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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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sample_name:"IRON/SULFUR CLUSTER" AND xref_links:"chembl" AND natural_source_ncbi_code:"246196"

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EMD-35992

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Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the pre-catalytic intermediate state

Release date: April 3, 2024
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8j5s
Q-score: 0.566

Yang X, Hu T, Liang J, Xiong Z, Lin Z, Zhao Y, Zhou X, Gao Y, Sun S, Yang X, Guddat LW, Yang H, Rao Z, Zhang B

Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01256-z Pubmed: 38548954 ]

Sample:

Iron/sulfur cluster (351 Da, Ligand)
Uncharacterized protein rv1280c (64 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Cryo-em structure of mycobacterium tuberculosis oppabcd in the pre-catalytic intermediate state (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Endogenous oligopeptide (698 Da, Protein from Mycolicibacterium smegmatis MC2 155)
Putative peptide transport permease protein rv1283c (35 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Magnesium ion (24 Da, Ligand)
Putative peptide transport permease protein rv1282c (31 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Uncharacterized abc transporter atp-binding protein rv1281c (65 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)

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EMD-27963

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Mycobacterial respiratory complex I with both quinone positions modelled

Release date: Oct. 12, 2022
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8e9g
Q-score: 0.537

Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL

PNAS (2023) 120 pp. e2214949120-e2214949120 [ Pubmed: 36952383 DOI: doi:10.1073/pnas.2214949120 ]

Sample:

Flavin mononucleotide (456 Da, Ligand)
Nadh-quinone oxidoreductase subunit d (48 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Mycobacterial respiratory complex i, consensus map (560 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
(2r)-3-{[(r)-hydroxy({(1s,2r,3r,4r,5s,6s)-3,4,5-trihydroxy-2-(alpha-d-mannopyranosyloxy)-6-[(6-o-undecanoyl-beta-d-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate (1 kDa, Ligand)
Guanosine-5'-triphosphate (523 Da, Ligand)
Fe2/s2 (inorganic) cluster (175 Da, Ligand)
Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Iron/sulfur cluster (351 Da, Ligand)
Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Zinc ion (65 Da, Ligand)
Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Menaquinone-9 (785 Da, Ligand)
Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)

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EMD-27964

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Mycobacterial respiratory complex I, fully-inserted quinone

Release date: Oct. 12, 2022
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8e9h
Q-score: 0.533

Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL

PNAS (2023) 120 pp. e2214949120-e2214949120 [ Pubmed: 36952383 DOI: doi:10.1073/pnas.2214949120 ]

Sample:

Flavin mononucleotide (456 Da, Ligand)
Nadh-quinone oxidoreductase subunit d (48 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
(2r)-3-{[(r)-hydroxy({(1s,2r,3r,4r,5s,6s)-3,4,5-trihydroxy-2-(alpha-d-mannopyranosyloxy)-6-[(6-o-undecanoyl-beta-d-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate (1 kDa, Ligand)
Mycobacterial respiratory complex i, fully-inserted quinone (560 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
Guanosine-5'-triphosphate (523 Da, Ligand)
Fe2/s2 (inorganic) cluster (175 Da, Ligand)
Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Iron/sulfur cluster (351 Da, Ligand)
Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Zinc ion (65 Da, Ligand)
Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Menaquinone-9 (785 Da, Ligand)
Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)

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EMD-27965

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Mycobacterial respiratory complex I, semi-inserted quinone

Release date: Oct. 12, 2022
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8e9i
Q-score: 0.509

Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL

PNAS (2023) 120 pp. e2214949120-e2214949120 [ DOI: doi:10.1073/pnas.2214949120 Pubmed: 36952383 ]

Sample:

Flavin mononucleotide (456 Da, Ligand)
Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Iron/sulfur cluster (351 Da, Ligand)
Zinc ion (65 Da, Ligand)
Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Fe2/s2 (inorganic) cluster (175 Da, Ligand)
Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit d (48 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Menaquinone-9 (785 Da, Ligand)
(2r)-3-{[(r)-hydroxy({(1s,2r,3r,4r,5s,6s)-3,4,5-trihydroxy-2-(alpha-d-mannopyranosyloxy)-6-[(6-o-undecanoyl-beta-d-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate (1 kDa, Ligand)
Guanosine-5'-triphosphate (523 Da, Ligand)
Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Mycobacterial respiratory complex i, semi-inserted quinone (560 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)

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EMD-20446

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Cryo-EM structure of AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and DNA

Release date: Nov. 20, 2019
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6ppr
Q-score: 0.505

Jia N, Unciuleac MC, Xue C, Greene EC, Patel DJ, Shuman S

PNAS (2019) 116 pp. 24507-24516 [ DOI: doi:10.1073/pnas.1913546116 Pubmed: 31740608 ]

Sample:

Uvrd/rep helicase (Complex from Mycolicibacterium smegmatis)
Iron/sulfur cluster (351 Da, Ligand)
Uvrd/rep helicase (118 kDa, Protein from Mycobacterium smegmatis)
Atp-dependent dna helicase (uvrd/rep) (110 kDa, Protein from Mycobacterium smegmatis)
Adnab-d934a-d1014a mutant in complex with amppnp and dna (200 kDa, Complex)
Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
Dna (Complex from Bacillus subtilis subsp. subtilis str. 168)
Atp-dependent dna helicase (uvrd/rep) (Complex from Mycolicibacterium smegmatis)
Dna (70-mer) (21 kDa, DNA from Mycolicibacterium smegmatis)

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Showing 1 - 5 of 5. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [5]

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