8IR9: Photosystem II protein D1

XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 30-microsecond delay. Determined by X-ray diffraction at 2.2 Å resolution. Released 17 Jan 2024.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Thermostichus vulcanus
Chains: 39
Atoms: 62,674
Mol. weight: 724.5 kDa
Ligands: FE2, CLA, PHO, BCR
Released: 17 Jan 2024

Explore 8IR9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8IR9 contains 303 α-helices and 175 β-strands across 39 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: 22 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-21	9
α-helix	31-54	24
α-helix	55-57	3
β-strand	58	1	44
β-strand	67	1	44
α-helix	71-73	3
β-strand	81-82	2	45
α-helix	83-86	4
α-helix	96-98	3
α-helix	102-107	6
α-helix	110-136	27
α-helix	143-155	13
α-helix	156-160	5
α-helix	161-165	5
α-helix	168-170	3
α-helix	172-173	2
β-strand	174-175	2	45
α-helix	176-190	15
α-helix	192-194	3
α-helix	196-221	26
β-strand	223	1	46
β-strand	224	1	47
α-helix	233-236	4
β-strand	243	1	48
β-strand	246	1	46
α-helix	248-258	11
α-helix	261-263	3
α-helix	268-293	26
β-strand	297-298	2	49
α-helix	300	1
β-strand	307	1	50
β-strand	313	1	50
α-helix	317-331	15

Chain A: 21 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-21	9
α-helix	31-54	24
α-helix	55-57	3
β-strand	58	1	1
β-strand	67	1	1
α-helix	71-73	3
β-strand	81-82	2	2
α-helix	83-86	4
α-helix	96-98	3
α-helix	102-107	6
α-helix	110-136	27
α-helix	143-155	13
α-helix	156-160	5
α-helix	161-165	5
α-helix	168-170	3
α-helix	172-173	2
β-strand	174-175	2	2
α-helix	176-190	15
α-helix	192-194	3
α-helix	196-221	26
β-strand	223	1	3
β-strand	224	1	4
α-helix	233-236	4
β-strand	243	1	5
β-strand	246	1	3
α-helix	248-258	11
α-helix	261-263	3
α-helix	268-293	26
β-strand	297-298	2	6
β-strand	307	1	7
β-strand	313	1	7
α-helix	317-331	15

Chain b: 27 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	51
α-helix	5-12	8
α-helix	16-44	29
α-helix	55-57	3
α-helix	63-68	6
β-strand	73	1	52
β-strand	78	1	53
β-strand	79	1	52
β-strand	84	1	53
α-helix	93-116	24
β-strand	120	1	54
α-helix	121-123	3
β-strand	124	1	55
β-strand	131	1	55
α-helix	135-152	18
α-helix	153-158	6
β-strand	166-168	3	56
β-strand	177-179	3	56
α-helix	187-190	4
α-helix	195-218	24
α-helix	220-221	2
β-strand	222	1	57
α-helix	223-228	6
α-helix	234-258	25
α-helix	265-268	4
α-helix	272-276	5
α-helix	279-293	15
α-helix	298-303	6
α-helix	307-312	6
β-strand	314	1	58
α-helix	315-317	3
β-strand	323	1	59
α-helix	330-332	3
β-strand	336-342	7	60
β-strand	343-347	5	61
β-strand	353-354	2	61
β-strand	355-356	2	62
α-helix	357-360	4
β-strand	369-371	3	62
β-strand	377-380	4	62
β-strand	391	1	62
α-helix	392-395	4
β-strand	398-402	5	61
β-strand	410-411	2	61
α-helix	414-424	11
β-strand	427	1	58
β-strand	429-433	5	60
α-helix	447-474	28
α-helix	476-478	3
β-strand	482	1	47
α-helix	488-491	4
β-strand	498	1	63
α-helix	502-504	3

