5EPP: Transitional endoplasmic reticulum ATPase

Structural Insights into the Interaction of p97 N-terminus Domain and VBM Motif in Rhomboid Protease, RHBDL4. Determined by X-ray diffraction at 1.88 Å resolution. Released 14 Sept 2016.

Method: X-ray diffraction
Resolution: 1.88 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,616
Mol. weight: 22.81 kDa
Released: 14 Sept 2016

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

Secondary structure: helices and β-sheets

5EPP contains 9 α-helices and 15 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: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	24-30	7	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	81-84	4	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	120-122	3
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	159-169	11	3
β-strand	173-176	4	2
β-strand	181-183	3	3
β-strand	189	1	4

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	301-313	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transitional endoplasmic reticulum ATPase	A	protein	184	Homo sapiens	P55072 (AlphaFold model)
Rhomboid-related protein 4	B	protein	15	Homo sapiens	Q8TEB9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5EPP_1 Transitional endoplasmic reticulum ATPase (chains A)
GAMGSNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDD
TCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYL
KPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEE
ESLN

Sequence of entity 2 (B), FASTA

>5EPP_2 Rhomboid-related protein 4 (chains B)
SPEEMRRQRLHRFDS

Primary citation

Structural insights into the interaction of p97 N-terminus domain and VBM in rhomboid protease, RHBDL4. Lim, J.J., Lee, Y., Ly, T.T. et al. Biochem J (2016) 473:2863-2880. DOI 10.1042/BCJ20160237 · 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
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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