Kalium channelrhodopsin 1 C110A mutant from Hyphochytrium catenoides, Dark State
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 9cdc
Q-score: 0.465
Morizumi T, Kim K, Li H, Nag P, Dogon T, Sineshchekov OA, Wang Y, Brown LS, Hwang S, Sun H, Bondar AN, Schapiro I, Govorunova EG, Spudich JL, Ernst OP
Nat Commun (2025) 16 pp. 1283-1283 [ DOI: doi:10.1038/s41467-025-56491-9 Pubmed: 39900567 ]
- Water (18 Da, Ligand)
- Retinal (284 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Kalium channelrhodopsin 1 c110a (30 kDa, Protein from Hyphochytrium catenoides)
- Cholesterol (386 Da, Ligand)
- Kalium channelrhodopin 1 c110a reconstituted in peptidisc, dark state (91 MDa, Complex from Hyphochytrium catenoides)
Kalium channelrhodopsin 1 C110A mutant from Hyphochytrium catenoides, Laser-Flash-Illuminated
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 9cdd
Q-score: 0.432
Morizumi T, Kim K, Li H, Nag P, Dogon T, Sineshchekov OA, Wang Y, Brown LS, Hwang S, Sun H, Bondar AN, Schapiro I, Govorunova EG, Spudich JL, Ernst OP
Nat Commun (2025) 16 pp. 1283-1283 [ DOI: doi:10.1038/s41467-025-56491-9 Pubmed: 39900567 ]
- Water (18 Da, Ligand)
- Retinal (284 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Kalium channelrhodopin 1 c110a reconstituted in peptidisc, laser-flash-illuminated (91 MDa, Complex from Hyphochytrium catenoides)
- Kalium channelrhodopsin 1 (30 kDa, Protein from Hyphochytrium catenoides)
- Cholesterol (386 Da, Ligand)
Kalium channelrhodopsin 1 C110A mutant from Hyphochytrium catenoides, Continuous Illumination State
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 9cde
Q-score: 0.395
Morizumi T, Kim K, Li H, Nag P, Dogon T, Sineshchekov OA, Wang Y, Brown LS, Hwang S, Sun H, Bondar AN, Schapiro I, Govorunova EG, Spudich JL, Ernst OP
Nat Commun (2025) 16 pp. 1283-1283 [ DOI: doi:10.1038/s41467-025-56491-9 Pubmed: 39900567 ]
- Water (18 Da, Ligand)
- Retinal (284 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Kalium channelrhodopin 1 c110a reconstituted in peptidisc, continuous illumination state (91 MDa, Complex from Hyphochytrium catenoides)
- Kalium channelrhodopsin 1 c110a - continuous illumination state (30 kDa, Protein from Hyphochytrium catenoides)
- Cholesterol (386 Da, Ligand)
Structure of the HrpA-bound E. coli disome, Class I
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9gft
Q-score: 0.385
Campbell A, Esser HF, Burroughs AM, Berninghausen O, Aravind L, Becker T, Green R, Beckmann R, Buskirk AR
Mol Cell (2025) [ Pubmed: 39922193 DOI: doi:10.1016/j.molcel.2025.01.018 ]
- Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
- A-site trna (24 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein ul23 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul10 (17 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs16 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 16s ribosomal rna (499 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl28 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us2 (26 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs6, fully modified isoform (15 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us7 (20 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl17 (14 kDa, Protein from Escherichia coli)
- P-site trna (24 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli)
- Hrpa-bound e. coli disome (Complex)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl25 (10 kDa, Protein from Escherichia coli)
- Vemp nascent chain (20 kDa, Protein from Vibrio alginolyticus)
- Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- Messenger rna (223 kDa, RNA from Vibrio alginolyticus)
- Vemp nascent chain (Complex from Vibrio alginolyticus)
- 23s rna (941 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul1 (24 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)
- Messenger rna (Complex from Vibrio alginolyticus)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl31a (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
- P-site trna (24 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
- A-site trna (24 kDa, RNA from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl36a (4 kDa, Protein from Escherichia coli)
- E. coli disome (Complex from Escherichia coli)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli)
- Atp-dependent rna helicase hrpa (152 kDa, Protein from Escherichia coli)
Structure of the HrpA-bound E. coli disome, Class II
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9ggr
Q-score: 0.311
Campbell A, Esser HF, Burroughs AM, Berninghausen O, Aravind L, Becker T, Green R, Beckmann R, Buskirk AR
Mol Cell (2025) [ Pubmed: 39922193 DOI: doi:10.1016/j.molcel.2025.01.018 ]
- Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
- A-site trna (24 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein ul23 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul10 (17 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs16 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 16s ribosomal rna (499 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl28 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us2 (26 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs6, fully modified isoform (15 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us7 (20 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl17 (14 kDa, Protein from Escherichia coli)