Chain B: 27 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	8
α-helix	5-12	8
α-helix	16-44	29
α-helix	55-57	3
α-helix	63-68	6
β-strand	73	1	9
β-strand	78	1	10
β-strand	79	1	9
β-strand	84	1	10
α-helix	93-116	24
β-strand	120	1	11
α-helix	121-123	3
β-strand	124	1	12
β-strand	131	1	12
α-helix	135-152	18
α-helix	153-158	6
β-strand	166-168	3	13
β-strand	177-179	3	13
α-helix	187-190	4
α-helix	195-218	24
α-helix	220-221	2
β-strand	222	1	14
α-helix	223-229	7
α-helix	234-258	25
α-helix	265-268	4
α-helix	272-276	5
α-helix	279-293	15
α-helix	298-303	6
α-helix	307-312	6
β-strand	314	1	15
α-helix	315-317	3
β-strand	323	1	16
α-helix	330-332	3
β-strand	336-342	7	17
β-strand	343-347	5	18
β-strand	353-354	2	18
β-strand	355-356	2	19
α-helix	357-360	4
β-strand	369-371	3	19
β-strand	377-380	4	19
α-helix	392-395	4
β-strand	398-402	5	18
β-strand	410-411	2	18
α-helix	414-424	11
β-strand	427	1	15
β-strand	429-433	5	17
α-helix	447-474	28
α-helix	476-478	3
β-strand	482	1	4
α-helix	488-491	4
β-strand	498	1	20
α-helix	502-504	3

Chain c: 26 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	28-31	4
α-helix	35-42	8
α-helix	46-74	29
α-helix	81-83	3
α-helix	89-94	6
β-strand	99	1	64
α-helix	101-103	3
β-strand	105	1	64
α-helix	109-130	22
α-helix	131-135	5
α-helix	154-181	28
β-strand	185-187	3	65
β-strand	195-197	3	65
α-helix	206-209	4
α-helix	223-226	4
α-helix	230-253	24
α-helix	258-263	6
α-helix	268-292	25
α-helix	299-302	4
α-helix	306-323	18
α-helix	328-330	3
β-strand	332	1	66
β-strand	338	1	66
β-strand	341-343	3	67
β-strand	349-351	3	67
α-helix	354-358	5
α-helix	367-369	3
β-strand	370-371	2	67
β-strand	374-375	2	67
α-helix	377-382	6
α-helix	386-396	11
β-strand	402-403	2	49
β-strand	407	1	68
β-strand	408	1	49
α-helix	413-414	2
β-strand	418	1	68
α-helix	422-453	32
β-strand	459	1	69
α-helix	461-463	3
α-helix	465-468	4
α-helix	470-471	2

Chain C: 26 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	28-31	4
α-helix	35-42	8
α-helix	46-73	28
α-helix	81-83	3
α-helix	89-94	6
β-strand	99	1	21
α-helix	101-103	3
β-strand	105	1	21
α-helix	109-130	22
α-helix	131-135	5
α-helix	154-181	28
β-strand	185-187	3	22
β-strand	195-197	3	22
α-helix	206-211	6
α-helix	212-214	3
α-helix	223-226	4
α-helix	230-253	24
α-helix	258-263	6
α-helix	268-292	25
α-helix	299-302	4
α-helix	306-323	18
β-strand	332	1	23
β-strand	338	1	23
β-strand	341-343	3	24
β-strand	349-351	3	24
α-helix	353-358	6
α-helix	367-369	3
β-strand	370-371	2	24
β-strand	374-375	2	24
α-helix	377-382	6
α-helix	386-396	11
β-strand	402-403	2	6
β-strand	407	1	25
β-strand	408	1	6
α-helix	413-414	2
β-strand	418	1	25
α-helix	422-453	32
β-strand	459	1	26
α-helix	461-463	3
α-helix	465-468	4
α-helix	470-471	2

Chain d: 24 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	14-22	9
β-strand	24	1	63
α-helix	31-54	24
β-strand	57	1	70
α-helix	58-61	4
β-strand	63	1	70
α-helix	67-69	3
β-strand	77-78	2	71
α-helix	79-82	4
α-helix	83-85	3
α-helix	101-107	7
α-helix	109-136	28
α-helix	141-145	5
α-helix	147-154	8
α-helix	155-159	5
α-helix	160-163	4
α-helix	167-169	3
α-helix	171-172	2
β-strand	173-174	2	71
α-helix	175-189	15
α-helix	191-193	3
α-helix	195-220	26
β-strand	222	1	72
β-strand	223	1	69
α-helix	231-233	3
β-strand	241	1	48
β-strand	244	1	72
α-helix	246-257	12
α-helix	264-290	27
β-strand	294	1	59
α-helix	299-307	9
α-helix	314-333	20
α-helix	335-337	3
α-helix	343-345	3

