9GRX: NDH-PSI-LHCI supercomplex from S. oleracea
NDH-PSI-LHCI supercomplex from S. oleracea. Determined by electron microscopy at 3.19 Å resolution. Released 12 Feb 2025.
- Method
- Electron microscopy
- Resolution
- 3.19 Å
- Organism
- Spinacia oleracea
- Chains
- 42
- Atoms
- 83,864
- Mol. weight
- 1246.9 kDa
- Ligands
- BCR, PGT, A1H1M, LMG
- Released
- 12 Feb 2025
Explore 9GRX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9GRX contains 468 α-helices and 251 β-strands across 42 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 0: 3 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 83-88 | 6 | 1 |
| β-strand | 93-98 | 6 | 1 |
| β-strand | 102-103 | 2 | 2 |
| β-strand | 108 | 1 | 3 |
| β-strand | 111-114 | 4 | 2 |
| β-strand | 122-125 | 4 | 2 |
| β-strand | 127-129 | 3 | 2 |
| α-helix | 135-138 | 4 | |
| α-helix | 141-151 | 11 | |
| β-strand | 159-170 | 12 | 2 |
| β-strand | 173-183 | 11 | 2 |
| β-strand | 188-198 | 11 | 2 |
| β-strand | 201-210 | 10 | 2 |
| α-helix | 214-225 | 12 | |
| β-strand | 229-230 | 2 | 1 |
Chain 1: 24 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 82-84 | 3 | |
| β-strand | 89 | 1 | 11 |
| β-strand | 100 | 1 | 11 |
| α-helix | 112-115 | 4 | |
| β-strand | 122-126 | 5 | 12 |
| α-helix | 131-136 | 6 | |
| α-helix | 138-147 | 10 | |
| β-strand | 152-157 | 6 | 12 |
| α-helix | 159-162 | 4 | |
| α-helix | 164-167 | 4 | |
| β-strand | 171-176 | 6 | 12 |
| α-helix | 186-199 | 14 | |
| β-strand | 203-210 | 8 | 12 |
| α-helix | 212-219 | 8 | |
| β-strand | 225-230 | 6 | 12 |
| α-helix | 234-236 | 3 | |
| β-strand | 245-247 | 3 | 12 |
| α-helix | 254-256 | 3 | |
| α-helix | 263-269 | 7 | |
| α-helix | 276-278 | 3 | |
| α-helix | 280-284 | 5 | |
| α-helix | 290-301 | 12 | |
| β-strand | 310-314 | 5 | 13 |
| β-strand | 316 | 1 | 14 |
| α-helix | 321-323 | 3 | |
| β-strand | 326 | 1 | 15 |
| β-strand | 329 | 1 | 15 |
| β-strand | 334 | 1 | 14 |
| α-helix | 336-343 | 8 | |
| β-strand | 350-355 | 6 | 13 |
| α-helix | 358-360 | 3 | |
| α-helix | 361-365 | 5 | |
| β-strand | 373-376 | 4 | 13 |
| α-helix | 380-389 | 10 | |
| β-strand | 392-396 | 5 | 13 |
| α-helix | 399-406 | 8 | |
| β-strand | 411-415 | 5 | 13 |
| α-helix | 418-424 | 7 | |
| β-strand | 433-437 | 5 | 13 |
| α-helix | 443-445 | 3 | |
| α-helix | 448-454 | 7 | |
| α-helix | 455-457 | 3 | |
Chain 2: 7 helices, 27 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-36 | 10 | |
| β-strand | 38 | 1 | 22 |
| β-strand | 41-44 | 4 | 22 |
| β-strand | 57-61 | 5 | 22 |
| β-strand | 67-71 | 5 | 22 |
| β-strand | 76-81 | 6 | 22 |
| β-strand | 83 | 1 | 23 |
| β-strand | 91 | 1 | 23 |
| β-strand | 95 | 1 | 22 |
| β-strand | 97-98 | 2 | 24 |
| β-strand | 102-103 | 2 | 24 |
| β-strand | 105-111 | 7 | 22 |
| β-strand | 147-154 | 8 | 25 |
| β-strand | 158-167 | 10 | 25 |
| β-strand | 170-179 | 10 | 25 |
| β-strand | 182-191 | 10 | 25 |
| β-strand | 197-209 | 13 | 22 |
| β-strand | 215-218 | 4 | 25 |
| β-strand | 224-227 | 4 | 22 |
| α-helix | 229-232 | 4 | |
| β-strand | 262 | 1 | 22 |
| β-strand | 266-267 | 2 | 22 |
| α-helix | 268 | 1 | |
| β-strand | 272-274 | 3 | 25 |
| β-strand | 279-283 | 5 | 22 |
| α-helix | 289-291 | 3 | |
| α-helix | 297-299 | 3 | |
| β-strand | 301-306 | 6 | 25 |
| β-strand | 311-318 | 8 | 25 |
| β-strand | 322-327 | 6 | 22 |
