1JB0: Photosystem I P700 chlorophyll a apoprotein A1
Crystal Structure of Photosystem I: a Photosynthetic Reaction Center and Core Antenna System from Cyanobacteria. Determined by X-ray diffraction at 2.5 Å resolution. Released 1 Aug 2001.
- Method
- X-ray diffraction
- Resolution
- 2.5 Å
- Organism
- Synechococcus elongatus
- Chains
- 12
- Atoms
- 24,198
- Mol. weight
- 359.7 kDa
- Ligands
- CLA, PQN, SF4, BCR
- Released
- 1 Aug 2001
Explore 1JB0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1JB0 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 | Synechococcus elongatus | P0A405 (AlphaFold model) |
| Photosystem I P700 chlorophyll a apoprotein A2 | B | protein | 740 | Synechococcus elongatus | P0A407 (AlphaFold model) |
| Photosystem I iron-sulfur center | C | protein | 80 | Synechococcus elongatus | P0A415 (AlphaFold model) |
| Photosystem 1 reaction centre subunit II | D | protein | 138 | Synechococcus elongatus | P0A420 (AlphaFold model) |
| Photosystem 1 reaction centre subunit IV | E | protein | 75 | Synechococcus elongatus | P0A423 |
| Photosystem 1 reaction centre subunit III | F | protein | 164 | Synechococcus elongatus | P0A401 |
| Photosystem 1 reaction centre subunit VIII | I | protein | 38 | Synechococcus elongatus | P0A427 |
| Photosystem 1 reaction centre subunit IX | J | protein | 41 | Synechococcus elongatus | P0A429 |
| Photosystem 1 reaction centre subunit X | K | protein | 83 | Synechococcus elongatus | P0A425 |
| Photosystem 1 reaction centre subunit XI | L | protein | 154 | Synechococcus elongatus | Q8DGB4 |
| Photosystem 1 reaction centre subunit XII | M | protein | 31 | Synechococcus elongatus | P0A403 |
| Photosystem I subunit psax | X | protein | 35 | Synechococcus elongatus | Q8DKP6 |
Sequence of entity 1 (A), FASTA
>1JB0_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
>1JB0_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
>1JB0_3 PHOTOSYSTEM I IRON-SULFUR CENTER (chains C)
AHTVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPTD
FLSIRVYLGAETTRSMGLAY
Sequence of entity 4 (D), FASTA
>1JB0_4 PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT II (chains D)
TTLTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFAR
KEQCLALAAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIG
QNPNPSQLKFTGKKPYDP
Sequence of entity 5 (E), FASTA
>1JB0_5 PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IV (chains E)
VQRGSKVKILRPESYWYNEVGTVASVDQTPGVKYPVIVRFDKVNYTGYSGSASGVNTNNF
ALHEVQEVAPPKKGK
Sequence of entity 6 (F), FASTA
>1JB0_6 PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III (chains F)
MRRFLALLLVLTLWLGFTPLASADVAGLVPCKDSPAFQKRAAAAVNTTADPASGQKRFER
YSQALCGEDGLPHLVVDGRLSRAGDFLIPSVLFLYIAGWIGWVGRAYLIAVRNSGEANEK
EIIIDVPLAIKCMLTGFAWPLAALKELASGELTAKDNEITVSPR
Sequence of entity 7 (I), FASTA
>1JB0_7 PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIII (chains I)
MMGSYAASFLPWIFIPVVCWLMPTVVMGLLFLYIEGEA
Sequence of entity 8 (J), FASTA
>1JB0_8 PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IX (chains J)
MKHFLTYLSTAPVLAAIWMTITAGILIEFNRFYPDLLFHPL
Sequence of entity 9 (K), FASTA
>1JB0_9 PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT X (chains K)
MVLATLPDTTWTPSVGLVVILCNLFAIALGRYAIQSRGKGPGLPIALPALFEGFGLPELL
ATTSFGHLLAAGVVSGLQYAGAL
Sequence of entity 10 (L), FASTA
>1JB0_10 PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI (chains L)
AEELVKPYNGDPFVGHLSTPISDSGLVKTFIGNLPAYRQGLSPILRGLEVGMAHGYFLIG
PWVKLGPLRDSDVANLGGLISGIALILVATACLAAYGLVSFQKGGSSSDPLKTSEGWSQF
TAGFFVGAMGSAFVAFFLLENFLVVDGIMTGLFN
Sequence of entity 11 (M), FASTA
>1JB0_11 PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XII (chains M)
MALTDTQVYVALVIALLPAVLAFRLSTELYK
Sequence of entity 12 (X), FASTA
>1JB0_12 PHOTOSYSTEM I SUBUNIT PSAX (chains X)
ATKSAKPTYAFRTFWAVLLLAINFLVAAYYFAAAA
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
Three-dimensional Structure of Cyanobacterial Photosystem I at 2.5 A Resolution. Jordan, P., Fromme, P., Witt, H.T. et al. Nature (2001) 411:909-917. DOI 10.1038/35082000 · 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…
- 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…
- 10EG 3.4 Å, Thermosynechococcus vestitus (BP-1) Photosystem I Complexed with Platinum Nanoparticles
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