Splicing factor 3B subunit 1
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein–RNA Heteromer Protein × 4 RNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts | Chain C； UniProt 453–1304 | Mutation：R625H | PHD finger-like domain-containing protein 5A × 1 （Q7RTV0） Splicing factor 3B subunit 3 × 1 （Q15393） Splicing factor 3B subunit 5 × 1 （Q9BWJ5） pre-mRNA intron × 1 U2 snRNA × 1 ZN ZINC ION × 3 | ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE | Resolution 3.10 Å |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 9K1Y | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2F9D 2.5 angstrom resolution structure of the spliceosomal protein p14 bound to region of SF3b155 Deposited 2005-12-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
373–415（43 aa）
Fragment：Residues: 373-415
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；14-18% PEG3350, MOPS buffer, 0.2M sodium formate
selenomethionine derivatized SF3b155 protein, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.50 Å R-free 0.276 |
| 2F9D 2.5 angstrom resolution structure of the spliceosomal protein p14 bound to region of SF3b155 Deposited 2005-12-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Q
373–415（43 aa）
Fragment：Residues: 373-415
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；14-18% PEG3350, MOPS buffer, 0.2M sodium formate
selenomethionine derivatized SF3b155 protein, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.50 Å R-free 0.276 |
| 2F9J 3.0 angstrom resolution structure of a Y22M mutant of the spliceosomal protein p14 bound to a region of SF3b155 Deposited 2005-12-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
381–415（35 aa）
Fragment：Residues: 381-415
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60% NaH2PO4/40% K2HPO4
0.5M beta-alanine, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.00 Å R-free 0.266 |
| 2F9J 3.0 angstrom resolution structure of a Y22M mutant of the spliceosomal protein p14 bound to a region of SF3b155 Deposited 2005-12-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Q
381–415（35 aa）
Fragment：Residues: 381-415
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60% NaH2PO4/40% K2HPO4
0.5M beta-alanine, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.00 Å R-free 0.266 |
| 2FHO NMR solution structure of the human spliceosomal protein complex p14-SF3b155 Deposited 2005-12-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
379–424（46 aa）
Fragment：residues in database 379-424
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；308 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition
20mM Sodium Phosphate buffer (pH 6.5), 100mM NaCl, 1mM d-DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2PEH Crystal structure of the UHM domain of human SPF45 in complex with SF3b155-ULM5 Deposited 2007-04-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
333–342（10 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；25% (w/v) PEG 1,500, 0.1 M Malonate, Imidazole, Borate buffer pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.11 Å R-free 0.273 |
| 2PEH Crystal structure of the UHM domain of human SPF45 in complex with SF3b155-ULM5 Deposited 2007-04-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
333–342（10 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；25% (w/v) PEG 1,500, 0.1 M Malonate, Imidazole, Borate buffer pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.11 Å R-free 0.273 |
| 2PEH Crystal structure of the UHM domain of human SPF45 in complex with SF3b155-ULM5 Deposited 2007-04-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
333–342（10 aa）
Chain D
333–342（10 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；25% (w/v) PEG 1,500, 0.1 M Malonate, Imidazole, Borate buffer pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.11 Å R-free 0.273 |
| 3LQV Branch Recognition by SF3b14 Deposited 2010-02-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
377–415（39 aa）
Fragment：UNP residues 377-415
|
Not recorded | ADE ADENINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；298 K；PEG3350, 0.2M NaCl, 20mM Adenine, pH 6, vapor diffusion, temperature 298K
|
Resolution 2.38 Å R-free 0.258 |
| 3LQV Branch Recognition by SF3b14 Deposited 2010-02-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Q
377–415（39 aa）
Fragment：UNP residues 377-415
|
Not recorded | ADE ADENINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；298 K；PEG3350, 0.2M NaCl, 20mM Adenine, pH 6, vapor diffusion, temperature 298K
|
Resolution 2.38 Å R-free 0.258 |
| 4OZ1 Crystal structure of human CAPERalpha UHM bound to SF3b155 ULM5 Deposited 2014-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–342（10 aa）
