U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 1–95 | Fragment：RNP DOMAIN RESIDUES 1-95 | No other associated polymer | X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；2M NA/K PHOSPHATE PH 5.5 | Resolution 2.40 Å R-free 0.242 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 1–95 | Fragment：RNP DOMAIN RESIDUES 1-95 | No other associated polymer | X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；2M NA/K PHOSPHATE PH 5.5 | Resolution 2.40 Å R-free 0.242 |
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 1OIA | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1AUD U1A-UTRRNA, NMR, 31 STRUCTURES Deposited 1997-08-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
2–102（101 aa）
Fragment：RESIDUES 1 - 102 OF U1A
|
Mutation：Y30H, Q35R | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
Ionic strength (raw mmCIF value) 50 mM NACL
|
Resolution not provided |
| 1DRZ U1A SPLICEOSOMAL PROTEIN/HEPATITIS DELTA VIRUS GENOMIC RIBOZYME COMPLEX Deposited 1998-09-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
2–98（97 aa）
Fragment：RNA BINDING DOMAIN
|
Mutation：Y31H, Q36R Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 3 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；pH 7.0
|
Resolution 2.30 Å R-free 0.284 |
| 1DZ5 The NMR structure of the 38KDa U1A protein-PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein Deposited 2000-02-16 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
2–102（101 aa）
Fragment：RESIDUES 2-102
Chain B
2–102（101 aa）
Fragment：RESIDUES 2-102
|
Mutation：YES Mutation：YES | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6；300 K；Ionic strength (raw mmCIF value) 10MM PHOSPHATE BUFFER；Pressure 1
NMR sample composition
10MM PHOSPHATE BUFFER
|
Resolution not provided |
| 1FHT RNA-BINDING DOMAIN OF THE U1A SPLICEOSOMAL PROTEIN U1A117, NMR, 43 STRUCTURES Deposited 1996-02-21 | Different construct Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–117（116 aa）
Fragment：N-TERMINAL DOMAIN
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1M5K Crystal structure of a hairpin ribozyme in the catalytically-active conformation Deposited 2002-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain F
1–100（100 aa）
Fragment：U1A RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | CA CALCIUM ION × 16 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；MPD, ammonium chloride, calcium chloride, pH 5.0, VAPOR DIFFUSION,
SITTING DROP at 300K, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.40 Å R-free 0.284 |
| 1M5K Crystal structure of a hairpin ribozyme in the catalytically-active conformation Deposited 2002-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain C
1–100（100 aa）
Fragment：U1A RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | CA CALCIUM ION × 17 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；MPD, ammonium chloride, calcium chloride, pH 5.0, VAPOR DIFFUSION,
SITTING DROP at 300K, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.40 Å R-free 0.284 |
| 1M5O Transition State Stabilization by a Catalytic RNA Deposited 2002-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain C
1–100（100 aa）
Fragment：U1A RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | CA CALCIUM ION × 20 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；MPD, calcium Chloride, ammonium chloride, meta-ammonium vanadate,
pH 5.0, VAPOR DIFFUSION, SITTING DROP at 300K
|
Resolution 2.20 Å R-free 0.264 |
| 1M5O Transition State Stabilization by a Catalytic RNA Deposited 2002-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain F
1–100（100 aa）
Fragment：U1A RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | CA CALCIUM ION × 17 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；MPD, calcium Chloride, ammonium chloride, meta-ammonium vanadate,
pH 5.0, VAPOR DIFFUSION, SITTING DROP at 300K
|
Resolution 2.20 Å R-free 0.264 |
| 1M5P Transition State Stabilization by a Catalytic RNA Deposited 2002-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain C
1–100（100 aa）
Fragment：U1A RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | CA CALCIUM ION × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；MPD, calcium Chloride, ammonium chloride, meta-ammonium vanadate,
pH 5.0, VAPOR DIFFUSION, SITTING DROP at 300K
|
Resolution 2.60 Å R-free 0.280 |
| 1M5P Transition State Stabilization by a Catalytic RNA Deposited 2002-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain F
1–100（100 aa）
Fragment：U1A RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | CA CALCIUM ION × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；MPD, calcium Chloride, ammonium chloride, meta-ammonium vanadate,
pH 5.0, VAPOR DIFFUSION, SITTING DROP at 300K
|
Resolution 2.60 Å R-free 0.280 |
| 1M5V Transition State Stabilization by a Catalytic RNA Deposited 2002-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain C
1–100（100 aa）
Fragment：U1A RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | CA CALCIUM ION × 13 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；MPD, ammonium chloride, calcium chloride,
