Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8vxh
Q-score: 0.573
Ashraf KU, Bunoro-Batista M, Ansell TB, Punetha A, Rosario-Garrido S, Firlar E, Kaelber JT, Stansfeld PJ, Petrou VI
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.29.634835 ]
- Undecaprenyl-phosphate 4-deoxy-4-formamido-l-arabinose transferase (40 kDa, Protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2)
- Salmonella enterica arnc in msp1e3d1 nanodisc in the apo state (162 kDa, Complex from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2)
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 9asc
Q-score: 0.5
Ashraf KU, Bunoro-Batista M, Ansell TB, Punetha A, Rosario-Garrido S, Firlar E, Kaelber JT, Stansfeld PJ, Petrou VI
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.29.634835 ]
- Uridine-5'-diphosphate (404 Da, Ligand)
- Salmonella enterica arnc in msp1e3d1 nanodisc bound to udp and mn2+ (162 kDa, Complex from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2)
- Undecaprenyl-phosphate 4-deoxy-4-formamido-l-arabinose transferase (40 kDa, Protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2)
- Manganese (ii) ion (54 Da, Ligand)
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 9b77
Q-score: 0.599
Ashraf KU, Bunoro-Batista M, Ansell TB, Punetha A, Rosario-Garrido S, Firlar E, Kaelber JT, Stansfeld PJ, Petrou VI
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.29.634835 ]
- Undecaprenyl-phosphate 4-deoxy-4-formamido-l-arabinose transferase (40 kDa, Protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2)
- Water (18 Da, Ligand)
- Salmonella enterica arnc in msp1e3d1 nanodisc in the apo state (162 kDa, Complex from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 9bct
Q-score: 0.554
You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH
Nature (2024) 635 pp. 229-236 [ DOI: doi:10.1038/s41586-024-07979-9 Pubmed: 39322680 ]
- Dna-directed rna polymerase subunit l (11 kDa, Protein from Thermococcus kodakarensis)
- Template strand dna (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit p (5 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit f (14 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit a' (103 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit n (7 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit k (6 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit e (21 kDa, Protein from Thermococcus kodakarensis)
- Ftta-dependent transcription termination complex (556 kDa, Complex from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit h (9 kDa, Protein from Thermococcus kodakarensis)
- Transcription termination factor ftta (73 kDa, Protein from Thermococcus kodakarensis)
- Non-template strand dna (11 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna (13 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit a" (43 kDa, Protein from Thermococcus kodakarensis)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt4 (8 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit b (127 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit d (29 kDa, Protein from Thermococcus kodakarensis)
- Transcription elongation factor spt5 (16 kDa, Protein from Thermococcus kodakarensis)
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 9bcu
Q-score: 0.613
You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH
Nature (2024) 635 pp. 229-236 [ DOI: doi:10.1038/s41586-024-07979-9 Pubmed: 39322680 ]
- Dna-directed rna polymerase subunit l (11 kDa, Protein from Thermococcus kodakarensis)
- Template strand dna (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit p (5 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit f (14 kDa, Protein from Thermococcus kodakarensis)
- Ftta-dependent transcription termination complex containing 52 nt rna (556 kDa, Complex from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit a' (103 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit n (7 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit k (6 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit e (21 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit h (9 kDa, Protein from Thermococcus kodakarensis)
- Rna (29-mer) (16 kDa, RNA from synthetic construct)
- Transcription termination factor ftta (73 kDa, Protein from Thermococcus kodakarensis)
- Non-template strand dna (11 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit a" (43 kDa, Protein from Thermococcus kodakarensis)
- Zinc ion (65 Da, Ligand)
- Transcription elongation factor spt4 (8 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit b (127 kDa, Protein from Thermococcus kodakarensis)
- Dna-directed rna polymerase subunit d (29 kDa, Protein from Thermococcus kodakarensis)
- Transcription elongation factor spt5 (16 kDa, Protein from Thermococcus kodakarensis)
Zophobas morio black wasting virus strain NJ2-molitor virion structure
Resolution: 2.0 Å
EM Method: Single-particle
Fitted PDBs: 8t9x
Q-score: 0.736
Penzes JJ, Holm M, Firlar E, Kaelber JT
To Be Published
- Dna (5'-d(p*tp*cp*gp*ap*a)-3') (1 kDa, DNA from Zophobas morio black wasting virus)
- Dna (5'-d(p*cp*ap*gp*gp*cp*cp*ap*ap*a)-3') (2 kDa, DNA from Zophobas morio black wasting virus)
- Major capsid protein (48 kDa, Protein from Zophobas morio black wasting virus)
- Zophobas morio densovirus (Virus from Zophobas morio densovirus)
- Dna (5'-d(p*cp*gp*a)-3') (886 Da, DNA from Zophobas morio black wasting virus)
- Water (18 Da, Ligand)
Colicin E1 fragment in nanodisc-embedded TolC
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 6wxh
Q-score: 0.478
Budiardjo SJ, Stevens JJ, Calkins AL, Ikujuni AP, Wimalasena VK, Firlar E, Case DA, Biteen JS, Kaelber JT, Slusky JSG
eLife (2022) 11 [ Pubmed: 35199644 DOI: doi:10.7554/eLife.73297 ]
- Outer membrane protein tolc (Complex from Escherichia coli K-12)
- Colicin e1 fragment cole1-t (Complex from Escherichia coli)
- Colicin e1 fragment cole1-t inside nanodisc-embedded tolc (21 kDa, Complex)
- Colicin-e1 (21 kDa, Protein from Escherichia coli)
- Outer membrane protein tolc (53 kDa, Protein from Escherichia coli (strain K12))
Colicin E1 fragment in nanodisc-embedded TolC
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 6wxi
Q-score: 0.471
Budiardjo SJ, Stevens JJ, Calkins AL, Ikujuni AP, Wimalasena VK, Firlar E, Case DA, Biteen JS, Kaelber JT, Slusky JSG
eLife (2022) 11 [ Pubmed: 35199644 DOI: doi:10.7554/eLife.73297 ]
- Outer membrane protein tolc (53 kDa, Protein from Escherichia coli (strain K12))
- Outer membrane protein tolc (53 kDa, Complex from Escherichia coli K-12)
Adeno-associated virus strain AAVhu.37 capsid icosahedral structure
Resolution: 2.56 Å
EM Method: Single-particle
Fitted PDBs: 6u95
Q-score: 0.57
Kaelber JT, Yost SA, Webber KA, Firlar E, Liu Y, Danos O, Mercer AC
Acta Crystallogr F Struct Biol Commun (2020) 76 pp. 58-64 [ Pubmed: 32039886 DOI: doi:10.1107/S2053230X20000308 ]
- Capsid protein vp1 (81 kDa, Protein from Adeno-associated virus)
- Adeno-associated virus (5 MDa, Virus from Adeno-associated virus)