CryoEM structure of GroEL-ADP.BeF3-Rubisco.
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8ba8
Q-score: 0.407
Gardner S, Darrow MC, Lukoyanova N, Thalassinos K, Saibil HR
PNAS (2023) 120 pp. e2308933120- [ DOI: doi:10.1073/pnas.2308933120 Pubmed: 38064510 ]
- Potassium ion (39 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Water (18 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Chaperonin groel (57 kDa, Protein from Escherichia coli K-12)
- Groel-adp.befx-rubisco (802 kDa, Complex from Escherichia coli)
CryoEM structure of GroEL-GroES-ADP.AlF3-Rubisco.
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8ba9
Q-score: 0.395
Gardner S, Darrow MC, Lukoyanova N, Thalassinos K, Saibil HR
PNAS (2023) 120 pp. e2308933120- [ DOI: doi:10.1073/pnas.2308933120 Pubmed: 38064510 ]
- 60 kda chaperonin (55 kDa, Protein from Escherichia coli K-12)
- Groel-adp.befx-rubisco (802 kDa, Complex from Escherichia coli)
- Potassium ion (39 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Co-chaperonin groes (10 kDa, Protein from Escherichia coli K-12)
- Aluminum fluoride (83 Da, Ligand)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8et3
Q-score: 0.382
Ghanbarpour A, Fei X, Baker TA, Davis JH, Sauer RT
PNAS (2023) 120 pp. e2219044120-e2219044120 [ DOI: doi:10.1073/pnas.2219044120 Pubmed: 36730206 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Atp-dependent clp protease atp-binding subunit clpx (46 kDa, Protein from Escherichia coli)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Green fluorescent protein (30 kDa, Protein from Escherichia coli)
- Clpxp aaa protease complex bound with sspb and gfp-ssra (Complex from Escherichia coli)
- Stringent starvation protein b (18 kDa, Protein from Escherichia coli)
- Atp-dependent clp protease proteolytic subunit (23 kDa, Protein from Escherichia coli)
Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP.BeF3-.
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 7xha
Q-score: 0.46
Dong L, Yang S, Chen J, Wu X, Sun D, Song C, Li L
PNAS (2023) 120 pp. e2208070120-e2208070120 [ Pubmed: 36598944 DOI: doi:10.1073/pnas.2208070120 ]
- Sece (Complex from Escherichia coli)
- Seca (Complex from Geobacillus thermodenitrificans NG80-2)
- Protein translocase subunit secy (47 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Complex of the seca/secye/proompa(4y)-sfgfp with adp.bef3- (180 kDa, Complex from Bacillus subtilis subsp. subtilis str. 168)
- Sfgfp (Complex)
- Beryllium trifluoride ion (66 Da, Ligand)
- Protein translocase subunit seca (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Translocating polypeptide (33 kDa, Protein from Escherichia coli)
- Secy (Complex from Geobacillus thermodenitrificans NG80-2)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Protein translocase subunit sece (7 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 7xhb
Q-score: 0.429
Dong L, Yang S, Chen J, Wu X, Sun D, Song C, Li L
PNAS (2023) 120 pp. e2208070120-e2208070120 [ Pubmed: 36598944 DOI: doi:10.1073/pnas.2208070120 ]
- Translocating peptide (37 kDa, Protein from Escherichia coli)
- Sece (Complex from Escherichia coli)
- Seca (Complex from Geobacillus thermodenitrificans NG80-2)
- Complex of the seca/secye/proompa(4y)-sfgfp with adp. (180 kDa, Complex from Bacillus subtilis subsp. subtilis str. 168)
- Protein translocase subunit secy (47 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
- Sfgfp (Complex)
- Protein translocase subunit seca (88 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Secy (Complex from Geobacillus thermodenitrificans NG80-2)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Protein translocase subunit sece (7 kDa, Protein from Geobacillus thermodenitrificans NG80-2)
Transcription antitermination complex: "pre-engaged" Qlambda-loading complex
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 7ubm
Q-score: 0.461
Yin Z, Bird JG, Kaelber JT, Nickels BE, Ebright RH
PNAS (2022) 119 pp. e2205278119-e2205278119 [ Pubmed: 35951650 DOI: doi:10.1073/pnas.2205278119 ]
