Resolution: 3.9 Å
EM Method: Helical reconstruction
Fitted PDBs: 7x54
Q-score: 0.375
Koh A, Ali S, Popp D, Tanaka K, Kitaoku Y, Miyazaki N, Iwasaki K, Mitsuoka K, Robert R, Narita A
To Be Published
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Cbg-parm filament with adp (Complex from Clostridium botulinum)
- Magnesium ion (24 Da, Ligand)
- Parm/stba family protein (32 kDa, Protein from Clostridium botulinum Bf)
A CBg-ParM filament with GTP and a short incubation time
Resolution: 8.6 Å
EM Method: Helical reconstruction
Fitted PDBs: 7x55
Q-score: 0.168
Koh A, Ali S, Popp D, Tanaka K, Kitaoku Y, Miyazaki N, Iwasaki K, Mitsuoka K, Robert R, Narita A
To Be Published
Resolution: 3.5 Å
EM Method: Helical reconstruction
Fitted PDBs: 7x56
Q-score: 0.486
Koh A, Ali S, Popp D, Tanaka K, Kitaoku Y, Miyazaki N, Iwasaki K, Mitsuoka K, Robert R, Narita A
To Be Published
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Cbg-parm filament with gdp (Complex from Clostridium botulinum)
- Magnesium ion (24 Da, Ligand)
- Parm/stba family protein (32 kDa, Protein from Clostridium botulinum Bf)
A CBg-ParM filament with GTP or GDPPi
Resolution: 6.5 Å
EM Method: Helical reconstruction
Fitted PDBs: 7x59
Q-score: 0.189
Koh A, Ali S, Popp D, Tanaka K, Kitaoku Y, Miyazaki N, Iwasaki K, Mitsuoka K, Robert R, Narita A
To Be Published
- Parm/stba family protein (32 kDa, Protein from Clostridium botulinum)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Cbg-parm filament with gtp or gdppi (Complex from Clostridium botulinum)
Structure of C2S2M2-type PSII-FCPII supercomplex from diatom
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7vd5
Q-score: 0.543
Nagao R, Kato K, Kumazawa M, Ifuku K, Yokono M, Suzuki T, Dohmae N, Akita F, Akimoto S, Miyazaki N, Shen JR
Nat Commun (2022) 13 pp. 1764- [ DOI: doi:10.1038/s41467-022-29294-5 ]
- Fcpb3, fucoxanthin chlorophyll a/c-binding protein (19 kDa, Protein from Chaetoceros gracilis)
- Fcpb5, fucoxanthin chlorophyll a/c-binding protein (24 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chaetoceros gracilis)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Fcpb6, fucoxanthin chlorophyll a/c-binding protein (16 kDa, Protein from Chaetoceros gracilis)
- Unknown ligand (Ligand)
- Photosystem ii subunit (4 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein j (3 kDa, Protein from Chaetoceros gracilis)
- Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii d2 protein (37 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
- Fcpb2, fucoxanthin chlorophyll a/c-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 Da, Ligand)
- Extrinsic protein in photosystem ii (16 kDa, Protein from Chaetoceros gracilis)
- Bicarbonate ion (61 Da, Ligand)
- Unknown protein 1 (2 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii cp47 reaction center protein (53 kDa, Protein from Chaetoceros gracilis)
- Fe (ii) ion (55 Da, Ligand)
- Cytochrome b559 subunit alpha (8 kDa, Protein from Chaetoceros gracilis)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Fcpb4, fucoxanthin chlorophyll a/c-binding protein (19 kDa, Protein from Chaetoceros gracilis)
- (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 (658 Da, Ligand)
- Photosystem ii reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Chaetoceros gracilis)
- Water (18 Da, Ligand)
- Cytochrome b559 subunit beta (3 kDa, Protein from Chaetoceros gracilis)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Photosystem ii protein d1 (37 kDa, Protein from Chaetoceros gracilis)
- Pheophytin a (871 Da, Ligand)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a (893 Da, Ligand)
- Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
- C2s2m2-type psii-fcpii supercomplex (1 MDa, Complex from Chaetoceros gracilis)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Cytochrome c-550 (14 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chaetoceros gracilis)
- Unknown protein 0 (2 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chaetoceros gracilis)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (19 kDa, Protein from Chaetoceros gracilis)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Photosystem ii reaction center protein w (5 kDa, Protein from Chaetoceros gracilis)
- Fcpb7, fucoxanthin chlorophyll a/c-binding protein (17 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chaetoceros gracilis)
- Ca-mn4-o5 cluster (339 Da, Ligand)
Structure of S1M1-type FCPII complex from diatom
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7vd6
Q-score: 0.565
Nagao R, Kato K, Kumazawa M, Ifuku K, Yokono M, Suzuki T, Dohmae N, Akita F, Akimoto S, Miyazaki N, Shen JR
Nat Commun (2022) 13 pp. 1764- [ DOI: doi:10.1038/s41467-022-29294-5 ]
- Fcpb5, fucoxanthin chlorophyll a/c-binding protein (29 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 Da, Ligand)
- Fcpb4, fucoxanthin chlorophyll a/c-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- S1m1-type fcpii complex (240 kDa, Complex from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- Fcpb6, fucoxanthin chlorophyll a/c-binding protein (23 kDa, Protein from Chaetoceros gracilis)
- Fcpb7, fucoxanthin chlorophyll a/c-binding protein (21 kDa, Protein from Chaetoceros gracilis)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Fcpb2, fucoxanthin chlorophyll a/c-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- Unknown ligand (Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Fcpb3, fucoxanthin chlorophyll a/c-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- (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 (658 Da, Ligand)
- Water (18 Da, Ligand)
