5B6C: Structural Details of Ufd1 binding to p97

Structural Details of Ufd1 binding to p97. Determined by X-ray diffraction at 1.55 Å resolution. Released 4 Jan 2017.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,740
Mol. weight: 20.94 kDa
Released: 4 Jan 2017

Explore 5B6C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5B6C contains 10 α-helices and 16 β-strands across 2 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: 10 helices, 15 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
β-strand	66-73	8	1
β-strand	81-83	3	1
α-helix	86-92	7
β-strand	99-104	6	1
α-helix	108-109	2
β-strand	110	1	2
α-helix	111	1
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	151-154	4	3
β-strand	161-169	9	3
β-strand	173-176	4	2
β-strand	181-183	3	3
α-helix	187-188	2
β-strand	189	1	4
α-helix	190-191	2

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	233	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transitional endoplasmic reticulum ATPase	A	protein	174	Homo sapiens	P55072 (AlphaFold model)
Peptide from Ubiquitin fusion degradation protein 1 homolog	B	protein	11	Homo sapiens	Q92890 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5B6C_1 Transitional endoplasmic reticulum ATPase (chains A)
GSNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCS
DEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPY
FLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKRA

Sequence of entity 2 (B), FASTA

>5B6C_2 Peptide from Ubiquitin fusion degradation protein 1 homolog (chains B)
FRAFSGSGNRL

Primary citation

Structural Details of Ufd1 Binding to p97 and Their Functional Implications in ER-Associated Degradation. Le, L.T.M., Kang, W., Kim, J.Y. et al. PLoS One (2016) 11:e0163394-e0163394. DOI 10.1371/journal.pone.0163394 · PubMed

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

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
6G2X 2.08 Å, Crystal structure of the p97 D2 domain in a helical split-washer conformation

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