7D1T: PSII

Cryo-EM Structure of PSII at 1.95 angstrom resolution. Determined by electron microscopy at 1.95 Å resolution. Released 31 Mar 2021.

Method: Electron microscopy
Resolution: 1.95 Å
Organism: Thermosynechococcus vulcanus
Chains: 40
Atoms: 52,994
Mol. weight: 709.09 kDa
Ligands: SQD, HEM, HEC, RRX
Released: 31 Mar 2021

Explore 7D1T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7D1T contains 300 α-helices and 182 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.

Chains a and A: 24 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	47
α-helix	66	1
β-strand	67	1	47
α-helix	68	1
α-helix	71-73	3
β-strand	81-82	2	48
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	48
α-helix	176-190	15
α-helix	192-194	3
α-helix	196-221	26
β-strand	223	1	49
β-strand	224	1	50
α-helix	225	1
α-helix	233-236	4
β-strand	243	1	51
β-strand	246	1	49
α-helix	248-258	11
α-helix	261-263	3
α-helix	268-293	26
β-strand	297-298	2	52
β-strand	307	1	53
β-strand	313	1	53
α-helix	317-331	15

Chains b and B: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	54
α-helix	5-12	8
α-helix	16-44	29
α-helix	55-57	3
α-helix	63-68	6
β-strand	73	1	55
β-strand	79	1	55
α-helix	93-116	24
β-strand	120	1	56
α-helix	121-123	3
β-strand	124	1	57
β-strand	131	1	57
α-helix	135-152	18
α-helix	153-158	6
β-strand	166-168	3	58
β-strand	177-179	3	58
α-helix	187-190	4
α-helix	195-218	24
α-helix	220-221	2
β-strand	222	1	59
α-helix	223-228	6
α-helix	234-258	25
α-helix	265-268	4
α-helix	272-276	5
α-helix	279-292	14
α-helix	298-303	6
α-helix	307-312	6
β-strand	314	1	60
α-helix	315-317	3
β-strand	323	1	61
α-helix	331-334	4
β-strand	336-340	5	62
β-strand	343-347	5	63
β-strand	353-354	2	63
β-strand	355-356	2	64
α-helix	357-360	4
β-strand	369-371	3	64
β-strand	377-380	4	64
β-strand	391	1	64
α-helix	392-395	4
β-strand	398-402	5	63
β-strand	410-411	2	63
α-helix	414-424	11
β-strand	427	1	60
β-strand	430-433	4	62
α-helix	447-474	28
α-helix	476-478	3
β-strand	482	1	50
α-helix	488-491	4
β-strand	498	1	65
α-helix	502-504	3

Chains c and C: 25 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	81-84	4
α-helix	89-94	6
β-strand	99	1	66
α-helix	101-103	3
β-strand	105	1	66
α-helix	109-130	22
α-helix	131-135	5
α-helix	154-181	28
β-strand	185-187	3	67
β-strand	195-197	3	67
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	306-324	19
α-helix	328-330	3
β-strand	332	1	68
β-strand	338	1	68
β-strand	341-343	3	69
β-strand	349-351	3	69
α-helix	353-358	6
α-helix	367-369	3
β-strand	370-371	2	69
β-strand	374-375	2	69
α-helix	377-382	6
α-helix	386-396	11
β-strand	402-403	2	52
β-strand	407	1	70
β-strand	408	1	52
α-helix	413-414	2
β-strand	418	1	70
α-helix	422-453	32
β-strand	459	1	71
α-helix	465-468	4
α-helix	470-471	2

Chains d and D: 22 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	14-22	9
β-strand	24	1	65
α-helix	33-54	22
β-strand	57	1	72
β-strand	63	1	72
α-helix	67-69	3
β-strand	77-78	2	73
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	73
α-helix	175-189	15
α-helix	191-193	3
α-helix	195-220	26
β-strand	222	1	74
β-strand	223	1	71
α-helix	232-234	3
β-strand	241	1	51
β-strand	244	1	74
α-helix	246-257	12
α-helix	264-290	27
β-strand	294	1	61
α-helix	299-307	9
α-helix	314-333	20
α-helix	335-337	3
α-helix	343-345	3

Chains e and E: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	8-9	2
α-helix	10-13	4
α-helix	17-39	23
α-helix	42-47	6
α-helix	49-51	3
α-helix	72-81	10

Chains f and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	18-40	23

Chains h and H: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	56
α-helix	6-11	6
α-helix	12-15	4
β-strand	22	1	59
α-helix	28-50	23

Chains i and I: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-24	23
α-helix	27-29	3