pH 5.0, VAPOR DIFFUSION, SITTING DROP at 300K
|
Resolution 2.40 Å R-free 0.265 |
| 1M5V Transition State Stabilization by a Catalytic RNA Deposited 2002-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain F
1–100（100 aa）
Fragment：U1A RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | CA CALCIUM ION × 21 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；MPD, ammonium chloride, calcium chloride,
pH 5.0, VAPOR DIFFUSION, SITTING DROP at 300K
|
Resolution 2.40 Å R-free 0.265 |
| 1NU4 U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix Deposited 2003-01-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–98（97 aa）
Fragment：U1A RBD1
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 2 MLA MALONIC ACID × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；Potassium Malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.80 Å R-free 0.234 |
| 1NU4 U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix Deposited 2003-01-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–98（97 aa）
Fragment：U1A RBD1
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 3 MLA MALONIC ACID × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；Potassium Malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.80 Å R-free 0.234 |
| 1NU4 U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix Deposited 2003-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
2–98（97 aa）
Fragment：U1A RBD1
Chain B
2–98（97 aa）
Fragment：U1A RBD1
|
Mutation：Y31H,Q36R Mutation：Y31H,Q36R | MG MAGNESIUM ION × 15 MLA MALONIC ACID × 36 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；Potassium Malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.80 Å R-free 0.234 |
| 1NU4 U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix Deposited 2003-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain B
2–98（97 aa）
Fragment：U1A RBD1
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 9 MLA MALONIC ACID × 18 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；Potassium Malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.80 Å R-free 0.234 |
| 1NU4 U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix Deposited 2003-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
2–98（97 aa）
Fragment：U1A RBD1
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 6 MLA MALONIC ACID × 18 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；Potassium Malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.80 Å R-free 0.234 |
| 1NU4 U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix Deposited 2003-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
2–98（97 aa）
Fragment：U1A RBD1
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 4 MLA MALONIC ACID × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；Potassium Malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.80 Å R-free 0.234 |
| 1NU4 U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix Deposited 2003-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
2–98（97 aa）
Fragment：U1A RBD1
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 6 MLA MALONIC ACID × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；Potassium Malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.80 Å R-free 0.234 |
| 1SJ3 Hepatitis Delta Virus Gemonic Ribozyme Precursor, with Mg2+ Bound Deposited 2004-03-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain P
1–100（100 aa）
Fragment：RNA binding domain
|
Mutation：Y31H, Q36R | MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；NaCl, MgCl2, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.282 |
| 1SJ4 Crystal structure of a C75U mutant Hepatitis Delta Virus ribozyme precursor, in Cu2+ solution Deposited 2004-03-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain P
1–100（100 aa）
Fragment：RNA binding domain
|
Mutation：Y31H, Q36R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；NaCl, CuSO4, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.70 Å R-free 0.282 |
| 1SJF Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in Cobalt Hexammine solution Deposited 2004-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
1–100（100 aa）
Fragment：U1A_RBD(residues 1-100)
|
Mutation：Y31H/Q36R | NCO COBALT HEXAMMINE(III) × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；Cobalt Herxammine, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.75 Å R-free 0.275 |
| 1U6B CRYSTAL STRUCTURE OF A SELF-SPLICING GROUP I INTRON WITH BOTH EXONS Deposited 2004-07-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–98（98 aa）
|
Mutation：Y31H,Q36R | K POTASSIUM ION × 5 MG MAGNESIUM ION × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；pH 6.80
|
Resolution 3.10 Å R-free 0.279 |
| 1URN U1A MUTANT/RNA COMPLEX + GLYCEROL Deposited 1995-01-04 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
2–98（97 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
CRYSTALLIZATION CONDITIONS: 1.8M (NH4)2 SO4, 40MM TRIS-HCL
PH 7.0, 5MM SPERMINE TRANSFERRED TO 1.9M (NH4)2 SO4, 40MM
TRIS-HCL PH 7.0, 5MM SPERMINE, 25% GLYCEROL FOR 15 MINUTES
BEFORE FREEZING.
