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EMBL

was set up in 1974 as Europe’s flagship laboratory for the life sciences – an intergovernmental organisation with more than 80 independent research groups covering the spectrum of molecular biology:

Research:

perform basic research in molecular biology

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offer vital services to scientists in the member states

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scientists, students and visitors at all levels

Transfer

and development of technology

Develop

new instruments and methods

Integrating

life science research in Europe

More about EMBL

Six sites

represent EMBL in Europe.

Barcelona

Tissue biology and disease modelling

Grenoble

Structural biology

Hamburg

Structural biology

Heidelberg

Main laboratory

Hinxton

EMBL-EBI: European Bioinformatics Institute

Rome

Epigenetics and neurobiology

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sample_name:"R2" AND xref_links:"scop2" AND author_name:"B"

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EMD-12681

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Cryo-EM structure of the RC-dLH complex (model_1b) from Gemmatimonas phototrophica at 2.47 A

Release date: March 2, 2022
Resolution: 2.47 Å
EM Method: Single-particle
Fitted PDBs: 7o0w
Q-score: 0.624

Qian P, Gardiner AT, Simova I, Naydenova K, Croll TI, Jackson PJ, Kloz M, Cubakova P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hajek J, Agirre J, Siebert CA, Bina D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polivka T, Hunter CN, Koblizek M

Sci Adv (2022) 8 pp. eabk3139-eabk3139 [ DOI: doi:10.1126/sciadv.abk3139 Pubmed: 35171663 ]

Sample:

Rc-u (13 kDa, Protein from Gemmatimonas phototrophica)
Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
Dodecyl-beta-d-maltoside (510 Da, Ligand)
Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
Bacteriochlorophyll a (911 Da, Ligand)
(1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
(2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
[(2~{s})-3-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
Rc-dlh model_1b (800 kDa, Complex from Gemmatimonas phototrophica)
(19r,22s)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9z)-hexadec-9-enoate (689 Da, Ligand)
Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
Menaquinone 8 (717 Da, Ligand)
Bacteriopheophytin a (889 Da, Ligand)
[(2~{s})-3-[(2~{r},3~{r},4~{r},5~{s},6~{r})-6-(hydroxymethyl)-5-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate (837 Da, Ligand)
(2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
(2~{e},4~{e},6~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{z},24~{e},26~{e},28~{e})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid (610 Da, Ligand)
Heme c (618 Da, Ligand)
Fe (iii) ion (55 Da, Ligand)
Spirilloxanthin (596 Da, Ligand)
Water (18 Da, Ligand)
2-acetamido-2-deoxy-alpha-d-glucopyranose (221 Da, Ligand)
Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)

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EMD-12682

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Cryo-EM structure (model_2b) of the RC-dLH complex from Gemmatimonas phototrophica at 2.44 A

Release date: March 2, 2022
Resolution: 2.44 Å
EM Method: Single-particle
Fitted PDBs: 7o0x
Q-score: 0.629

Qian P, Gardiner AT, Simova I, Naydenova K, Croll TI, Jackson PJ, Kloz M, Cubakova P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hajek J, Agirre J, Siebert CA, Bina D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polivka T, Hunter CN, Koblizek M

Sci Adv (2022) 8 pp. eabk3139-eabk3139 [ DOI: doi:10.1126/sciadv.abk3139 Pubmed: 35171663 ]

Sample:

Rc-u (13 kDa, Protein from Gemmatimonas phototrophica)
Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
Dodecyl-beta-d-maltoside (510 Da, Ligand)
Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
Bacteriochlorophyll a (911 Da, Ligand)
(1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
(2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
[(2~{s})-3-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
(19r,22s)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9z)-hexadec-9-enoate (689 Da, Ligand)
Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
Menaquinone 8 (717 Da, Ligand)
Bacteriopheophytin a (889 Da, Ligand)
[(2~{s})-3-[(2~{r},3~{r},4~{r},5~{s},6~{r})-6-(hydroxymethyl)-5-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate (837 Da, Ligand)
(2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
(2~{e},4~{e},6~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{z},24~{e},26~{e},28~{e})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid (610 Da, Ligand)
Heme c (618 Da, Ligand)
Fe (iii) ion (55 Da, Ligand)
Spirilloxanthin (596 Da, Ligand)
Rc-dlh model_2b (800 kDa, Complex from Gemmatimonas phototrophica)
Water (18 Da, Ligand)
2-acetamido-2-deoxy-alpha-d-glucopyranose (221 Da, Ligand)
Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)

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EMD-9610

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Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis

Release date: Nov. 14, 2018
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6adq
Q-score: 0.458

Gong H, Li J, Xu A, Tang Y, Ji W, Gao R, Wang S, Yu L, Tian C, Li J, Yen HY, Man Lam S, Shui G, Yang X, Sun Y, Li X, Jia M, Yang C, Jiang B, Lou Z, Robinson CV, Wong LL, Guddat LW, Sun F, Wang Q, Rao Z

Science (2018) 362 [ DOI: doi:10.1126/science.aat8923 Pubmed: 30361386 ]

Sample:

Copper (ii) ion (63 Da, Ligand)
Lpqe protein (19 kDa, Protein from Mycobacterium smegmatis MC2 51)
Fe2/s2 (inorganic) cluster (175 Da, Ligand)
Cytochrome bc1 complex cytochrome c subunit (30 kDa, Protein from Mycobacterium smegmatis MC2 51)
(2r)-2-(hexadecanoyloxy)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9s)-9-methyloctadecanoate (853 Da, Ligand)
(2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycobacterium smegmatis MC2 51)
Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
Superoxide dismutase in complex with bcc-aa3 type ciii-civ supercomplex from mycobacterium smegmatis (800 kDa, Complex from Mycobacterium smegmatis MC2 51)
Palmitic acid (256 Da, Ligand)
Menaquinone-9 (785 Da, Ligand)
Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
Cardiolipin (1 kDa, Ligand)
Heme c (618 Da, Ligand)
Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycobacterium smegmatis MC2 51)
Heme-a (852 Da, Ligand)
Protoporphyrin ix containing fe (616 Da, Ligand)
Rieske iron-sulfur protein qcra (46 kDa, Protein from Mycobacterium smegmatis MC2 51)
(2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
Cytochrome c oxidase subunit 2 (38 kDa, Protein from Mycobacterium smegmatis MC2 51)
Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycobacterium smegmatis MC2 51)
Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycobacterium smegmatis MC2 51)
Ubiquinol-cytochrome c reductase cytochrome b subunit (60 kDa, Protein from Mycobacterium smegmatis MC2 51)

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Sort by: Download

Showing 1 - 3 of 3. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [3]

Format:

Select the script type:

Shell (Unix-based) Batch (Windows-based)

Preview first 10

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