| α-helix | 329-331 | 3 | |
| α-helix | 332-335 | 4 | |
| β-strand | 339-354 | 16 | 22 |
| β-strand | 359-368 | 10 | 25 |
Chain 3: 7 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 78-87 | 10 | 28 |
| α-helix | 88 | 1 | |
| α-helix | 92 | 1 | |
| β-strand | 93-100 | 8 | 28 |
| β-strand | 105 | 1 | 29 |
| α-helix | 106-110 | 5 | |
| α-helix | 119-122 | 4 | |
| α-helix | 135-137 | 3 | |
| β-strand | 138-143 | 6 | 28 |
| β-strand | 148 | 1 | 30 |
| α-helix | 153-158 | 6 | |
| β-strand | 166-168 | 3 | 28 |
| β-strand | 173 | 1 | 29 |
| β-strand | 174 | 1 | 30 |
| β-strand | 182-186 | 5 | 28 |
| α-helix | 189-191 | 3 | |
| β-strand | 196-198 | 3 | 31 |
| β-strand | 204-206 | 3 | 31 |
Chain 4: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 35 |
| β-strand | 13-19 | 7 | 35 |
| α-helix | 25-48 | 24 | |
| α-helix | 57-60 | 4 | |
| α-helix | 70-92 | 23 | |
Chain 5: 12 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 67-70 | 4 | |
| α-helix | 85-87 | 3 | |
| α-helix | 105-107 | 3 | |
| α-helix | 108-118 | 11 | |
| α-helix | 125-142 | 18 | |
| α-helix | 147-167 | 21 | |
| α-helix | 169-170 | 2 | |
| α-helix | 172-174 | 3 | |
| α-helix | 177-180 | 4 | |
| α-helix | 184-194 | 11 | |
| α-helix | 199-205 | 7 | |
| α-helix | 208-210 | 3 | |
Chain 6: 6 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 82-87 | 6 | |
| α-helix | 94-110 | 17 | |
| α-helix | 112-116 | 5 | |
| α-helix | 120-140 | 21 | |
| α-helix | 150-169 | 20 | |
| β-strand | 175 | 1 | 3 |
| α-helix | 177-197 | 21 | |
Chain 7: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 80 | 1 | 40 |
| β-strand | 85 | 1 | 41 |
| α-helix | 86 | 1 | |
| α-helix | 89-91 | 3 | |
| α-helix | 117-131 | 15 | |
| α-helix | 143-166 | 24 | |
| α-helix | 173-195 | 23 | |
| α-helix | 199-220 | 22 | |
34 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 |
|---|
| Photosynthetic NDH subunit of lumenal location 1, chloroplastic | 0 | protein | 157 | Spinacia oleracea | A0A9R0JJI5 (AlphaFold model) |
| Photosynthetic NDH subunit of subcomplex B 1, chloroplastic | 1 | protein | 403 | Spinacia oleracea | A0A9R0JDZ5 (AlphaFold model) |
| Photosynthetic NDH subunit of subcomplex B 2, chloroplastic | 2 | protein | 372 | Spinacia oleracea | A0A9R0KAG7 (AlphaFold model) |
| Photosynthetic NDH subunit of subcomplex B 3, chloroplastic | 3 | protein | 139 | Spinacia oleracea | A0A9R0J911 (AlphaFold model) |
| Photosynthetic NDH subunit of subcomplex B 4, chloroplastic | 4 | protein | 93 | Spinacia oleracea | A0A9R0J426 |
| Photosynthetic NDH subunit of subcomplex B 5, chloroplastic | 5 | protein | 154 | Spinacia oleracea | A0A9R0JS52 |
| Photosynthetic NDH subunit of lumenal location 2, chloroplastic | 6 | protein | 125 | Spinacia oleracea | A0A9R0I5E4 |
| Photosynthetic NDH subunit of lumenal location 3, chloroplastic | 7 | protein | 144 | Spinacia oleracea | A0A9R0JBH0 |
| peptidylprolyl isomerase | 8 | protein | 143 | Spinacia oleracea | A0A9R0IC28 |
| Peptidyl-prolyl cis-trans isomerase | 9 | protein | 174 | Spinacia oleracea | A0A9R0IB03 |
| NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic | A | protein | 350 | Spinacia oleracea | Q9M3I6 |
| NAD(P)H-quinone oxidoreductase subunit 2 A, chloroplastic | B | protein | 488 | Spinacia oleracea | P0CD52 |
30 more molecules are not listed.
