6DHF: Photosystem II protein D1 1

RT XFEL structure of the one-flash state of Photosystem II (1F, S2-rich) at 2.08 Angstrom resolution. Determined by X-ray diffraction at 2.08 Å resolution. Released 21 Nov 2018.

Method: X-ray diffraction
Resolution: 2.08 Å
Organisms: Thermosynechococcus elongatus (strain BP-1), Thermosynechococcus elongatus
Chains: 40
Atoms: 52,207
Mol. weight: 732.69 kDa
Ligands: FE2, BCT, CLA, PHO
Released: 21 Nov 2018

Explore 6DHF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DHF contains 297 α-helices and 178 β-strands across 40 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: 21 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-21	9
α-helix	31-54	24
β-strand	58	1	44
α-helix	66	1
β-strand	67	1	44
α-helix	68	1
α-helix	71-73	3
β-strand	81-82	2	45
α-helix	83-86	4
α-helix	96-98	3
α-helix	102-108	7
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	268-293	26
β-strand	297-298	2	49
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
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	225	1
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: 28 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	51
α-helix	5-12	8
α-helix	16-42	27
α-helix	55-57	3
α-helix	63-67	5
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	272-277	6
α-helix	279-291	13
α-helix	298-303	6
α-helix	307-312	6
β-strand	314	1	58
α-helix	315-317	3
α-helix	319-321	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	496	1	63
β-strand	498	1	64
α-helix	502-504	3
β-strand	505	1	63

Chain B: 27 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	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	223-228	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	15
α-helix	315-317	3
α-helix	319-321	3
β-strand	323	1	16
α-helix	331-334	4
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
β-strand	391	1	19
α-helix	392-395	4
β-strand	398-402	5	18
β-strand	409-411	3	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

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	65
α-helix	101-103	3
β-strand	105	1	65
α-helix	109-130	22
α-helix	131-135	5
α-helix	154-180	27
β-strand	185-187	3	66
β-strand	195-197	3	66
α-helix	206-209	4
α-helix	211-214	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	306-324	19
β-strand	332	1	67
β-strand	338	1	67
β-strand	341-343	3	68
β-strand	349-351	3	68
α-helix	353-358	6
α-helix	367-369	3
β-strand	370-371	2	68
β-strand	374-375	2	68
α-helix	377-382	6
α-helix	386-396	11
β-strand	402-403	2	49
β-strand	407	1	69
β-strand	408	1	49
α-helix	413-414	2
β-strand	418	1	69
α-helix	422-453	32
β-strand	459	1	70
α-helix	461-463	3
α-helix	465-468	4
α-helix	470-471	2

Chain C: 24 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	35-42	8
α-helix	46-74	29
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	206-214	9
α-helix	223-226	4
α-helix	230-253	24
α-helix	258-261	4
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	354-358	5
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: 23 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	14-22	9
β-strand	24	1	64
α-helix	31-54	24
β-strand	57	1	71
α-helix	58-61	4
β-strand	63	1	71
β-strand	77-78	2	72
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	147-153	7
α-helix	154-159	6
α-helix	160-163	4
α-helix	167-169	3
α-helix	171-172	2
β-strand	173-174	2	72
α-helix	175-189	15
α-helix	191-193	3
α-helix	195-220	26
β-strand	222	1	73
β-strand	223	1	70
α-helix	231-233	3
β-strand	241	1	48
β-strand	244	1	73
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: 23 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	101-106	6
α-helix	109-136	28
α-helix	141-153	13
α-helix	154-159	6
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	195-220	26
β-strand	222	1	29
β-strand	223	1	26
α-helix	231-234	4
β-strand	241	1	5
β-strand	244	1	29
α-helix	246-256	11
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

27 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 1	A, a	protein	334	Thermosynechococcus elongatus (strain BP-1)	P0A444 (AlphaFold model)
Photosystem II CP47 reaction center protein	B, b	protein	505	Thermosynechococcus elongatus (strain BP-1)	Q8DIQ1 (AlphaFold model)
Photosystem II CP43 reaction center protein	C, c	protein	451	Thermosynechococcus elongatus (strain BP-1)	Q8DIF8 (AlphaFold model)
Photosystem II D2 protein	D, d	protein	341	Thermosynechococcus elongatus (strain BP-1)	Q8CM25 (AlphaFold model)
Cytochrome b559 subunit alpha	E, e	protein	82	Thermosynechococcus elongatus (strain BP-1)	Q8DIP0
Cytochrome b559 subunit beta	F, f	protein	34	Thermosynechococcus elongatus (strain BP-1)	Q8DIN9
Photosystem II reaction center protein H	H, h	protein	65	Thermosynechococcus elongatus (strain BP-1)	Q8DJ43
Photosystem II reaction center protein I	I, i	protein	36	Thermosynechococcus elongatus	Q8DJZ6
Photosystem II reaction center protein J	J, j	protein	36	Thermosynechococcus elongatus (strain BP-1)	P59087
Photosystem II reaction center protein K	K, k	protein	37	Thermosynechococcus elongatus (strain BP-1)	Q9F1K9
Photosystem II reaction center protein L	L, l	protein	37	Thermosynechococcus elongatus (strain BP-1)	Q8DIN8
Photosystem II reaction center protein M	M, m	protein	33	Thermosynechococcus elongatus	Q8DHA7

8 more molecules are not listed.