|
Resolution 1.92 Å |
| 1URN U1A MUTANT/RNA COMPLEX + GLYCEROL Deposited 1995-01-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain B
2–98（97 aa）
|
Not recorded | CL CHLORIDE ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
CRYSTALLIZATION CONDITIONS: 1.8M (NH4)2 SO4, 40MM TRIS-HCL
PH 7.0, 5MM SPERMINE TRANSFERRED TO 1.9M (NH4)2 SO4, 40MM
TRIS-HCL PH 7.0, 5MM SPERMINE, 25% GLYCEROL FOR 15 MINUTES
BEFORE FREEZING.
|
Resolution 1.92 Å |
| 1URN U1A MUTANT/RNA COMPLEX + GLYCEROL Deposited 1995-01-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain C
2–98（97 aa）
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
CRYSTALLIZATION CONDITIONS: 1.8M (NH4)2 SO4, 40MM TRIS-HCL
PH 7.0, 5MM SPERMINE TRANSFERRED TO 1.9M (NH4)2 SO4, 40MM
TRIS-HCL PH 7.0, 5MM SPERMINE, 25% GLYCEROL FOR 15 MINUTES
BEFORE FREEZING.
|
Resolution 1.92 Å |
| 1VBX Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in EDTA solution Deposited 2004-03-03 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
1–100（100 aa）
Fragment：U1A_RBD(residues 1-100)
|
Mutation：Y31H/Q36R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；NaCl, EDTA, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.70 Å R-free 0.285 |
| 1VBY Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, and Mn2+ bound Deposited 2004-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
1–100（100 aa）
Fragment：U1A_RBD(residues 1-100)
|
Mutation：Y31H/Q36R | MN MANGANESE (II) ION × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；MnCl2, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.90 Å R-free 0.284 |
| 1VBZ Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in Ba2+ solution Deposited 2004-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
1–100（100 aa）
Fragment：U1A_RBD(residues 1-100)
|
Mutation：Y31H/Q36R | BA BARIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；BaCl2, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.268 |
| 1VC0 Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in Imidazole and Sr2+ solution Deposited 2004-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
1–100（100 aa）
Fragment：U1A_RBD(residues 1-100)
|
Mutation：Y31H/Q36R | SR STRONTIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；SrCl2, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.50 Å R-free 0.273 |
| 1VC5 Crystal Structure of the Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in EDTA solution Deposited 2004-03-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
1–100（100 aa）
Fragment：U1A_RBD(residues 1-100)
|
Mutation：Y31H/Q36R | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；EDTA, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.40 Å R-free 0.327 |
| 1VC6 Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Product with C75U Mutaion, cleaved in Imidazole and Mg2+ solutions Deposited 2004-03-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
1–100（100 aa）
Fragment：U1A_RBD(residues 1-100)
|
Mutation：Y31H/Q36R | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Imidazole, Mg2+, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.284 |
| 1ZZN Crystal structure of a group I intron/two exon complex that includes all catalytic metal ion ligands. Deposited 2005-06-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–97（97 aa）
Fragment：RRM 1
|
Mutation：Y31H, Q36R | MG MAGNESIUM ION × 5 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；MPD, sodium cacodylate, magnesium acetate, potassium chloride, cobalt heximine, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.37 Å R-free 0.307 |
| 2A3J Structure of URNdesign, a complete computational redesign of human U1A protein Deposited 2005-06-24 | Different construct Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–80（78 aa）
Fragment：RNA binding domain, residues 2-97
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；298 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate；Pressure ambient
NMR sample composition
U-15N,variant of U1A, 50 mM Sodium Phosphate,5% D2O | 5% D2O in water
NMR sample composition
U-15N, 13C, variant of U1A, 50 mM Sodium Phosphate, 5% D2O | 5% D2O in water
|
Resolution not provided |
| 2NZ4 Structural investigation of the GlmS ribozyme bound to its catalytic cofactor Deposited 2006-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
4–97（94 aa）
Fragment：RNA Binding Domain
|
Mutation：Y31H, Q36R | GLP 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 1 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M sodium cacodylate pH 6.8, 0.02M magnesium chloride, 0.15M potassium chloride, 0.002M glucosamine 6 phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.50 Å R-free 0.269 |
