Structure of photosystem I-light-harvesting supercomplex from a red-lineage diatom
Nagao, R., Kato, K., Ifuku, K., Suzuki, T., Kumazawa, M., Uchiyama, I., Kashino, Y., Dohmae, N., Akimoto, S., Shen, J.R., Miyazaki, N., Akita, F.(2020) Nat Commun
Experimental Data Snapshot
wwPDB Validation 3D Report Full Report
(2020) Nat Commun
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I P700 chlorophyll a apoprotein A1 | 751 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() | |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I P700 chlorophyll a apoprotein A2 | 733 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() | |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I iron-sulfur center | 81 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() | |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit II | 139 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() | |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 5 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit IV | 67 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() | |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 6 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit III | 185 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() | |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 7 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit VIII | G [auth I] | 36 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 8 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit IX | H [auth J] | 41 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 9 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit XI | I [auth L] | 151 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 10 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit XII | J [auth M] | 30 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 11 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Unknown protein 1 | K [auth 1u] | 130 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
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Entity ID: 12 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photosystem I reaction center subunit Psa28 | L [auth 2u] | 121 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 13 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcr15 | M [auth 1] | 227 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 14 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcr8 | N [auth 2] | 205 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 15 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcr2 | O [auth 3] | 200 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 16 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcr9 | P [auth 4] | 215 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 17 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcr11 | Q [auth 5] | 266 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 18 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcr12 | R [auth 6] | 208 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 19 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcr10 | S [auth 7] | 296 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 20 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcr4 | T [auth 8] | 270 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 21 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcf6 | U [auth 9] | 214 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 22 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcr3 | V [auth 10] | 207 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 23 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcq13 | W [auth 11] | 229 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 24 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcq3 | X [auth 12] | 204 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 25 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcq11 | Y [auth 13] | 244 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 26 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcq10 | Z [auth 14] | 249 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 27 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcq8 | AA [auth 15] | 281 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 28 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fucoxanthin chlorophyll a/c-binding protein Lhcq5 | BA [auth 16] | 218 | Chaetoceros neogracilis | Mutation(s): 0 | ![]() |
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Ligands 11 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CLA Query on CLA | AB [auth A] AD [auth B] AG [auth 2] AH [auth 4] AI [auth 5] | CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M | |||
CL0 Query on CL0 | CA [auth A] | CHLOROPHYLL A ISOMER C55 H72 Mg N4 O5 VIQFHHZSLDFWDU-DVXFRRMCSA-M | |||
LMG Query on LMG | AP [auth 14] BE [auth B] BF [auth 2u] DE [auth B] FC [auth A] | 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N | |||
LHG Query on LHG | BC [auth A] CC [auth A] CE [auth B] DJ [auth 6] GI [auth 5] | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N | |||
A86 Query on A86 | AF [auth 2u] BJ [auth 6] BM [auth 10] CF [auth 2u] CM [auth 10] | (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-
yl acetate C42 H58 O6 SJWWTRQNNRNTPU-XJUZQKKNSA-N | |||
KC1 Query on KC1 | AN [auth 12] AO [auth 13] BG [auth 2] BI [auth 5] BO [auth 13] | Chlorophyll c1 C35 H30 Mg N4 O5 DGNIJJSSARBJSH-QIEHNWLWSA-L | |||
DD6 Query on DD6 | AJ [auth 6] AM [auth 10] CG [auth 2] CI [auth 5] CJ [auth 6] | (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol C40 H54 O3 OGHZCSINIMWCSB-WMTIXGNLSA-N | |||
BCR Query on BCR | AC [auth A] AE [auth B] ME [auth F] OE [auth I] QE [auth J] | BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N | |||
LMT Query on LMT | BP [auth 15] DC [auth A] EC [auth A] EE [auth B] EJ [auth 7] | DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N | |||
PQN Query on PQN | UB [auth A], UD [auth B] | PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N | |||
SF4 Query on SF4 | HE [auth C], IE [auth C], VB [auth A] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N |
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | RELION | 3 |
MODEL REFINEMENT | PHENIX | 1.13_2998 |