Sequence of entity 1 (A, a), FASTA

>6DHF_1 Photosystem II protein D1 1 (chains A, a)
ANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSGS
LLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQ
WELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEH
NILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFGQEEETYNIVA
AHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFTALGISTMAFNLNGFNFNHSVIDAK
GNVINTWADIINRANLGMEVMHERNAHNFPLDLA

Sequence of entity 2 (B, b), FASTA

>6DHF_2 Photosystem II CP47 reaction center protein (chains B, b)
GLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGMF
VLPFMARLGVTGSWSGWSITGETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDLE
LFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTGLFGPGMWVSDPYGLTGSVQPV
APEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSSS
IAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDSSYFQQEINRRVQASLASGATLEEA
WSAIPEKLAFYDYIGNNPAKGGLFRTGPMNKGDGIAQAWKGHAVFRNKEGEELFVRRMPA
FFESFPVILTDKNGVVKADIPFRRAESKYSFEQQGVTVSFYGGELNGQTFTDPPTVKSYA
RKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFSG
IDPELSPEQVEWGFYQKVGDVTTRR

Sequence of entity 3 (C, c), FASTA

>6DHF_3 Photosystem II CP43 reaction center protein (chains C, c)
ATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFELAHFIPEKPMY
EQGLILIPHIATLGWGVGPGGEVVDTFPFFVVGVVHLISSAVLGFGGVYHAIRGPETLEE
YSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAMFFGGLYDTWAPGGGDVRVITNP
TLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWIGLICIAGGIWHILTTPFGWARR
AFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPSEFYGPTGPEASQAQAMTFLIRDQ
KLGANVGSAQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLNKIKN
DIQPWQERRAAEYMTHAPLGSLNSVGGVATEINSVNFVSPRSWLATSHFVLAFFFLVGHL
WHAGRARAAAAGFEKGIDRESEPVLSMPSLD

Sequence of entity 4 (D, d), FASTA

>6DHF_4 Photosystem II D2 protein (chains D, d)
RGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEGC
NFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQFE
IARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQGFHNW
TLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTANR
FWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPEF
ETFYTKNLLLNEGIRAWMAPQDQPHENFVFPEEVLPRGNAL

Sequence of entity 5 (E, e), FASTA

>6DHF_5 Cytochrome b559 subunit alpha (chains E, e)
GTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQRS
IPLVTDRFEAKQQVETFLEQLK

Sequence of entity 6 (F, f), FASTA

>6DHF_6 Cytochrome b559 subunit beta (chains F, f)
SYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR

Sequence of entity 7 (H, h), FASTA

>6DHF_7 Photosystem II reaction center protein H (chains H, h)
ARRTWLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFLVFLLIILEIYNSTLILDGVNVS
WKALG

Sequence of entity 8 (I, i), FASTA

>6DHF_8 Photosystem II reaction center protein I (chains I, i)
METLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKD

Sequence of entity 9 (J, j), FASTA

>6DHF_9 Photosystem II reaction center protein J (chains J, j)
GGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL

Sequence of entity 10 (K, k), FASTA

>6DHF_10 Photosystem II reaction center protein K (chains K, k)
KLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR

Sequence of entity 11 (L, l), FASTA

>6DHF_11 Photosystem II reaction center protein L (chains L, l)
MEPNPNRQPVELNRTSLYLGLLLILVLALLFSSYFFN

Sequence of entity 12 (M, m), FASTA

>6DHF_12 Photosystem II reaction center protein M (chains M, m)
MEVNQLGLIATALFVLVPSVFLIILYVQTESQQ

Ligands and cofactors

ID	Name	Formula	Copies
FE2	FE (II) ion	Fe	2
BCT	Bicarbonate ion	C H O3	2
CLA	Chlorophyll a	C55 H72 Mg N4 O5	70
PHO	Pheophytin a	C55 H74 N4 O5	4
BCR	Beta-carotene	C40 H56	22
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
SQD	1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol	C41 H78 O12 S	8
DGD	Digalactosyl diacyl glycerol (DGDG)	C51 H96 O15	10
OEX	Ca-MN4-O5 cluster	Ca Mn4 O5	2
LMG	1,2-distearoyl-monogalactosyl-diglyceride	C45 H86 O10	13
LHG	1,2-dipalmitoyl-phosphatidyl-glycerole	C38 H75 O10 P	10
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	2
HEC	Heme C	C34 H36 Fe N4 O4	2

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

Primary citation

Structures of the intermediates of Kok's photosynthetic water oxidation clock. Kern, J., Chatterjee, R., Young, I.D. et al. Nature (2018) 563:421-425. DOI 10.1038/s41586-018-0681-2 · PubMed

Other PDB entries of the same protein (UniProt P0A444 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5OJ5 1.08 Å, YCF48 bound to D1 peptide
9EVX 1.71 Å, cryoEM structure of Photosystem II averaged across S2-S3 states at 1.71 Angstrom…
7RF1 1.89 Å, RT XFEL structure of Photosystem II averaged across all S-states at 1.89 Angstrom…
9Z35 1.93 Å, RT XFEL structure of two-flash state of Photosystem II (2F, S3 rich) at 1.93 Angstrom…
9Z6A 1.93 Å, RT XFEL structure of the two-flash state of Photosystem II (2F, S3 rich) at 1.93…
9Z33 1.97 Å, RT XFEL structure of dark-stable state of Photosystem II (0F, S1 rich) at 1.97 Angstrom…
9Z68 1.97 Å, RT XFEL structure of the dark-stable state of Photosystem II (0F, S1 rich) at 1.97…
9Z34 1.98 Å, RT XFEL structure of one-flash state of Photosystem II (1F, S2 rich) at 1.98 Angstrom…
9Z69 1.98 Å, RT XFEL structure of the one-flash state of Photosystem II (1F, S2 rich) at 1.98…
8F4C 2.0 Å, RT XFEL structure of the two-flash state of Photosystem II (2F, S3-rich) at 2.00…
8F4I 2.0 Å, RT XFEL structure of Photosystem II 2000 microseconds after the third illumination at…
8F4J 2.0 Å, RT XFEL structure of Photosystem II 4000 microseconds after the third illumination at…

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