Fragment：333-342
|
Not recorded | K POTASSIUM ION × 1 CL CHLORIDE ION × 1 LYS LYSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.8 M sodium phosphate, 0.8 M potassium phosphate, 0.1 M HEPES pH 7.5
|
Resolution 1.74 Å R-free 0.180 |
| 5IFE Crystal structure of the human SF3b core complex Deposited 2016-02-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 3 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；0.05 M HEPES-NaOH pH=6.91-7.05, 40% Pentaerythritol propoxylate (5/4 PO/OH), 0.2M KCl
|
Resolution 3.10 Å R-free 0.260 |
| 5O9Z Cryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex) Deposited 2017-06-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric |
Chain v
1–1304（1304 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 5Z56 cryo-EM structure of a human activated spliceosome (mature Bact) at 5.1 angstrom. Deposited 2018-01-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric |
Chain 1
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 13 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；20 mM HEPES-KOH, 150 mM NaCl, 1.5 mM MgCl2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.10 Å |
| 5Z57 Cryo-EM structure of the human activated spliceosome (late Bact) at 6.5 angstrom Deposited 2018-01-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 57-meric |
Chain 1
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 ALA ALANINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 10 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；20 mM HEPES-KOH, pH 7.9, 150 mM NaCl, 1.5 mM MgCl2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.50 Å |
| 5Z58 Cryo-EM structure of a human activated spliceosome (early Bact) at 4.9 angstrom. Deposited 2018-01-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 46-meric |
Chain 1
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；20 mM HEPES-KOH, pH 7.9, 150 mM NaCl, 1.5 mM MgCl2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.90 Å |
| 5ZYA SF3b spliceosomal complex bound to E7107 Deposited 2018-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
1–1304（1304 aa）
|
Not recorded | 9B0 [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate × 1 ZN ZINC ION × 3 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.95 Å |
| 6AH0 The Cryo-EM Structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex) Deposited 2018-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric |
Chain 1
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.70 Å |
| 6AHD The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom resolution Deposited 2018-08-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 63-meric |
Chain 1
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6EN4 SF3b core in complex with a splicing modulator Deposited 2017-10-04 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
453–1304（852 aa）
|
Mutation：deletion 1-452 | ZN ZINC ION × 3 BGZ [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{S})-6-methyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] ethanoate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；50 mM HEPES-NaOH, pH 7-7.4, 200 mM KCl, and 38-39% (v/v) pentaerythritol propoxylate (5/4 PO/OH)
|
Resolution 3.08 Å R-free 0.266 |
| 6FF4 human Bact spliceosome core structure Deposited 2018-01-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 28-meric |
Chain u
1–1304（1304 aa）
|
Not recorded | MG MAGNESIUM ION × 4 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 10 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE；blot with blotting sensor
|
Resolution 3.40 Å |
| 6FF7 human Bact spliceosome core structure Deposited 2018-01-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 61-meric |
Chain u
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 11 MG MAGNESIUM ION × 5 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 6QX9 Structure of a human fully-assembled precatalytic spliceosome (pre-B complex). Deposited 2019-03-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 65 PDB declaration: 71-meric |
Chain B1
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 6 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.28 Å |
| 6Y50 5'domain of human 17S U2 snRNP Deposited 2020-02-24 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric |
Chain u
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6Y53 human 17S U2 snRNP low resolution part Deposited 2020-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 18 PDB declaration: nonadecameric |
Chain u
1–1304（1304 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.10 Å |
| 6Y5Q human 17S U2 snRNP Deposited 2020-02-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 21 PDB declaration: 22-meric |