Chain D: 24 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	14-22	9
β-strand	24	1	20
α-helix	33-54	22
β-strand	57	1	27
α-helix	58-61	4
β-strand	63	1	27
α-helix	67-69	3
β-strand	77-78	2	28
α-helix	79-82	4
α-helix	83-85	3
α-helix	101-107	7
α-helix	109-136	28
α-helix	141-145	5
α-helix	147-154	8
α-helix	155-159	5
α-helix	160-163	4
α-helix	167-169	3
α-helix	171-172	2
β-strand	173-174	2	28
α-helix	175-189	15
α-helix	191-193	3
α-helix	195-219	25
β-strand	222	1	29
β-strand	223	1	26
α-helix	231-233	3
β-strand	241	1	5
β-strand	244	1	29
α-helix	246-257	12
α-helix	264-290	27
β-strand	294	1	16
α-helix	299-307	9
α-helix	314-333	20
α-helix	335-337	3
α-helix	343-345	3

22 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Photosystem II protein D1	A, a	protein	344	Thermostichus vulcanus	P51765 (AlphaFold model)
Photosystem II CP47 reaction center protein	B, b	protein	505	Thermostichus vulcanus	D0VWR1 (AlphaFold model)
Photosystem II CP43 reaction center protein	C, c	protein	455	Thermostichus vulcanus	D0VWR7 (AlphaFold model)
Photosystem II D2 protein	D, d	protein	342	Thermostichus vulcanus	D0VWR8 (AlphaFold model)
Cytochrome b559 subunit alpha	E, e	protein	84	Thermostichus vulcanus	P12238
Cytochrome b559 subunit beta	F, f	protein	44	Thermostichus vulcanus	P12239
Photosystem II reaction center protein H	H, h	protein	65	Thermostichus vulcanus	P19052
Photosystem II reaction center protein I	I, i	protein	38	Thermostichus vulcanus	P12240
Photosystem II reaction center protein J	J, j	protein	39	Thermostichus vulcanus	Q7DGD4
Photosystem II reaction center protein K	K, k	protein	37	Thermostichus vulcanus	P19054
Photosystem II reaction center protein L	L, l	protein	37	Thermostichus vulcanus	P12241
Photosystem II reaction center protein M	M, m	protein	36	Thermostichus vulcanus	P12312

8 more molecules are not listed.

Sequence of entity 1 (A, a), FASTA

>8IR9_1 Photosystem II protein D1 (chains A, a)
MTTTLQRRESANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDI
DGIREPVSGSLLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFL
LGASCYMGRQWELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSDGMPLGISGTF
NFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFG
QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFAALGISTMAFNLNGF
NFNHSVIDAKGNVINTWADIINRANLGMEVMHERNAHNFPLDLA

Sequence of entity 2 (B, b), FASTA

>8IR9_2 Photosystem II CP47 reaction center protein (chains B, b)
GLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGMF
VLPFMARLGVTGSWSGWSITGETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDLE
LFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTGLFGPGMWVSDPYGLTGSVQPV
APEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSSS
IAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDSSYFQQEINRRVQASLASGATLEEA
WSAIPEKLAFYDYIGNNPAKGGLFRTGPMNKGDGIAQAWKGHAVFRNKEGEELFVRRMPA
FFESFPVILTDKNGVVKADIPFRRAESKYSFEQQGVTVSFYGGELNGQTFTDPPTVKSYA
RKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFSG
IDPELSPEQVEWGFYQKVGDVTTRK

Sequence of entity 3 (C, c), FASTA

>8IR9_3 Photosystem II CP43 reaction center protein (chains C, c)
NSIFATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFELAHFIPE
KPMYEQGLILIPHIATLGWGVGPGGEVVDTFPFFVVGVVHLISSAVLGFGGVYHAIRGPE
TLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAMFFGGLYDTWAPGGGDVRV
ITNPTLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWIGLICIAGGIWHILTTPFG
WARRAFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPSEFYGPTGPEASQAQAMTFL
IRDQKLGANVGSAQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLN
KIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINSVNFVSPRSWLATSHFVLAFFFL
VGHLWHAGRARAAAAGFEKGIDRESEPVLSMPSLD

