S. thermodepolymerans KpsMT(E151Q)-KpsE in complex with ATP
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8tsh
Q-score: 0.499
Nature (2024) 628 pp. 901-909 [ DOI: doi:10.1038/s41586-024-07248-9 Pubmed: 38570679 ]
- Abc transporter atp-binding protein (26 kDa, Protein from Caldimonas thermodepolymerans)
- Capsular biosynthesis protein (44 kDa, Protein from Caldimonas thermodepolymerans)
- Abc transporter kpsmt(e151q) in complex with polysaccharide co-polymerase kpse in atp-bound state (Complex from Caldimonas thermodepolymerans)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Transport permease protein (30 kDa, Protein from Caldimonas thermodepolymerans)
S. thermodepolymerans KpsMT-KpsE in complex with ADP:AlF4-
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 8tsi
Q-score: 0.428
Nature (2024) 628 pp. 901-909 [ Pubmed: 38570679 DOI: doi:10.1038/s41586-024-07248-9 ]
- Capsular biosynthesis protein (44 kDa, Protein from Caldimonas thermodepolymerans)
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Abc transporter atp-binding protein (26 kDa, Protein from Caldimonas thermodepolymerans)
- Abc transporter kpsmt in complex with polysaccharide co-polymerase kpse in adp:alf4- -bound state (Complex from Caldimonas thermodepolymerans)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Transport permease protein (30 kDa, Protein from Caldimonas thermodepolymerans)
S. thermodepolymerans KpsM-KpsE in Apo 2 state with rigid body fitted KpsT
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8tsl
Q-score: 0.444
Nature (2024) 628 pp. 901-909 [ Pubmed: 38570679 DOI: doi:10.1038/s41586-024-07248-9 ]
- Capsular biosynthesis protein (44 kDa, Protein from Caldimonas thermodepolymerans)
- Abc transporter kpsmt in complex with polysaccharide co-polymerase kpse in apo 2 state (Complex from Caldimonas thermodepolymerans)
- Abc transporter atp-binding protein (26 kDa, Protein from Caldimonas thermodepolymerans)
- Transport permease protein (30 kDa, Protein from Caldimonas thermodepolymerans)
S. thermodepolymerans KpsMT-KpsE Apo 1
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8tsw
Q-score: 0.476
Nature (2024) 628 pp. 901-909 [ DOI: doi:10.1038/s41586-024-07248-9 Pubmed: 38570679 ]
- Capsular biosynthesis protein (44 kDa, Protein from Caldimonas thermodepolymerans)
- Abc transporter atp-binding protein (26 kDa, Protein from Caldimonas thermodepolymerans)
- Transport permease protein (30 kDa, Protein from Caldimonas thermodepolymerans)
- Abc transporter kpsmt in complex with polysaccharide co-polymerase kpse in apo 1 state (Complex from Caldimonas thermodepolymerans)
S. thermodepolymerans KpsM-KpsE in Glycolipid 2 state with rigid body fitted KpsT
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8tt3
Q-score: 0.421
Nature (2024) 628 pp. 901-909 [ Pubmed: 38570679 DOI: doi:10.1038/s41586-024-07248-9 ]
- Capsular biosynthesis protein (44 kDa, Protein from Caldimonas thermodepolymerans)
- Abc transporter kpsmt in complex with polysaccharide co-polymerase kpse bound to the glycolipid in state 2 (Complex from Caldimonas thermodepolymerans)
- Abc transporter atp-binding protein (26 kDa, Protein from Caldimonas thermodepolymerans)
- (2r,5s,8s)-2,5-dihydroxy-5,10-dioxo-8-[(undecanoyloxy)methyl]-4,6,9-trioxa-5lambda~5~-phosphahenicosan-1-yl 3-deoxy-alpha-l-altro-oct-2-ulopyranosidonic acid (816 Da, Ligand)
- Transport permease protein (30 kDa, Protein from Caldimonas thermodepolymerans)
S. thermodepolymerans KpsM-KpsE in Glycolipid 1 state with rigid body fitted KpsT
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8tun
Q-score: 0.439
Nature (2024) 628 pp. 901-909 [ DOI: doi:10.1038/s41586-024-07248-9 Pubmed: 38570679 ]
- Capsular biosynthesis protein (44 kDa, Protein from Caldimonas thermodepolymerans)
- Abc transporter atp-binding protein (26 kDa, Protein from Caldimonas thermodepolymerans)
- (2r,5s,8s)-2,5-dihydroxy-5,10-dioxo-8-[(undecanoyloxy)methyl]-4,6,9-trioxa-5lambda~5~-phosphahenicosan-1-yl 3-deoxy-alpha-l-altro-oct-2-ulopyranosidonic acid (816 Da, Ligand)
- Transport permease protein (30 kDa, Protein from Caldimonas thermodepolymerans)
- Abc transporter kpsmt in complex with polysaccharide co-polymerase kpse bound to the glycolipid in state 1 (Complex from Caldimonas thermodepolymerans)
Mechanistic Insights Revealed by YbtPQ in the Occluded State
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8vsi
Q-score: 0.547
Biomolecules (2024) 14 [ Pubmed: 38540742 DOI: doi:10.3390/biom14030322 ]
- Magnesium ion (24 Da, Ligand)
- Ybtpq (Complex from Escherichia coli)
- Abc transporter atp-binding protein (66 kDa, Protein from Escherichia coli)
- Adp orthovanadate (544 Da, Ligand)
- Permease and atp-binding protein of yersiniabactin-iron abc transporter ybtq (66 kDa, Protein from Escherichia coli)
Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the pre-translocation state
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 8j5q
Q-score: 0.519
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) 31 pp. 1072-1082 [ Pubmed: 38548954 DOI: doi:10.1038/s41594-024-01256-z ]
- Iron/sulfur cluster (351 Da, Ligand)
- Uncharacterized protein rv1280c (64 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Putative peptide transport permease protein rv1282c (31 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Cryo-em structure of mycobacterium tuberculosis oppabcd in the pre-translocation state (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Endogenous oligopeptide (783 Da, Protein from Mycolicibacterium smegmatis MC2 155)
- Uncharacterized abc transporter atp-binding protein rv1281c (65 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Putative peptide transport permease protein rv1283c (35 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the resting state
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 8j5r
Q-score: 0.534
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) 31 pp. 1072-1082 [ Pubmed: 38548954 DOI: doi:10.1038/s41594-024-01256-z ]
- Iron/sulfur cluster (351 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))
- Uncharacterized protein rv1280c (64 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Cryo-em structure of mycobacterium tuberculosis oppabcd in the resting state (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Putative peptide transport permease protein rv1283c (35 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the pre-catalytic intermediate state
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) 31 pp. 1072-1082 [ Pubmed: 38548954 DOI: doi:10.1038/s41594-024-01256-z ]
- Iron/sulfur cluster (351 Da, Ligand)
- Cryo-em structure of mycobacterium tuberculosis oppabcd in the pre-catalytic intermediate state (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Uncharacterized protein rv1280c (64 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Putative peptide transport permease protein rv1282c (31 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Magnesium ion (24 Da, Ligand)
- Uncharacterized abc transporter atp-binding protein rv1281c (65 kDa, Protein 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))