5OJR: YCF48

YCF48 bound to D1 peptide. Determined by X-ray diffraction at 1.96 Å resolution. Released 8 Aug 2018.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: Thermosynechococcus elongatus
Chains: 6
Atoms: 10,323
Mol. weight: 148.43 kDa
Released: 8 Aug 2018

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

Secondary structure: helices and β-sheets

5OJR contains 28 α-helices and 133 β-strands across 6 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: 7 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	40	1
β-strand	41	1	1
α-helix	42	1
β-strand	47-51	5	2
α-helix	57	1
β-strand	58-63	6	3
β-strand	69-73	5	3
β-strand	77-81	5	3
β-strand	89-90	2	3
β-strand	101-108	8	4
β-strand	111-117	7	4
β-strand	120-124	5	4
β-strand	132-133	2	4
α-helix	135-137	3
β-strand	144-151	8	5
β-strand	154-159	6	5
β-strand	164-167	4	5
β-strand	173-176	4	5
β-strand	180-182	3	6
β-strand	185-190	6	7
β-strand	196-200	5	7
β-strand	205-209	5	7
β-strand	215	1	6
β-strand	217-220	4	7
α-helix	226	1
β-strand	227-232	6	8
β-strand	238-242	5	8
β-strand	246-249	4	8
β-strand	250-251	2	9
β-strand	254-258	5	9
α-helix	260-261	2
β-strand	262	1	8
β-strand	272-277	6	1
β-strand	283-287	5	1
β-strand	292-295	4	1
β-strand	303-304	2	1
α-helix	307-310	4
β-strand	317-322	6	2
β-strand	325-329	5	2
β-strand	334-338	5	2

Chain B: 8 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	40	1
β-strand	41	1	10
α-helix	42	1
β-strand	47-51	5	11
α-helix	57	1
β-strand	58-63	6	12
β-strand	69-73	5	12
β-strand	77-81	5	12
β-strand	89-90	2	12
β-strand	101-108	8	13
β-strand	111-117	7	13
β-strand	120-124	5	13
β-strand	132-133	2	13
α-helix	135-137	3
β-strand	144-151	8	14
β-strand	154-159	6	14
β-strand	164-167	4	14
β-strand	173-176	4	14
β-strand	180-182	3	15
β-strand	185-190	6	16
β-strand	196-200	5	16
β-strand	205-209	5	16
β-strand	215	1	15
β-strand	217-220	4	16
α-helix	226	1
β-strand	227-232	6	17
β-strand	238-242	5	17
β-strand	246-249	4	17
β-strand	250-251	2	18
β-strand	254-258	5	18
α-helix	260-261	2
β-strand	262	1	17
α-helix	270-271	2
β-strand	272-277	6	10
β-strand	283-287	5	10
β-strand	292-295	4	10
β-strand	303-304	2	10
α-helix	306-310	5
β-strand	317-322	6	11
β-strand	325-329	5	11
β-strand	334-338	5	11

Chain C: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	40	1
β-strand	41	1	19
α-helix	42	1
β-strand	47-51	5	20
α-helix	57	1
β-strand	58-63	6	21
β-strand	69-73	5	21
β-strand	77-81	5	21
β-strand	89-90	2	21
β-strand	101-108	8	22
β-strand	111-117	7	22
β-strand	120-124	5	22
β-strand	132-133	2	22
β-strand	144-151	8	23
β-strand	154-159	6	23
β-strand	164-167	4	23
β-strand	175-178	4	23
β-strand	185-190	6	24
β-strand	196-200	5	24
β-strand	205-209	5	24
β-strand	217-220	4	24
α-helix	226	1
β-strand	227-232	6	25
β-strand	238-242	5	25
β-strand	246-249	4	25
β-strand	250-251	2	26
β-strand	254-258	5	26
β-strand	262	1	25
β-strand	272-277	6	19
β-strand	283-287	5	19
β-strand	292-295	4	19
β-strand	303-304	2	19
α-helix	307-310	4
β-strand	317-322	6	20
β-strand	325-329	5	20
β-strand	334-338	5	20

Chain D: 6 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	39-40	2
β-strand	41	1	27
α-helix	42	1
β-strand	47-51	5	28
α-helix	57	1
β-strand	58-63	6	29
β-strand	69-73	5	29
β-strand	77-81	5	29
β-strand	89-90	2	29
β-strand	101-108	8	30
β-strand	111-117	7	30
β-strand	120-124	5	30
β-strand	132-133	2	30
β-strand	144-151	8	31
β-strand	154-159	6	31
β-strand	164-167	4	31
β-strand	175-178	4	31
β-strand	185-190	6	32
β-strand	196-200	5	32
β-strand	205-209	5	32
β-strand	217-220	4	32
α-helix	226	1
β-strand	227-232	6	33
β-strand	238-242	5	33
β-strand	246-249	4	33
β-strand	250-251	2	34
β-strand	254-258	5	34
β-strand	262	1	33
α-helix	271	1
β-strand	272-277	6	27
β-strand	283-287	5	27
β-strand	292-295	4	27
β-strand	303-304	2	27
α-helix	306-310	5
β-strand	317-322	6	28
β-strand	325-329	5	28
β-strand	334-338	5	28

Chain E: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	336-338	3	6
β-strand	342-344	3	5
α-helix	346-348	3
β-strand	349-350	2	4

Chain F: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	336-338	3	15
β-strand	342-344	3	14
α-helix	345-348	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ycf48-like protein	A, B, C, D	protein	326	Thermosynechococcus elongatus	Q8DI95 (AlphaFold model)
Photosystem II protein D1 3	E, F	protein	18	Thermosynechococcus elongatus	Q8DIV4 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5OJR_1 Ycf48-like protein (chains A, B, C, D)
MRGSHHHHHHGLVPRGSIPALDYNPWEAIQLPTTATILDMSFIDRHHGWLVGVNATLMET
RDGGQTWEPRTLVLDHSDYRFNSVSFQGNEGWIVGEPPIMLHTTDGGQSWSQIPLDPKLP
GSPRLIKALGNGSAEMITNVGAIYRTKDSGKNWQALVQEAIGVMRNLNRSPSGEYVAVSS
RGSFYSTWEPGQTAWEPHNRTTSRRLHNMGFTPDGRLWMIVNGGKIAFSDPDNSENWGEL
LSPLRRNSVGFLDLAYRTPNEVWLAGGAGALLCSQDGGQTWQQDVDVKKVPSNFYKILFF
SPDQGFILGQKGILLRYVTDLTAAPA

Sequence of entity 2 (E, F), FASTA

>5OJR_2 Photosystem II protein D1 3 (chains E, F)
NAHNFPLDLASAESAPVA

Primary citation

Ycf48 involved in the biogenesis of the oxygen-evolving photosystem II complex is a seven-bladed beta-propeller protein. Yu, J., Knoppova, J., Michoux, F. et al. Proc Natl Acad Sci U S A (2018) 115:E7824-E7833. DOI 10.1073/pnas.1800609115 · PubMed

Other PDB entries of the same protein (UniProt Q8DI95 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5OJ5 1.08 Å, YCF48 bound to D1 peptide
2XBG 1.5 Å, Crystal Structure of YCF48 from Thermosynechococcus elongatus
5OJP 1.86 Å, YCF48 bound to D1 peptide

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