Sequence of entity 4 (D, d), FASTA

>8IR9_4 Photosystem II D2 protein (chains D, d)
ERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEG
CNFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQF
EIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQGFHN
WTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTAN
RFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPE
FETFYTKNLLLNEGIRAWMAPQDQPHENFVFPEEVLPRGNAL

Sequence of entity 5 (E, e), FASTA

>8IR9_5 Cytochrome b559 subunit alpha (chains E, e)
MAGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQ
RSIPLVTDRFEAKQQVETFLEQLK

Sequence of entity 6 (F, f), FASTA

>8IR9_6 Cytochrome b559 subunit beta (chains F, f)
TSNTPNQEPVSYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR

Sequence of entity 7 (H, h), FASTA

>8IR9_7 Photosystem II reaction center protein H (chains H, h)
ARRTWLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFLVFLLIILEIYNSTLILDGVNVS
WKALG

Sequence of entity 8 (I, i), FASTA

>8IR9_8 Photosystem II reaction center protein I (chains I, i)
METLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKDLE

Sequence of entity 9 (J, j), FASTA

>8IR9_9 Photosystem II reaction center protein J (chains J, j)
MSEGGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL

Sequence of entity 10 (K, k), FASTA

>8IR9_10 Photosystem II reaction center protein K (chains K, k)
KLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR

Sequence of entity 11 (L, l), FASTA

>8IR9_11 Photosystem II reaction center protein L (chains L, l)
MEPNPNRQPVELNRTSLYLGLLLILVLALLFSSYFFN

Sequence of entity 12 (M, m), FASTA

>8IR9_12 Photosystem II reaction center protein M (chains M, m)
MEVNQLGLIATALFVLVPSVFLIILYVQTESQQKSS

Ligands and cofactors

ID	Name	Formula	Copies
FE2	FE (II) ion	Fe	2
CLA	Chlorophyll a	C55 H72 Mg N4 O5	70
PHO	Pheophytin a	C55 H74 N4 O5	4
BCR	Beta-carotene	C40 H56	22
OEX	Ca-MN4-O5 cluster	Ca Mn4 O5	2
PL9	2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-he…	C53 H80 O2	4
BCT	Bicarbonate ion	C H O3	2
LHG	1,2-dipalmitoyl-phosphatidyl-glycerole	C38 H75 O10 P	10
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	14
LMG	1,2-distearoyl-monogalactosyl-diglyceride	C45 H86 O10	12
HTG	heptyl 1-thio-beta-D-glucopyranoside	C13 H26 O5 S	11
DGD	Digalactosyl diacyl glycerol (DGDG)	C51 H96 O15	8
CA	Calcium ion	Ca	7
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	2
MG	Magnesium ion	Mg	2
HEC	Heme C	C34 H36 Fe N4 O4	2
SQD	1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol	C41 H78 O12 S	8

Water and common crystallization additives (CL, GOL, UNL) are not listed.

Primary citation

Oxygen-evolving photosystem II structures during S 1 -S 2 -S 3 transitions. Li, H., Nakajima, Y., Nango, E. et al. Nature (2024) 626:670-677. DOI 10.1038/s41586-023-06987-5 · PubMed

Other PDB entries of the same protein (UniProt P51765 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5B66 1.85 Å, Crystal structure analysis of Photosystem II complex
5B5E 1.87 Å, Crystal structure analysis of Photosystem II complex
3WU2 1.9 Å, Crystal structure analysis of Photosystem II complex
5V2C 1.9 Å, Re-refinement of crystal structure of photosystem II complex
4UB6 1.95 Å, Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser
4UB8 1.95 Å, Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser
7D1T 1.95 Å, Cryo-EM Structure of PSII at 1.95 angstrom resolution
8GN2 1.95 Å, Crystal structure of PPBQ-bound photosystem II complex
9LP8 2.0 Å, Extrinsic-protein reconstituted PSII of Thermosynechococcus vulcanus NIES-2134
7D1U 2.08 Å, Cryo-EM Structure of PSII at 2.08 angstrom resolution
4IL6 2.1 Å, Structure of Sr-substituted photosystem II
8GN1 2.1 Å, Crystal structure of DBBQ-bound photosystem II complex

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