12 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	334	Thermosynechococcus vulcanus	P51765 (AlphaFold model)
Photosystem II CP47 reaction center protein	B, b	protein	505	Thermosynechococcus vulcanus	D0VWR1 (AlphaFold model)
Photosystem II CP43 reaction center protein	C, c	protein	451	Thermosynechococcus vulcanus	D0VWR7 (AlphaFold model)
Photosystem II D2 protein	D, d	protein	342	Thermosynechococcus vulcanus	D0VWR8 (AlphaFold model)
Cytochrome b559 subunit alpha	E, e	protein	81	Thermosynechococcus vulcanus	P12238
Cytochrome b559 subunit beta	F, f	protein	34	Thermosynechococcus vulcanus	P12239
Photosystem II reaction center protein H	H, h	protein	63	Thermosynechococcus vulcanus	P19052
Photosystem II reaction center protein I	I, i	protein	36	Thermosynechococcus vulcanus	P12240
Photosystem II reaction center protein J	J, j	protein	37	Thermosynechococcus vulcanus	Q7DGD4
Photosystem II reaction center protein K	K, k	protein	37	Thermosynechococcus vulcanus	P19054
Photosystem II reaction center protein L	L, l	protein	37	Thermosynechococcus vulcanus	P12241
Photosystem II reaction center protein M	M, m	protein	34	Thermosynechococcus vulcanus	P12312

8 more molecules are not listed.

Sequence of entity 1 (A, a), FASTA

>7D1T_1 Photosystem II protein D1 (chains A, a)
ANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSGS
LLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQ
WELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEH
NILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFGQEEETYNIVA
AHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFAALGISTMAFNLNGFNFNHSVIDAK
GNVINTWADIINRANLGMEVMHERNAHNFPLDLA

Sequence of entity 2 (B, b), FASTA

>7D1T_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

>7D1T_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

>7D1T_4 Photosystem II D2 protein (chains D, d)
ERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEG
CNFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQF
EIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQGFHN
WTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTAN
RFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPE
FETFYTKNLLLNEGIRAWMAPQDQPXENFVFPEEVLPRGNAL

Sequence of entity 5 (E, e), FASTA

>7D1T_5 Cytochrome b559 subunit alpha (chains E, e)
TTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQRSI
PLVTDRFEAKQQVETFLEQLK

Sequence of entity 6 (F, f), FASTA

>7D1T_6 Cytochrome b559 subunit beta (chains F, f)
SYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR

Sequence of entity 7 (H, h), FASTA

>7D1T_7 Photosystem II reaction center protein H (chains H, h)
ARRTWLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFLVFLLIILEIYNSTLILDGVNVS
WKA

Sequence of entity 8 (I, i), FASTA

>7D1T_8 Photosystem II reaction center protein I (chains I, i)
METLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKD

Sequence of entity 9 (J, j), FASTA

>7D1T_9 Photosystem II reaction center protein J (chains J, j)
EGGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL

Sequence of entity 10 (K, k), FASTA

>7D1T_10 Photosystem II reaction center protein K (chains K, k)
KLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR

Sequence of entity 11 (L, l), FASTA

>7D1T_11 Photosystem II reaction center protein L (chains L, l)
MEPNPNRQPVELNRTSLYLGLLLILVLALLFSSYFFN

Sequence of entity 12 (M, m), FASTA

>7D1T_12 Photosystem II reaction center protein M (chains M, m)
MEVNQLGLIATALFVLVPSVFLIILYVQTESQQK

Ligands and cofactors

ID	Name	Formula	Copies
SQD	1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol	C41 H78 O12 S	8
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	2
HEC	Heme C	C34 H36 Fe N4 O4	2
RRX	(3R)-beta,beta-caroten-3-ol	C40 H56 O	2
MG	Magnesium ion	Mg	2
LHG	1,2-dipalmitoyl-phosphatidyl-glycerole	C38 H75 O10 P	10
BCT	Bicarbonate ion	C H O3	2
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	8
DGD	Digalactosyl diacyl glycerol (DGDG)	C51 H96 O15	8
LMG	1,2-distearoyl-monogalactosyl-diglyceride	C45 H86 O10	10
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
BCR	Beta-carotene	C40 H56	20
PHO	Pheophytin a	C55 H74 N4 O5	4
CLA	Chlorophyll a	C55 H72 Mg N4 O5	70
FE2	FE (II) ion	Fe	2
OEX	Ca-MN4-O5 cluster	Ca Mn4 O5	2

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

Primary citation

High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams. Kato, K., Miyazaki, N., Hamaguchi, T. et al. Commun Biol (2021) 4:382-382. DOI 10.1038/s42003-021-01919-3 · 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
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
6JLJ 2.15 Å, XFEL structure of cyanobacterial photosystem II (dark state, dataset1)

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