3PCQ: Femtosecond X-ray protein Nanocrystallography

Femtosecond X-ray protein Nanocrystallography. Determined by X-ray diffraction at 8.98 Å resolution. Released 2 Feb 2011.

Method: X-ray diffraction
Resolution: 8.98 Å
Organism: Thermosynechococcus elongatus
Chains: 12
Atoms: 24,196
Mol. weight: 359.83 kDa
Ligands: CLA, PQN, SF4, BCR
Released: 2 Feb 2011

Explore 3PCQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PCQ contains 138 α-helices and 62 β-strands across 12 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: 42 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	16-18	3	1
α-helix	36-38	3
β-strand	44	1	2
α-helix	46-53	8
α-helix	58-60	3
α-helix	65-96	32
α-helix	100-105	6
β-strand	113-114	2	3
α-helix	123-126	4
β-strand	128-131	4	4
β-strand	134-136	3	4
β-strand	137-138	2	3
α-helix	139	1
α-helix	143-150	8
α-helix	155-177	23
α-helix	178-182	5
β-strand	183-185	3	1
α-helix	187-190	4
α-helix	193-198	6
α-helix	199-207	9
α-helix	208-215	8
α-helix	216-220	5
α-helix	221-227	7
α-helix	237-238	2
α-helix	241-244	4
α-helix	246-251	6
α-helix	272-275	4
α-helix	294-311	18
β-strand	315	1	5
β-strand	323	1	5
α-helix	325-331	7
α-helix	344-350	7
α-helix	352-376	25
α-helix	387-418	32
α-helix	422-425	4
α-helix	429-434	6
α-helix	437-468	32
α-helix	471-473	3
β-strand	475	1	6
β-strand	480	1	6
α-helix	485-496	12
β-strand	498	1	7
β-strand	502	1	7
β-strand	518-520	3	8
β-strand	523-526	4	8
α-helix	533-558	26
α-helix	569-572	4
α-helix	591-620	30
β-strand	623-625	3	8
β-strand	631-633	3	8
α-helix	639-642	4
α-helix	646-648	3
α-helix	649-655	7
α-helix	656-657	2
α-helix	659-663	5
α-helix	670-691	22
α-helix	694-710	17
β-strand	718	1	2
α-helix	721-723	3
α-helix	724-754	31

Chain B: 50 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	9
α-helix	9-12	4
β-strand	16	1	10
α-helix	18-26	9
α-helix	30-32	3
α-helix	38-70	33
α-helix	73-78	6
α-helix	83-85	3
β-strand	86-89	4	11
α-helix	97-103	7
β-strand	112-114	3	11
α-helix	119-125	7
α-helix	131-154	24
α-helix	158-160	3
α-helix	161-163	3
α-helix	164-167	4
α-helix	170-175	6
α-helix	176-184	9
α-helix	185-192	8
α-helix	193-197	5
α-helix	198-201	4
α-helix	211-213	3
α-helix	222-225	4
α-helix	229-233	5
α-helix	269-286	18
β-strand	290	1	12
β-strand	298	1	12
α-helix	300-305	6
β-strand	309	1	13
β-strand	312	1	13
α-helix	317-319	3
α-helix	325-331	7
α-helix	333-357	25
α-helix	364-366	3
α-helix	368-395	28
α-helix	396-400	5
α-helix	404-406	3
α-helix	410-416	7
α-helix	418-448	31
α-helix	452-454	3
β-strand	458	1	14
α-helix	461-469	9
α-helix	473-475	3
α-helix	487-490	4
α-helix	500-508	9
α-helix	520-545	26
α-helix	556-559	4
α-helix	569-571	3
α-helix	578-609	32
α-helix	612-618	7
α-helix	622-625	4
α-helix	626-631	6
α-helix	632-633	2
α-helix	637-639	3
β-strand	641-642	2	15
β-strand	645-646	2	15
α-helix	650-671	22
α-helix	674-689	16
α-helix	694-696	3
β-strand	702	1	10
α-helix	705-707	3
α-helix	708-736	29

Chain C: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
α-helix	15-19	5
β-strand	26-29	4	17
β-strand	37-40	4	17
α-helix	44-46	3
α-helix	52-56	5
β-strand	64-67	4	16

Chain D: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	18
α-helix	7-8	2
β-strand	9	1	19
β-strand	13	1	20
β-strand	17	1	21
α-helix	20-23	4
β-strand	26-33	8	18
β-strand	37-40	4	19
β-strand	46-49	4	19
α-helix	50	1
β-strand	52-58	7	18
α-helix	61-67	7
α-helix	68-72	5
α-helix	73-75	3
β-strand	81-85	5	18
β-strand	91-95	5	18
α-helix	109-111	3
β-strand	114-115	2	16
α-helix	119-121	3
α-helix	122-124	3
α-helix	125-128	4

Chain E: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	22
β-strand	17	1	22
β-strand	20-26	7	22
β-strand	36-39	4	22
β-strand	57-60	4	22
α-helix	62-64	3
β-strand	65-67	3	22