Structure of alpha6beta1 integrin in complex with laminin-511
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7cec
Q-score: 0.347
Arimori T, Miyazaki N, Mihara E, Takizawa M, Taniguchi Y, Cabanas C, Sekiguchi K, Takagi J
Nat Commun (2021) 12 pp. 4012-4012 [ Pubmed: 34188035 DOI: doi:10.1038/s41467-021-24184-8 ]
- Laminin subunit beta-1 (8 kDa, Protein from Homo sapiens)
- Ts2/16 vl-sarah(s37c),ts2/16 vl-sarah(s37c) (18 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Ts2/16 vh(s112c)-sarah,ts2/16 vh(s112c)-sarah (19 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Integrin beta-1 (50 kDa, Protein from Homo sapiens)
- Integrin alpha-6 (69 kDa, Protein from Homo sapiens)
- Laminin subunit gamma-1 (9 kDa, Protein from Homo sapiens)
- Quaternary complex of alpha6beta1 integrin, laminin-511, ts2/16 fv-clasp, and huts-4 fv-clasp (286 kDa, Complex from Homo sapiens)
- Huts-4 vh(s112c)-sarah,huts-4 vh(s112c)-sarah (19 kDa, Protein from Homo sapiens)
- Huts-4 vl(c87y)-sarah(s37c),huts-4 vl(c87y)-sarah(s37c) (17 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Laminin subunit alpha-5 (73 kDa, Protein from Homo sapiens)
Cryo-EM structure of phosphoketolase from Bifidobacterium longum
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 6lxv
Q-score: 0.763
Nakata K, Miyazaki N, Yamaguchi H, Hirose M, Kashiwagi T, Kutumbarao NHV, Miyashita O, Tama F, Miyano H, Mizukoshi T, Iwasaki K
J Struct Biol (2022) 214 pp. 107842-107842 [ DOI: doi:10.1016/j.jsb.2022.107842 Pubmed: 35181457 ]
- Thiamine diphosphate (425 Da, Ligand)
- Water (18 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Phosphoketolase with thiamine-diphophate (Complex from Bifidobacterium longum subsp. longum F8)
- Phosphoketolase (93 kDa, Protein from Bifidobacterium longum subsp. longum F8)
Structure of the peripheral FCPI from diatom
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 6l4t
Q-score: 0.563
Nagao R, Kato K, Ifuku K, Suzuki T, Kumazawa M, Uchiyama I, Kashino Y, Dohmae N, Akimoto S, Shen JR, Miyazaki N, Akita F
Nat Commun (2020) [ DOI: doi:10.1038/s41467-020-16324-3 ]
- Fucoxanthin chlorophyll a/c-binding protein lhcq5 (23 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq3 (21 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr12 (22 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr4 (29 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 Da, Ligand)
- (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 (658 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcq13 (24 kDa, Protein from Chaetoceros gracilis)
- Water (18 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcq11 (25 kDa, Protein from Chaetoceros gracilis)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Peripheral fcpi (170 kDa, Complex from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq8 (30 kDa, Protein from Chaetoceros gracilis)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcr3 (22 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq10 (26 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a (893 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcr10 (32 kDa, Protein from Chaetoceros gracilis)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Structure of the PSI-FCPI supercomplex from diatom
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 6l4u
Q-score: 0.587
Nagao R, Kato K, Ifuku K, Suzuki T, Kumazawa M, Uchiyama I, Kashino Y, Dohmae N, Akimoto S, Shen JR, Miyazaki N, Akita F
Nat Commun (2020) [ DOI: doi:10.1038/s41467-020-16324-3 ]
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq5 (23 kDa, Protein from Chaetoceros gracilis)
- Iron/sulfur cluster (351 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcq3 (21 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr9 (22 kDa, Protein from Chaetoceros gracilis)
- Phylloquinone (450 Da, Ligand)
- Unknown protein 1 (11 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr8 (21 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr15 (24 kDa, Protein from Chaetoceros gracilis)
- Photosystem i iron-sulfur center (8 kDa, Protein from Chaetoceros gracilis)
- Beta-carotene (536 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcr12 (22 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr4 (29 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Chaetoceros gracilis)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Chaetoceros gracilis)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- (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 (658 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcq13 (24 kDa, Protein from Chaetoceros gracilis)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Chaetoceros gracilis)
- Water (18 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcq11 (25 kDa, Protein from Chaetoceros gracilis)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Chaetoceros gracilis)
- Psi-fcpi (640 kDa, Complex from Chaetoceros gracilis)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit psa28 (12 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq8 (30 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Chaetoceros gracilis)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr3 (22 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq10 (26 kDa, Protein from Chaetoceros gracilis)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr2 (21 kDa, Protein from Chaetoceros gracilis)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcf6 (23 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr11 (29 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr10 (32 kDa, Protein from Chaetoceros gracilis)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)