Chain u
1–1304（1304 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.10 Å |
| 7ABG Human pre-Bact-1 spliceosome Deposited 2020-09-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric |
Chain u
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTG 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.80 Å |
| 7ABH Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion) Deposited 2020-09-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
Chain u
1–1304（1304 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 7ABI Human pre-Bact-2 spliceosome Deposited 2020-09-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric |
Chain u
1–1304（1304 aa）
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.00 Å |
| 7B0I Structure of a minimal SF3B core in complex with spliceostatin A (form II) Deposited 2020-11-19 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
453–1304（852 aa）
|
Not recorded | SJT spliceostatin A (form II) × 1 ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.17；277.15 K；0.1 M HEPES pH=7.17, 0.2 M MgCl2, 25% (v/v) PEG-400
|
Resolution 3.00 Å R-free 0.247 |
| 7B91 Structure of a minimal SF3B core in complex with pladienolide D (form I) Deposited 2020-12-13 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
453–1304（852 aa）
|
Not recorded | T2Z [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] ethanoate × 1 ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1M Bis-Tris Propane pH 7.63, PEG-3350 11%, Glycerol 15%, KSCN 0.2M
|
Resolution 3.00 Å R-free 0.255 |
| 7B92 Structure of a minimal SF3B core in complex with sudemycin D6 (form II) Deposited 2020-12-14 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
453–1304（852 aa）
|
Not recorded | ZN ZINC ION × 3 T2W [(~{Z},2~{S})-5-[[4-[(2~{E},4~{E})-3-methyl-5-[(2~{S},4~{R})-4,6,6-trimethyl-4-oxidanyl-oxan-2-yl]penta-2,4-dienyl]cyclohexyl]amino]-5-oxidanylidene-pent-3-en-2-yl] ~{N}-methylcarbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 M HEPES pH=7.42, 0.2 M Magnesium chloride, 27.75% (v/v) PEG-400
|
Resolution 3.00 Å R-free 0.258 |
| 7B9C Structure of a minimal SF3B core in complex with spliceostatin A (form I) Deposited 2020-12-14 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
453–1304（852 aa）
|
Not recorded | ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 SJT spliceostatin A (form II) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 M Bis-Tris Propane pH 7.1-7.45, 0.2 M Potassium thiocyanate (KSCN), 11-12% (w/v) PEG-3350, 10-15% (v/v) Glycerol
|
Resolution 2.40 Å R-free 0.248 |
| 7DVQ Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex) Deposited 2021-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric |
Chain 1
1–1304（1304 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 5 K POTASSIUM ION × 2 G5J 5'-O-[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(methoxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine × 1 ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.89 Å |
| 7EVN The cryo-EM structure of the DDX42-SF3b complex Deposited 2021-05-21 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
452–1304（853 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7EVO The cryo-EM structure of the human 17S U2 snRNP Deposited 2021-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 20 PDB declaration: 21-meric |
Chain 1
1–1304（1304 aa）
|
Not recorded | 9B0 [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate × 1 ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 7OMF Structure of a minimal SF3B core in complex with sudemycin D6 (form I) Deposited 2021-05-21 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
453–1304（852 aa）
|
Not recorded | ZN ZINC ION × 3 T2W [(~{Z},2~{S})-5-[[4-[(2~{E},4~{E})-3-methyl-5-[(2~{S},4~{R})-4,6,6-trimethyl-4-oxidanyl-oxan-2-yl]penta-2,4-dienyl]cyclohexyl]amino]-5-oxidanylidene-pent-3-en-2-yl] ~{N}-methylcarbamate × 1 SCN THIOCYANATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1M Bis-tris propane pH 7.4, 0.2M KSCN, 12% (w/v) PEG-3350, 10%(v/v) Glycerol
|
Resolution 3.00 Å R-free 0.266 |
| 7ONB Structure of the U2 5' module of the A3'-SSA complex Deposited 2021-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–RNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain C
1–1304（1304 aa）
|
Not recorded | SJT spliceostatin A (form II) × 1 ZN ZINC ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE；The A3'-SSA complex was frozen in vitreous ice by applying ~2.2 uL crosslinked sample to both sides of a glow-discharged UltrAufoil R1.2/1.3 gold grid. The excess sample was blotted away for 2s using a blot force of 7 and the grid was snap frozen in liquid ethane cooled by liquid nitrogen.
