4KDI: P97/VCP N

Crystal structure of p97/VCP N in complex with OTU1 UBXL. Determined by X-ray diffraction at 1.86 Å resolution. Released 19 Mar 2014.

Method: X-ray diffraction
Resolution: 1.86 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae
Chains: 4
Atoms: 3,863
Mol. weight: 63 kDa
Released: 19 Mar 2014

Explore 4KDI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KDI contains 19 α-helices and 44 β-strands across 4 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: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	1
β-strand	38-41	4	1
α-helix	43-49	7
α-helix	51-52	2
β-strand	53	1	2
β-strand	56-60	5	1
β-strand	66-73	8	1
β-strand	81-83	3	1
α-helix	86-91	6
β-strand	99-104	6	1
α-helix	108-109	2
β-strand	110	1	3
α-helix	111	1
β-strand	113-118	6	4
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	3
β-strand	151-154	4	4
β-strand	161-169	9	4
β-strand	173-176	4	3
β-strand	181-184	4	4

Chain B: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	5
β-strand	38-41	4	5
α-helix	43-48	6
α-helix	51-52	2
β-strand	53	1	6
β-strand	56-60	5	5
β-strand	66-73	8	5
β-strand	81-84	4	5
α-helix	86-91	6
β-strand	99-104	6	5
β-strand	110	1	7
β-strand	113-118	6	8
β-strand	121-122	2	4
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	7
β-strand	151-156	6	8
β-strand	159-169	11	8
β-strand	173-176	4	7
β-strand	181-184	4	8

Chain C: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	2
β-strand	10-14	5	2
β-strand	21	1	9
α-helix	22-28	7
β-strand	35-38	4	2
β-strand	43-46	4	2
β-strand	58	1	9
α-helix	59-62	4
β-strand	68-72	5	2

Chain D: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	0-7	8	10
β-strand	10-17	8	10
β-strand	21	1	11
α-helix	22-28	7
β-strand	35-38	4	10
β-strand	43-46	4	10
α-helix	52-55	4
β-strand	58	1	11
α-helix	60-62	3
β-strand	68	1	6
β-strand	69-72	4	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transitional endoplasmic reticulum ATPase	A, B	protein	193	Homo sapiens	P55072 (AlphaFold model)
Ubiquitin thioesterase OTU1	C, D	protein	90	Saccharomyces cerevisiae	P43558 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4KDI_1 Transitional endoplasmic reticulum ATPase (chains A, B)
GSHMASMTGGQQMGRGSNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKK
RREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTV
EGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIH
CEGEPIKREDEEE

Sequence of entity 2 (C, D), FASTA

>4KDI_2 Ubiquitin thioesterase OTU1 (chains C, D)
GSHMASMTGGQQMGRGSMKLKVTGAGINQVVTLKQDATLNDLIEHINVDVKTMRFGYPPQ
RINLQGEDASLGQTQLDELGINSGEKITIE

Primary citation

Structural Basis for Ovarian Tumor Domain-containing Protein 1 (OTU1) Binding to p97/Valosin-containing Protein (VCP). Kim, S.J., Cho, J., Song, E.J. et al. J Biol Chem (2014) 289:12264-12274. DOI 10.1074/jbc.M113.523936 · 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
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
6G2X 2.08 Å, Crystal structure of the p97 D2 domain in a helical split-washer conformation

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