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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:

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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

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and development of technology

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new instruments and methods

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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

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Hinxton

EMBL-EBI: European Bioinformatics Institute

Rome

Epigenetics and neurobiology

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primary_citation_author:"Cubakova P" AND author_name:"D"

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EMD-12679

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Cryo-EM structure (model_1a) of the RC-dLH complex from Gemmatimonas phototrophica at 2.4 A

Release date: March 2, 2022
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 7o0u
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:

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-dlh model_1a (800 kDa, Complex 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)
(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)
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)
Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
Spirilloxanthin (596 Da, Ligand)
Water (18 Da, Ligand)
2-acetamido-2-deoxy-alpha-d-glucopyranose (221 Da, Ligand)
Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)

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EMD-12680

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Cryo-EM structure (model_2a) of the RC-dLH complex from Gemmatimonas phototrophica at 2.5 A

Release date: March 2, 2022
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7o0v
Q-score: 0.62

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:

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 (4 kDa, Protein from Gemmatimonas phototrophica)
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-dlh (model_2a) (800 kDa, Complex from Gemmatimonas phototrophica)
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)

[Show more]

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)

[Show more]

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)

[Show more]

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Showing 1 - 4 of 4. Page 1 of 1

Display: Statistics

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EMDB [4]

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

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