Sequence of entity 1 (0), FASTA
>9GRX_1 Photosynthetic NDH subunit of lumenal location 1, chloroplastic (chains 0)
KETPERYTAFVDKADGYSYVYPSDWREFDFRAHDSAFKDRYLQLQNVRLSFIPTDKNDVH
DLGPMEDVIQTLVKNILAAPNQMTDIREIQERSVDGKNYWTFEYNLTSPNFSVTHFTTLA
IANGRYYTLTVSANERRWKRYRNKLKVVADSFKVFEI
Sequence of entity 2 (1), FASTA
>9GRX_2 Photosynthetic NDH subunit of subcomplex B 1, chloroplastic (chains 1)
NPWLDLFYDGEDEPETEYGSMFSDGKQDEDPYPRDNPENPYGFLKFPQGYAVEMASLGSK
VRGDVRRCCCVVSGGVYDNLLFFPAIQLIKDRYPGVQIDIITSARGKQTYEMNKNVRWAT
VYDLDDNFPDPAEYTDMLGLLKNRYYDMVLSTKLAGLGHAAFLFMTTARDRVSYVYPNVN
AAGAGLLLSETFTPDSMNLSEGGYNMYHQMIEWLGRPVKDIPQHLASPLKVSISRKLKEA
VEAKYKEAGAEKGKYVVIHGIKCDSKASMQSEGDTDSLLPIEIWAEISQAIRGVTPIFVI
PHEKLREDVEEIVGEETSIVFITTPGQLAALINDSVGVIATNTAAIQLALAREKPSIALF
CSEEKGKCFVPDAEGKKCTVIASKTGNLADIDVAVVKDTLKVF
Sequence of entity 3 (2), FASTA
>9GRX_3 Photosynthetic NDH subunit of subcomplex B 2, chloroplastic (chains 2)
MASLLPFSLLKPTTICKASSTAAPPAALVESLNDQFARKGINFLESTDTSTNISSPIVEL
SVRNGSSLKLQLSNAHVTSYKPKVYWKDDGFEEVLYTLPLSKGGIGLVLNDVTQPVTTTK
KPDPFRRSEPAAAAAAKGSLLAGAEWSVRDVDSDSFDAVQVELSCTSGSLEITYVVSLYP
ESMASAVLVKNNGNKAIGLTSAILSHIQFKKRSGSGIQGLQGCSYCSHPPLSSPFEIVSP
AEAMKAEDPGMFSFSSESPSKLGEWTTQEVPITILKNKLSRVYTAPPSERSKKFYRTTPS
KYETVDQGRELVFRVIRMGYDDILVSSPGSLSEKYGRDYFICTGPASILVPVTVNPGEEW
RGAQVIEHDNLT
Sequence of entity 4 (3), FASTA
>9GRX_4 Photosynthetic NDH subunit of subcomplex B 3, chloroplastic (chains 3)
EEEELEPPYVGFAFVSSVLLPDGTPDMHLRSATGGQKLRDIMLDNDIDLYGPYARPLLNC
AGGGTCASCMVEVIEGKELLNPRTEKEKEHLKKKPKNWRLACQITVGTPESRGMVVIQQL
PEWKAHEWKYEKDGPIVSE
Sequence of entity 5 (4), FASTA
>9GRX_5 Photosynthetic NDH subunit of subcomplex B 4, chloroplastic (chains 4)
MAVLVEHVEGQRDLITHKSIWHLSDAAIKNVYLFYMMFTCWGCCVFGAAKDPYYDSEQYR
GDGGDGTGHWVYEKQEDIEEAGRAALWREELIE
Sequence of entity 6 (5), FASTA
>9GRX_6 Photosynthetic NDH subunit of subcomplex B 5, chloroplastic (chains 5)
GLTDIEPDLNEDPRDRWATNGVAPEDFVYGKYDEHHTFYESSEKGSFWGAVAEEYNSMDP
PTGFQGLISWLFLPAVAAGMYFNVPGDYLFIGAGLFVIIFCIIEMDKPDQPHNFEPQIYN
MERGARDKLIADYNTMDIWDFNEKYGDLWDFTLK
Sequence of entity 7 (6), FASTA
>9GRX_7 Photosynthetic NDH subunit of lumenal location 2, chloroplastic (chains 6)
EFKWGTRSFIWERFFEPGLSPEDAVSRIKNTAEGLHSLRHMLETMSWRYVIFYIRLKQAY
LKQDMKSAMIMVPEGRRDDYSNAANELVDNMAEFDYYVRTPKVYESYVSYEKTLKSIDNL
LGFLA
Sequence of entity 8 (7), FASTA
>9GRX_8 Photosynthetic NDH subunit of lumenal location 3, chloroplastic (chains 7)
QLWLDGPLPGLRPAENKIGNEETGTRTFLKKGIYMANIGTKGSALRLRKYAFDLLAMEDL
IGQDTLNYVRRYLRFKGTFMYYDFDKVISAAPVADKPPLTNLANRLFDNFEKLQEAVKLK
DVPLTRSCYDDTAVTLQEVMNRMA
Sequence of entity 9 (8), FASTA
>9GRX_9 peptidylprolyl isomerase (chains 8)