|
Resolution 3.10 Å |
| 7OPI Structure of a minimal SF3B core in complex with the inactive modulator spliceostatin E (form I) Deposited 2021-05-31 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
453–1304（852 aa）
|
Not recorded | 07I Spliceostatin E (form I) × 1 ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.15；277.15 K；0.1 M Bis-tris propane pH=7.15, 0.2 M KSCN, PEG-3350 11% (w/v), Glycerol (v/v) 10%
|
Resolution 3.10 Å R-free 0.269 |
| 7Q3L Human 17S U2 snRNP 5' domain Deposited 2021-10-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric |
Chain A
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；Sample after desalting may have also contained up to 5% glycerol.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.21 Å |
| 7Q4O Substrate-bound A-like U2 snRNP Deposited 2021-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；Sample after desalting may have also contained up to 5% glycerol.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.10 Å |
| 7Q4P U2 snRNP after ATP-dependent remodelling Deposited 2021-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: octameric |
Chain A
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；Sample after desalting may have also contained up to 5% glycerol.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.15 Å |
| 7QTT Structural organization of a late activated human spliceosome (Baqr, core region) Deposited 2022-01-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 37-meric |
Chain C
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 12 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；All solutions were sterile filtered using a 0.22um vacuum filtration unit.
cryo-EM vitrification conditions
Cryogen ETHANE；Volumes of 4 ul of the concentrated sample were applied to one side of glow-discharged UltrAuFoil 200 2/2 grids (Quantifoil) in a Vitrobot Mark IV (FEI) operating at 4 degrees Celsius and 100% humidity. The grids were blotted for 2s with blotting force 5 and immediately frozen by plunging into liquid ethane.
|
Resolution 3.10 Å |
| 7SN6 U2AF65 UHM BOUND TO SF3B155 ULM5 Deposited 2021-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
333–351（19 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 15% V/V 2-PROPANOL, 20% PEG 4000
|
Resolution 1.80 Å R-free 0.217 |
| 7SN6 U2AF65 UHM BOUND TO SF3B155 ULM5 Deposited 2021-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
333–351（19 aa）
|
Not recorded | IPA ISOPROPYL ALCOHOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 15% V/V 2-PROPANOL, 20% PEG 4000
|
Resolution 1.80 Å R-free 0.217 |
| 7VPX The cryo-EM structure of the human pre-A complex Deposited 2021-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 35-meric |
Chain 1
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 6 SJT spliceostatin A (form II) × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8CH6 Structure of a late-stage activated spliceosome (BAqr) arrested with a dominant-negative Aquarius mutant (state B complex). Deposited 2023-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric |
Chain C
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 12 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；All solutions were sterile-filtered using a 0.22um vacuum filtration unit.
cryo-EM vitrification conditions
Cryogen ETHANE；Volumes of 4 ul of the concentrated sample were applied to one side of glow-discharged UltrAuFoil 200 2/2 grids (Quantifoil) in a Vitrobot Mark IV (FEI), operated at 4 degrees Celsius and 100% humidity. The grids were blotted for 2s with blotting force 5 and immediately frozen by plunging into liquid ethane.
|
Resolution 5.90 Å |
| 8H6E Cryo-EM structure of human exon-defined spliceosome in the late pre-B state. Deposited 2022-10-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric |
Chain 2G
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8H6J Cryo-EM structure of human exon-defined spliceosome in the mature pre-B state. Deposited 2022-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric |
Chain 2G
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 8H6K Cryo-EM structure of human exon-defined spliceosome in the mature B state. Deposited 2022-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 63-meric |
Chain 2G
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8H6L Cryo-EM structure of human exon-defined spliceosome in the early B state. Deposited 2022-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 59-meric |
Chain 2G
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8HK1 The cryo-EM structure of human pre-17S U2 snRNP Deposited 2022-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 20 PDB declaration: 21-meric |
Chain 1
1–1304（1304 aa）
|
Not recorded | 9B0 [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate × 1 ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8I0P The cryo-EM structure of human pre-Bact complex Deposited 2023-01-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 51-meric |
Chain 1
1–1304（1304 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8I0R The cryo-EM structure of human Bact-I complex Deposited 2023-01-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 55-meric |
Chain 1
1–1304（1304 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8I0S The cryo-EM structure of human Bact-II complex Deposited 2023-01-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric |
Chain 1
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7 ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 8I0T The cryo-EM structure of human Bact-III complex Deposited 2023-01-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric |
Chain 1
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7 ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8I0U The cryo-EM structure of human Bact-IV complex Deposited 2023-01-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric |
Chain 1
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7 ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8I0V The cryo-EM structure of human post-Bact complex Deposited 2023-01-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 51-meric |
Chain 1
1–1304（1304 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7 ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8QO9 Cryo-EM structure of a human spliceosomal B complex protomer Deposited 2023-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 71-meric |
Chain B1
1–1304（1304 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.29 Å |
| 8QXD Cryo-EM structure of the cross-exon pre-B complex Deposited 2023-10-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric |
Chain B1
1–1304（1304 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.60 Å |
| 8QZS Cryo-EM structure of the cross-exon B-like complex Deposited 2023-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 68-meric |
Chain B1
1–1304（1304 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8R08 Cryo-EM structure of the cross-exon pre-B+AMPPNP complex Deposited 2023-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 71-meric |
Chain B1
1–1304（1304 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.10 Å |
| 8R09 Cryo-EM structure of the cross-exon pre-B+5'ss+ATPgammaS complex Deposited 2023-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 60-meric |
Chain B1
1–1304（1304 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 8R0A Cryo-EM structure of the cross-exon pre-B+5'ss complex Deposited 2023-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 62-meric |
Chain B1
1–1304（1304 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.80 Å |
| 8R0B Cryo-EM structure of the cross-exon pre-B+ATP complex Deposited 2023-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 60-meric |
Chain B1
1–1304（1304 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 8RM5 Cryo-EM structure of the cross-exon pre-B+5'ssLNG+ATPyS complex Deposited 2024-01-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 60-meric |
Chain B1
1–1304（1304 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.90 Å |
| 8Y7E Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U12 snRNP part Deposited 2024-02-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 15 PDB declaration: heptadecameric |
Chain 1
1–1304（1304 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 4.66 Å |
| 9K1O Structure of SF3B core in complex with the 22-nt histone mRNA(SF3B-22-nt histone mRNA) Deposited 2024-10-16 | Different mutation/modification Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric |
Chain C
453–1304（852 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9K1Q Structure of SF3B core in complex with the 101-nt histone mRNA(SF3B-101-nt histone mRNA) Deposited 2024-10-16 | Different mutation/modification Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric |
Chain C
453–1304（852 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 9K1R Structure of SF3B core in complex with the intron-U2 snRNA (SF3B-intron-U2 snRNA) Deposited 2024-10-16 | Different mutation/modification Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric |
Chain C
453–1304（852 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 9K1W Structure of the SF3B core, harboring the K700E mutation in SF3B1, in complex with intron-U2 snRNA Deposited 2024-10-16 | Different mutation/modification Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric |
Chain C
453–1304（852 aa）
|
Mutation：K700E | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9R8V Cryo-EM structure of the human pre-Bact-OTS complex (whole map) Deposited 2025-05-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 63-meric |
Chain B1
1–1304（1304 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.50 Å |
| 9ZE0 Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (Proximal DHX15 state) Deposited 2025-11-26 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain B1
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；20 mM HEPES-KOH pH 7.9, 150 mM NaCl, 1.5 mM MgCl2, 10 mM DTT, 4.5% glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.43 Å |
| 9ZE2 Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (core) Deposited 2025-11-27 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain B1
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；20 mM HEPES-KOH pH 7.9, 150 mM NaCl, 1.5 mM MgCl2, 10 mM DTT, 4.5% glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.26 Å |
| 9ZE3 Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (Distal DHX15 state) Deposited 2025-11-27 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain B1
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；20 mM HEPES-KOH pH 7.9, 150 mM NaCl, 1.5 mM MgCl2, 10 mM DTT, 4.5% glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.93 Å |
| 9ZEC Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (SF3A state 1) Deposited 2025-11-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain B1
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；20 mM HEPES-KOH pH 7.9, 150 mM NaCl, 1.5 mM MgCl2, 10 mM DTT, 4.5% glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.61 Å |
| 9ZED Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (SF3A state 2) Deposited 2025-11-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain B1
1–1304（1304 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；20 mM HEPES-KOH pH 7.9, 150 mM NaCl, 1.5 mM MgCl2, 10 mM DTT, 4.5% glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.94 Å |
71 other PDB entries and 77 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | SF3B1_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain C； PDBConstruct 46–897； UniProt 453–1304 |