- P-site trna (24 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl25 (10 kDa, Protein from Escherichia coli)
- Vemp nascent chain (20 kDa, Protein from Vibrio alginolyticus)
- Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
- Atp-dependent rna helicase hrpa (149 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul1 (24 kDa, Protein from Escherichia coli)
- Messenger rna (17 kDa, RNA from Vibrio alginolyticus)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl31a (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
- P-site trna (24 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
- A-site trna (24 kDa, RNA from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
- Hrpa-bound e. coli disome (Complex from Escherichia coli)
- Large ribosomal subunit protein bl36a (4 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli)
- Atp-dependent rna helicase hrpa (152 kDa, Protein from Escherichia coli)
CryoEM structure of canonical rice nucleosome core particle
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8q15
Q-score: 0.401
Hari Sundar G V, Sotelo-Parrilla P, Raju S, Jha S, Gireesh A, Gut F, Vinothkumar KR, Berger F, Jeyaprakash AA, Shivaprasad PV
To Be Published
- Histone h3.2 (15 kDa, Protein from Oryza)
- Widom 601 (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Oryza)
- Widom 601 (44 kDa, DNA from synthetic construct)
- Histone h2a.2 (13 kDa, Protein from Oryza)
- Rice canonical nucleosome core particle with widom 601 dna sequence (Complex from Oryza)
- Histone h2b.4 (16 kDa, Protein from Oryza)
CryoEM structure of rice nucleosome containing a H4 variant chimera
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8q16
Q-score: 0.441
Hari Sundar G V, Sotelo-Parrilla P, Raju S, Jha S, Gireesh A, Gut F, Vinothkumar KR, Berger F, Jeyaprakash AA, Shivaprasad PV
To Be Published
- Rice nucleosome core particle containing a histone h4 variant chimera with widom 601 dna (Complex from Oryza)
- Histone h3.2 (15 kDa, Protein from Oryza)
- Histone h2a.2 (13 kDa, Protein from Oryza)
- Widom 601 (45 kDa, DNA from synthetic construct)
- Widom 601 (45 kDa, DNA from synthetic construct)
- Chimeric h4.v (11 kDa, Protein from Oryza)
- Histone h2b.4 (16 kDa, Protein from Oryza)
Homo sapiens Xenotropic and Polytropic Retrovirus Receptor 1 (XPR1) with Y22A/E23A/K26A mutations
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 9ijy
Q-score: 0.524
He Q, Zhang R, Tury S, Courgnaud V, Liu F, Battini JL, Li B, Chen Q
Nat Commun (2025) 16 pp. 683-683 [ Pubmed: 39814721 DOI: doi:10.1038/s41467-025-55995-8 ]
- Dimer of xpr1 mutant (81 kDa, Complex from Homo sapiens)
- Solute carrier family 53 member 1 (83 kDa, Protein from Homo sapiens)
- (4s,7r)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide (763 Da, Ligand)
- Phosphate ion (94 Da, Ligand)
Wild type Homo sapiens Xenotropic and Polytropic Retrovirus Receptor 1 (XPR1)
Resolution: 2.91 Å
EM Method: Single-particle
Fitted PDBs: 9ijz
Q-score: 0.497
He Q, Zhang R, Tury S, Courgnaud V, Liu F, Battini JL, Li B, Chen Q
Nat Commun (2025) 16 pp. 683-683 [ Pubmed: 39814721 DOI: doi:10.1038/s41467-025-55995-8 ]
- Phosphate ion (94 Da, Ligand)
- (4s,7r)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide (763 Da, Ligand)
- Dimer of xpr1 (81 kDa, Complex from Homo sapiens)
- Solute carrier family 53 member 1 (83 kDa, Protein from Homo sapiens)
Human RNA Polymerase III Class III Open Pre-initiation Complex 1 (OC1)
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 9fso
Q-score: 0.342
Shah SZ, Perry TN, Graziadei A, Cecatiello V, Kaliyappan T, Misiaszek AD, Muller CW, Ramsay EP, Vannini A
Nat Commun (2025) 16 pp. 141-141 [ Pubmed: 39747245 DOI: doi:10.1038/s41467-024-55553-8 ]
- Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 4 (165 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc10 (12 kDa, Protein from Homo sapiens)
- U6_2_template (30 kDa, DNA from Homo sapiens)
- Transcription factor iiib 50 kda subunit (46 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc9 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc6 (35 kDa, Protein from Homo sapiens)
- Transcription factor tfiiib component b'' homolog (55 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac1 (39 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc1 (155 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Tfiiib (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Snapc (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc7 (25 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc4 (44 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (22 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Rna polymerase iii class iii open pre-initiation complex 1 (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc8 (22 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase iii subunit rpc2 (127 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc3 (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac2 (15 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Isoform 2 of dna-directed rna polymerase iii subunit rpc5 (74 kDa, Protein from Homo sapiens)
- U6_2_non template (30 kDa, DNA from Homo sapiens)
- Human rna polymerase iii (Complex from Homo sapiens)