Chain F: 12 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	6-7	2	23
α-helix	8-10	3
α-helix	12-19	8
α-helix	30-38	9
β-strand	42-43	2	23
β-strand	49	1	23
β-strand	51	1	14
α-helix	57-59	3
α-helix	64-88	25
α-helix	89-93	5
α-helix	96-99	4
β-strand	100	1	24
α-helix	103-111	9
α-helix	113-115	3
α-helix	116-125	10
α-helix	133-135	3

Chain I: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	10-16	7
α-helix	17-21	5
α-helix	22-35	14
β-strand	37	1	9

Chain J: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-7	6
β-strand	10	1	24
α-helix	11-32	22

4 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 I P700 chlorophyll a apoprotein A1	A	protein	755	Thermosynechococcus elongatus	P0A405 (AlphaFold model)
Photosystem I P700 chlorophyll a apoprotein A2	B	protein	740	Thermosynechococcus elongatus	P0A407 (AlphaFold model)
Photosystem I iron-sulfur center	C	protein	80	Thermosynechococcus elongatus	P0A415 (AlphaFold model)
Photosystem I reaction center subunit II	D	protein	138	Thermosynechococcus elongatus	P0A420 (AlphaFold model)
Photosystem I reaction center subunit IV	E	protein	75	Thermosynechococcus elongatus	P0A423
Photosystem I reaction center subunit III	F	protein	164	Thermosynechococcus elongatus	P0A401
Photosystem I reaction center subunit VIII	I	protein	38	Thermosynechococcus elongatus	P0A427
Photosystem I reaction center subunit IX	J	protein	41	Thermosynechococcus elongatus	P0A429
Photosystem I reaction center subunit PsaK	K	protein	83	Thermosynechococcus elongatus	P0A425
Photosystem I reaction center subunit XI	L	protein	154	Thermosynechococcus elongatus	Q8DGB4
Photosystem I reaction center subunit XII	M	protein	31	Thermosynechococcus elongatus	P0A403
Photosystem I 4.8K protein	X	protein	35	Thermosynechococcus elongatus	Q8DKP6

Sequence of entity 1 (A), FASTA

>3PCQ_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains A)
MTISPPEREPKVRVVVDNDPVPTSFEKWAKPGHFDRTLARGPQTTTWIWNLHALAHDFDT
HTSDLEDISRKIFSAHFGHLAVVFIWLSGMYFHGAKFSNYEAWLADPTGIKPSAQVVWPI
VGQGILNGDVGGGFHGIQITSGLFQLWRASGITNEFQLYCTAIGGLVMAGLMLFAGWFHY
HKRAPKLEWFQNVESMLNHHLAGLLGLGSLAWAGHQIHVSLPINKLLDAGVAAKDIPLPH
EFILNPSLMAELYPKVDWGFFSGVIPFFTFNWAAYSDFLTFNGGLNPVTGGLWLSDTAHH
HLAIAVLFIIAGHMYRTNWGIGHSLKEILEAHKGPFTGAGHKGLYEVLTTSWHAQLAINL
AMMGSLSIIVAQHMYAMPPYPYLATDYPTQLSLFTHHMWIGGFLVVGGAAHGAIFMVRDY
DPAMNQNNVLDRVLRHRDAIISHLNWVCIFLGFHSFGLYVHNDTMRAFGRPQDMFSDTGI
QLQPVFAQWVQNLHTLAPGGTAPNAAATASVAFGGDVVAVGGKVAMMPIVLGTADFMVHH
IHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSGWDHVFLGLF
WMYNCISVVIFHFSWKMQSDVWGTVAPDGTVSHITGGNFAQSAITINGWLRDFLWAQASQ
VIGSYGSALSAYGLLFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPR
ALSIIQGRAVGVAHYLLGGIATTWAFFLARIISVG

Sequence of entity 2 (B), FASTA

>3PCQ_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains B)
ATKFPKFSQDLAQDPTTRRIWYAIAMAHDFESHDGMTEENLYQKIFASHFGHLAIIFLWV
SGSLFHVAWQGNFEQWVQDPVNTRPIAHAIWDPQFGKAAVDAFTQAGASNPVDIAYSGVY
HWWYTIGMRTNGDLYQGAIFLLILASLALFAGWLHLQPKFRPSLSWFKNAESRLNHHLAG
LFGVSSLAWAGHLIHVAIPESRGQHVGWDNFLSTMPHPAGLAPFFTGNWGVYAQNPDTAS
HVFGTAQGAGTAILTFLGGFHPQTESLWLTDMAHHHLAIAVLFIVAGHMYRTQFGIGHSI
KEMMDAKDFFGTKVEGPFNMPHQGIYETYNNSLHFQLGWHLACLGVITSLVAQHMYSLPP
YAFIAQDHTTMAALYTHHQYIAGFLMVGAFAHGAIFLVRDYDPAQNKGNVLDRVLQHKEA
IISHLSWVSLFLGFHTLGLYVHNDVVVAFGTPEKQILIEPVFAQFIQAAHGKLLYGFDTL
LSNPDSIASTAWPNYGNVWLPGWLDAINSGTNSLFLTIGPGDFLVHHAIALGLHTTTLIL
VKGALDARGSKLMPDKKDFGYAFPCDGPGRGGTCDISAWDAFYLAMFWMLNTIGWVTFYW
HWKHLGVWEGNVAQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGTNNLSVWAWMFLFGH
LVWATGFMFLISWRGYWQELIETLVWAHERTPLANLVRWKDKPVALSIVQARLVGLAHFS
VGYILTYAAFLIASTAAKFG