- Transcription antitermination complex: "pre-engaged" qlambda-loading complex (500 kDa, Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Antitermination protein q (22 kDa, Protein from Escherichia phage Lambda)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna (53-mer) (18 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna (52-mer) (18 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (71 kDa, Protein from Escherichia coli)
- Rna (5'-r(*up*gp*gp*gp*ap*gp*ap*gp*gp*up*a)-3') (3 kDa, RNA from Escherichia coli)
Resolution: 2.58 Å
EM Method: Single-particle
Fitted PDBs: 7ug7
Q-score: 0.536
Wieland M, Holm M, Rundlet EJ, Morici M, Koller TO, Maviza TP, Pogorevc D, Osterman IA, Muller R, Blanchard SC, Wilson DN
PNAS (2022) 119 pp. e2114214119-e2114214119 [ DOI: doi:10.1073/pnas.2114214119 Pubmed: 35500116 ]
- Trna-phe (24 kDa, RNA from Escherichia coli)
- Mrna (19 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 23s rrna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 1,4-diaminobutane (88 Da, Ligand)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- N-formylmethionine (177 Da, Ligand)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- Elongation factor g (77 kDa, Protein from Escherichia coli K-12)
- Spermidine (145 Da, Ligand)
- 70s ribosome in an intermediate state of translocation bound to ef-g(gdp) and argyrinb (Complex from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l1 (24 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal subunit (Complex from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- Trna-fmet (24 kDa, RNA from Escherichia coli)
- 16s rrna (497 kDa, RNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
- Phenylalanine (165 Da, Ligand)
- Argyrin b (874 Da, Protein from Actinoplanes sp.)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal subunit (Complex from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- Ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
CryoEM structure of the Rix7 D2 Walker B mutant
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 7t3i
Q-score: 0.38
Kocaman S, Lo YH, Krahn JM, Sobhany M, Dandey VP, Petrovich ML, Etigunta SK, Williams JG, Deterding LJ, Borgnia MJ, Stanley RE
Pnas Nexus (2022) 1 pp. pgac118-pgac118 [ Pubmed: 36090660 DOI: doi:10.1093/pnasnexus/pgac118 ]
- Substrate peptide (2 kDa, Protein from Escherichia coli)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Cryoem structure of rix7 d2 walker b mutant (Complex from Chaetomium thermophilum)
- Phosphate ion (94 Da, Ligand)
- Rix7 (89 kDa, Protein from Chaetomium thermophilum)
Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR promoter DNA (class 1)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7mkd
Q-score: 0.495
Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2112877118 Pubmed: 34599106 ]
- Escherichia coli sigma 70 rna polymerase bound to lambda pr promoter dna (Complex)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Template strand of lambda pr promoter dna (27 kDa, DNA from Escherichia virus Lambda)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Chapso (631 Da, Ligand)
- Lambda pr promoter dna (Complex from Escherichia virus Lambda)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Rna polymerase (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Nontemplate strand of lambda pr promoter dna (27 kDa, DNA from Escherichia virus Lambda)
Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR promoter DNA (class 2)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7mke
Q-score: 0.412
Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2112877118 Pubmed: 34599106 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Lambda pr promoter dna (class 2) (Complex from Escherichia virus Lambda)
- Rna polymerase (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Template strand of lambda pr dna promoter (27 kDa, DNA from Escherichia virus Lambda)
- Magnesium ion (24 Da, Ligand)
- Escherichia coli rna polymerase bound to lambda pr promoter dna (Complex)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Nontemplate strand of lambda pr dna promoter (27 kDa, DNA from Escherichia virus Lambda)