-N/D1 Hexamer Complexed with FAF1 UBX Domain. Kang, W. J Korean Chem Soc (2024). DOI 10.5012/jkcs.2023.67.5.348

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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