Sequence of entity 3 (C), FASTA

>3PCQ_3 Photosystem I iron-sulfur center (chains C)
AHTVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPTD
FLSIRVYLGAETTRSMGLAY

Sequence of entity 4 (D), FASTA

>3PCQ_4 Photosystem I reaction center subunit II (chains D)
TTLTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFAR
KEQCLALAAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIG
QNPNPSQLKFTGKKPYDP

Sequence of entity 5 (E), FASTA

>3PCQ_5 Photosystem I reaction center subunit IV (chains E)
VQRGSKVKILRPESYWYNEVGTVASVDQTPGVKYPVIVRFDKVNYTGYSGSASGVNTNNF
ALHEVQEVAPPKKGK

Sequence of entity 6 (F), FASTA

>3PCQ_6 Photosystem I reaction center subunit III (chains F)
MRRFLALLLVLTLWLGFTPLASADVAGLVPCKDSPAFQKRAAAAVNTTADPASGQKRFER
YSQALCGEDGLPHLVVDGRLSRAGDFLIPSVLFLYIAGWIGWVGRAYLIAVRNSGEANEK
EIIIDVPLAIKCMLTGFAWPLAALKELASGELTAKDNEITVSPR

Sequence of entity 7 (I), FASTA

>3PCQ_7 Photosystem I reaction center subunit VIII (chains I)
MMGSYAASFLPWIFIPVVCWLMPTVVMGLLFLYIEGEA

Sequence of entity 8 (J), FASTA

>3PCQ_8 Photosystem I reaction center subunit IX (chains J)
MKHFLTYLSTAPVLAAIWMTITAGILIEFNRFYPDLLFHPL

Sequence of entity 9 (K), FASTA

>3PCQ_9 Photosystem I reaction center subunit PsaK (chains K)
MVLATLPDTTWTPSVGLVVILCNLFAIALGRYAIQSRGKGPGLPIALPALFEGFGLPELL
ATTSFGHLLAAGVVSGLQYAGAL

Sequence of entity 10 (L), FASTA

>3PCQ_10 Photosystem I reaction center subunit XI (chains L)
AEELVKPYNGDPFVGHLSTPISDSGLVKTFIGNLPAYRQGLSPILRGLEVGMAHGYFLIG
PWVKLGPLRDSDVANLGGLISGIALILVATACLAAYGLVSFQKGGSSSDPLKTSEGWSQF
TAGFFVGAMGSAFVAFFLLENFLVVDGIMTGLFN

Sequence of entity 11 (M), FASTA

>3PCQ_11 Photosystem I reaction center subunit XII (chains M)
MALTDTQVYVALVIALLPAVLAFRLSTELYK

Sequence of entity 12 (X), FASTA

>3PCQ_12 Photosystem I 4.8K protein (chains X)
ATKSAKPTYAFRTFWAVLLLAINFLVAAYYFGILK

Ligands and cofactors

ID	Name	Formula	Copies
CLA	Chlorophyll a	C55 H72 Mg N4 O5	96
PQN	Phylloquinone	C31 H46 O2	2
SF4	Iron/sulfur cluster	Fe4 S4	3
BCR	Beta-carotene	C40 H56	22
LHG	1,2-dipalmitoyl-phosphatidyl-glycerole	C38 H75 O10 P	3
LMG	1,2-distearoyl-monogalactosyl-diglyceride	C45 H86 O10	1
CA	Calcium ion	Ca	1

Primary citation

Femtosecond X-ray protein nanocrystallography. Chapman, H.N., Fromme, P., Barty, A. et al. Nature (2011) 470:73-77. DOI 10.1038/nature09750 · PubMed

Other PDB entries of the same protein (UniProt P0A405 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9QFP 1.74 Å, Monomeric Photosystem I Cryo-EM structure at 1.8 A resolution
7FIX 1.97 Å, Cryo-EM structure of cyanobacterial photosystem I in the presence of ferredoxin and…
1JB0 2.5 Å, Crystal Structure of Photosystem I: a Photosynthetic Reaction Center and Core Antenna…
7M75 2.75 Å, Room Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two…
6TRA 2.85 Å, Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of…
6PFY 2.9 Å, Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I at…
6PGK 2.9 Å, Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I XFEL at…
6TRC 2.98 Å, Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of…
7M76 3.0 Å, Room Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two…
7M78 3.0 Å, Room Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two…
6TRD 3.16 Å, Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of…
6LU1 3.2 Å, Cyanobacterial PSI Monomer from T. elongatus by Single Particle CRYO-EM at 3.2 A…

Browse structure collections

About this viewer

MolViewer shows 3PCQ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.