5GLF: Transitional endoplasmic reticulum ATPase

Structural insights into the interaction of p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease. Determined by X-ray diffraction at 2.25 Å resolution. Released 9 Nov 2016.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 8
Atoms: 6,171
Mol. weight: 89.22 kDa
Released: 9 Nov 2016

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

Secondary structure: helices and β-sheets

5GLF contains 41 α-helices and 62 β-strands across 8 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	24-29	6	1
β-strand	38-41	4	1
α-helix	43-49	7
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
α-helix	187-188	2
β-strand	189	1	4
α-helix	190-191	2

Chains B, D, F and H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	245-247	3	3

Chain C: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	24-29	6	5
β-strand	38-41	4	5
α-helix	43-49	7
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
α-helix	108-109	2
β-strand	110	1	6
α-helix	111	1
β-strand	113-118	6	7
α-helix	123-125	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	6
β-strand	151-154	4	7
β-strand	161-169	9	7
β-strand	173-176	4	6
α-helix	180	1
β-strand	181-183	3	7
α-helix	187-191	5

Chain E: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	8
β-strand	38-41	4	8
α-helix	43-49	7
β-strand	56-60	5	8
β-strand	66-73	8	8
β-strand	81-84	4	8
α-helix	86-92	7
β-strand	99-104	6	8
α-helix	108-109	2
β-strand	110	1	9
α-helix	111	1
β-strand	113-118	6	10
β-strand	119	1	11
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	9
β-strand	151-155	5	10
β-strand	160-169	10	10
β-strand	173-176	4	9
α-helix	180	1
β-strand	181-183	3	10
α-helix	187-188	2
β-strand	189	1	11
α-helix	190-191	2

Chain G: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	12
β-strand	38-41	4	12
α-helix	43-49	7
β-strand	56-60	5	12
β-strand	66-73	8	12
β-strand	81-84	4	12
α-helix	86-91	6
β-strand	99-104	6	12
α-helix	108-109	2
β-strand	110	1	13
α-helix	111	1
β-strand	113-118	6	14
β-strand	119	1	15
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	13
β-strand	151-156	6	14
β-strand	159-169	11	14
β-strand	173-176	4	13
α-helix	180	1
β-strand	181-183	3	14
α-helix	187-188	2
β-strand	189	1	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transitional endoplasmic reticulum ATPase	A, C, E, G	protein	184	Homo sapiens	P55072 (AlphaFold model)
Derlin-1	B, D, F, H	protein	12	Homo sapiens	Q9BUN8 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>5GLF_1 Transitional endoplasmic reticulum ATPase (chains A, C, E, G)
GAMGSNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDD
TCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYL
KPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEE
ESLN

Sequence of entity 2 (B, D, F, H), FASTA

>5GLF_2 Derlin-1 (chains B, D, F, H)
RHNWGQGFRLGD

Primary citation

Structural insights into the interaction of human p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease. Lim, J.J., Lee, Y., Yoon, S.Y. et al. FEBS Lett (2016) 590:4402-4413. DOI 10.1002/1873-3468.12447 · 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

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