LRVEYYATTAEPSCELNLVRSGLGYCDLVVGSGVPAPYNTLINVHYTARFSDETVFDSSY
KRGRPLTMRIGVGKVIKGLDQGIFGGDGVPPMQVGGKRKLRIPPHLGYGPEPAGCFSGDC
NVPANATLLYDVTFMGVYSGNRA
Sequence of entity 10 (9), FASTA
>9GRX_10 Peptidyl-prolyl cis-trans isomerase (chains 9)
PLQSKVTNKVYFDISIGNPVGKLVGRVVIGLFGDDVPQTAENFRALCTGEKGFGYKGSAF
HRVIKDFMIQGGDFDKGNGTGGKSIYGRTFKDENFNLTHTGPGTVSMANAGPNTNGSQFF
ICTVKTPWLDNRHVVFGQVLEGMDIVKLIESSETDRGDRPKKRVVISECGELPA
Sequence of entity 11 (A), FASTA
>9GRX_11 NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic (chains A)
FSRLEFLKEVYETIWMLFPILILVLGITIGVLVIVWLEREISASIQQRIGPEYAGPLGIL
QALADGTKLLFKENLLPSRGDTYLFSIGPSIAVISILLGYLIIPFGSRLVLADLSIGVFL
WIAVSSIAPIGLLMSGYGSNNKYSFLGGLRAAAQSISYEIPLTLCVLSISLLSNSSSTVD
IVEAQSKYGFWGWNLWRQPIGFIVFIISSLAECERLPFDLPEAEEELVAGYQTEYSGIKF
GLFYVASYLNLLISSLFVTVLYLGGWNLSIPYIFISEFFEINKIDGVFGTTIGIFITLAK
TFLFLFIPITTRWTLPRLRMDQLLNLGWKFLLPISLGNLLLTTSSQLFSL
Sequence of entity 12 (B), FASTA
>9GRX_12 NAD(P)H-quinone oxidoreductase subunit 2 A, chloroplastic (chains B)
KAFHLLLFDGSLIFPECILIFGLILLLMIDSTSDQKDIPWLYFISSTSLVMSITALLFRW
REEPMISFSGNFQTNNFNEIFQFLILLCSTLCIPLSVEYIECTEMALTEFLLFILTATLG
GMFLCGANDLITIFVAPECFSLCSYLLSGYTKKDVRSNEATTKYLLMGGASSSILVHGFS
WLYGSSGGEIELQEIVNGLINTQMYNSPGISIALIFITVGIGFKLSPAPSHQWTPDVYEG
SPTPVVAFLSVTSKVAASASATRIFDIPFYFSSNEWHLLLEILAILSMILGNLIAITQTS
MKRMLAYSSIGQIGYVIIGIIVGDSNDGYASMITYMLFYISMNLGTFACIVLFGLRTGTD
NIRDYAGLYTKDPFLALSLALCLLSLGGLPPLAGFFGKIYLFWCGWQAGLYFLVLIGLLT
SVLSIYYYLKIIKLLMTGRNQEITPHVRNYRRSPLRSKNSIEFSMIVCVIASTIPGISMN
PIITIAQD
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| BCR | Beta-carotene | C40 H56 | 29 |
| PGT | (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoylo… | C40 H79 O10 P | 24 |
| A1H1M | 4-trans-(4-trans-Propylcyclohexyl)-cyclohexyl alpha-maltoside | C27 H48 O11 | 2 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 12 |
| PQ9 | 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18,… | C43 H64 O2 | 1 |
| SQD | 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol | C41 H78 O12 S | 7 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 6 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 144 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 3 |
| CL0 | Chlorophyll a isomer | C55 H72 Mg N4 O5 | 1 |
| PQN | Phylloquinone | C31 H46 O2 | 2 |
| CHL | Chlorophyll B | C55 H70 Mg N4 O6 | 9 |
| LUT | (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | C40 H56 O2 | 8 |
Primary citation
Cryo-EM structure of the NDH-PSI-LHCI supercomplex from Spinacia oleracea. Introini, B., Hahn, A., Kuhlbrandt, W. Nat Struct Mol Biol (2025) 32:968-978. DOI 10.1038/s41594-024-01478-1 · PubMed
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