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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

Services:

offer vital services to scientists in the member states

Training

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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EMD-25178

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Sub-tomogram averaged structure of HIV-1 Envelope protein in native membrane

Release date: March 9, 2022
Resolution: 9.1 Å
EM Method: Subtomogram averaging
Fitted PDBs: 7ska
Q-score: 0.067

Mangala Prasad V, Leaman DP, Lovendahl KN, Croft JT, Benhaim MA, Hodge EA, Zwick MB, Lee KK

Cell (2022) 185 pp. 641-653.e17 [ Pubmed: 35123651 DOI: doi:10.1016/j.cell.2022.01.013 ]

Sample:

Human immunodeficiency virus 1 (430 kDa, Virus from Human immunodeficiency virus 1)
Envelope glycoprotein gp120 (52 kDa, Protein from Human immunodeficiency virus 1)
Alpha-l-fucopyranose (164 Da, Ligand)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Envelope glycoprotein gp41 (16 kDa, Protein from Human immunodeficiency virus 1)

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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-13110

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Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex

Release date: Sept. 22, 2021
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7oy8
Q-score: 0.551

Qian P, Croll TI, Swainsbury DJK, Castro-Hartmann P, Moriarty NW, Sader K, Hunter CN

Biochem J (2021) 478 pp. 3253-3263 [ Pubmed: 34402504 DOI: doi:10.1042/BCJ20210511 ]

Sample:

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EMD-30314

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STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF THIORHODOVIBRIO STRAIN 970

Release date: Oct. 7, 2020
Resolution: 2.82 Å
EM Method: Single-particle
Fitted PDBs: 7c9r
Q-score: 0.632

Tani K, Kanno R, Makino Y, Hall M, Takenouchi M, Imanishi M, Yu LJ, Overmann J, Madigan MT, Kimura Y, Mizoguchi A, Humbel BM, Wang-Otomo ZY

Nat Commun (2020) 11 pp. 4955-4955 [ DOI: doi:10.1038/s41467-020-18748-3 Pubmed: 33009385 ]

Sample:

Reaction center protein m chain (36 kDa, Protein from Thiorhodovibrio sp. 970)
Light-harvesting-reaction center complex from the purple phototrophic bacterium thiorhodovibrio strain 970 (400 kDa, Complex from Thiorhodovibrio sp. 970)
Photosynthetic reaction center, subunit h, bacterial (28 kDa, Protein from Thiorhodovibrio sp. 970)
Antenna complex alpha/beta subunit (5 kDa, Protein from Thiorhodovibrio sp. 970)
Dodecyl-beta-d-maltoside (510 Da, Ligand)
Alpha subunit 2 of light-harvesting 1 complex (9 kDa, Protein from Thiorhodovibrio sp. 970)
Magnesium ion (24 Da, Ligand)
Octadecane (254 Da, Ligand)
(6~{e},8~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{e},24~{e},26~{e})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26-undecaene (600 Da, Ligand)
Photosynthetic reaction center cytochrome c subunit (42 kDa, Protein from Thiorhodovibrio sp. 970)
Lhc domain-containing protein (8 kDa, Protein from Thiorhodovibrio sp. 970)
Calcium ion (40 Da, Ligand)
Antenna complex alpha/beta subunit (5 kDa, Protein from Thiorhodovibrio sp. 970)
L subunit of the reaction center (30 kDa, Protein from Thiorhodovibrio sp. 970)
Bacteriochlorophyll a (911 Da, Ligand)
Cardiolipin (1 kDa, Ligand)
Menaquinone 8 (717 Da, Ligand)
Protoporphyrin ix containing fe (616 Da, Ligand)
Bacteriopheophytin a (889 Da, Ligand)
Ubiquinone-8 (727 Da, Ligand)
(1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
Fe (iii) ion (55 Da, Ligand)
Diacyl glycerol (625 Da, Ligand)
Alpha subunit 1 of light-harvesting 1 complex (8 kDa, Protein from Thiorhodovibrio sp. 970)
Antenna complex alpha/beta subunit (9 kDa, Protein from Thiorhodovibrio sp. 970)

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EMD-4255

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human Bact spliceosome core structure

Release date: Aug. 29, 2018
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6ff4
Q-score: 0.443

Haselbach D, Komarov I, Agafonov DE, Hartmuth K, Graf B, Dybkov O, Urlaub H, Kastner B, Luhrmann R, Stark H

Cell (2018) 172 pp. 454-464.e11 [ Pubmed: 29361316 DOI: doi:10.1016/j.cell.2018.01.010 ]

Sample:

Bud13 homolog (70 kDa, Protein from Homo sapiens)
Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
U5 snrna (36 kDa, RNA from Homo sapiens)
Splicing factor 3b subunit 3 (135 kDa, Protein from Homo sapiens)
Pre mrna (153 kDa, RNA from Homo sapiens)
Cell division cycle 5-like protein (92 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 6 (14 kDa, Protein from Homo sapiens)
Crooked neck-like protein 1 (100 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
Pre-mrna-processing factor 17 (65 kDa, Protein from Homo sapiens)
116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 1 (146 kDa, Protein from Homo sapiens)
Rna-binding motif protein, x-linked 2 (37 kDa, Protein from Homo sapiens)
Pleiotropic regulator 1 (57 kDa, Protein from Homo sapiens)
U6 snrna (34 kDa, RNA from Homo sapiens)
Splicing factor 3b subunit 5 (10 kDa, Protein from Homo sapiens)
Splicing factor 3a subunit 2 (49 kDa, Protein from Homo sapiens)
Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Homo sapiens)
Serine/arginine repetitive matrix protein 2 (300 kDa, Protein from Homo sapiens)
Peptidyl-prolyl cis-trans isomerase-like 1 (18 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Serine/arginine repetitive matrix protein 1 (102 kDa, Protein from Homo sapiens)
Splicing factor 3b subunit 2 (100 kDa, Protein from Homo sapiens)
Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Homo sapiens)
Ring finger protein 113a (38 kDa, Protein from Homo sapiens)
Human bact spliceosome state 1 unmasked (4 MDa, Complex from Homo sapiens)
Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Homo sapiens)
Inositol hexakisphosphate (660 Da, Ligand)
Phd finger-like domain-containing protein 5a (12 kDa, Protein from Homo sapiens)
U2 snrna (60 kDa, RNA from Homo sapiens)
Guanosine-5'-triphosphate (523 Da, Ligand)
Peptidyl-prolyl cis-trans isomerase cwc27 homolog (53 kDa, Protein from Homo sapiens)
Snw domain-containing protein 1 (61 kDa, Protein from Homo sapiens)

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