| 2NZ4 Structural investigation of the GlmS ribozyme bound to its catalytic cofactor Deposited 2006-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain B
4–97（94 aa）
Fragment：RNA Binding Domain
|
Mutation：Y31H, Q36R | GLP 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 1 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M sodium cacodylate pH 6.8, 0.02M magnesium chloride, 0.15M potassium chloride, 0.002M glucosamine 6 phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.50 Å R-free 0.269 |
| 2NZ4 Structural investigation of the GlmS ribozyme bound to its catalytic cofactor Deposited 2006-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain C
4–97（94 aa）
Fragment：RNA Binding Domain
|
Mutation：Y31H, Q36R | GLP 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 1 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M sodium cacodylate pH 6.8, 0.02M magnesium chloride, 0.15M potassium chloride, 0.002M glucosamine 6 phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.50 Å R-free 0.269 |
| 2NZ4 Structural investigation of the GlmS ribozyme bound to its catalytic cofactor Deposited 2006-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain D
4–97（94 aa）
Fragment：RNA Binding Domain
|
Mutation：Y31H, Q36R | GLP 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 1 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M sodium cacodylate pH 6.8, 0.02M magnesium chloride, 0.15M potassium chloride, 0.002M glucosamine 6 phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.50 Å R-free 0.269 |
| 2OIH Hepatitis Delta Virus gemonic ribozyme precursor with C75U mutation and bound to monovalent cation Tl+ Deposited 2007-01-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
1–99（99 aa）
|
Not recorded | TL THALLIUM (I) ION × 15 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；containing 5-10% (v/v) MPD, 50 mM sodium cacodylate, pH 6.0, 40-80 mM NaCl, 30 mM SrCl2, and 15-50 mM spermine HCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.40 Å R-free 0.288 |
| 2OJ3 Hepatitis Delta Virus ribozyme precursor structure, with C75U mutation, bound to Tl+ and cobalt hexammine (Co(NH3)63+) Deposited 2007-01-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
1–99（99 aa）
|
Not recorded | NCO COBALT HEXAMMINE(III) × 2 TL THALLIUM (I) ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；5-10% (v/v) MPD, 50 mM sodium cacodylate, pH 6.0, 40-80 mM NaCl, 30 mM SrCl2, and 15-50 mM spermine HCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.90 Å R-free 0.263 |
| 2U1A RNA BINDING DOMAIN 2 OF HUMAN U1A PROTEIN, NMR, 20 STRUCTURES Deposited 1997-03-26 | Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
195–282（88 aa）
Fragment：RNA BINDING DOMAIN 2, RBD2
|
Mutation：P2A | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 5.5；298 K
|
Resolution not provided |
| 3BO2 A relaxed active site following exon ligation by a group I intron Deposited 2007-12-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: pentameric |
Chain A
4–98（95 aa）
Fragment：RRM 1 domain
|
Not recorded | MG MAGNESIUM ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；298 K；MPD, Sodium Cacodylate, Magnesium Acetate, Potassium Acetate, Cobalt Hexamine, Potassium Vanadate, pH 6.80, vapor diffusion, hanging drop, temperature 298K
|
Resolution 3.31 Å R-free 0.321 |
| 3BO3 A relaxed active site following exon ligation by a group I intron Deposited 2007-12-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
4–98（95 aa）
Fragment：RRM 1 domain
|
Not recorded | MG MAGNESIUM ION × 13 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；298 K；MPD, Sodium Cacodylate, Magnesium Acetate, Potassium Acetate, Cobalt Hexamine, pH 6.80, vapor diffusion, hanging drop, temperature 298K
|
Resolution 3.40 Å R-free 0.325 |
| 3BO4 A relaxed active site following exon ligation by a group I intron Deposited 2007-12-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
4–98（95 aa）
Fragment：RRM 1 domain
|
Not recorded | MG MAGNESIUM ION × 12 K POTASSIUM ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；298 K；MPD, Sodium Cacodylate, Magnesium Acetate, Potassium Acetate, Cobalt Hexamine, Potassium Vanadate, pH 6.80, vapor diffusion, hanging drop, temperature 298K
|
Resolution 3.33 Å R-free 0.296 |
| 3CUL Aminoacyl-tRNA synthetase ribozyme Deposited 2008-04-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
1–98（98 aa）
Fragment：UNP residues 1-98
|
Mutation：Y31H, Q36R Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 8 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；295 K；100 mM magnesium formate, 15% PEG 3000, 1 M lithium chloride, pH 7.0, VAPOR DIFFUSION, temperature 295K
|
Resolution 2.80 Å R-free 0.283 |
| 3CUL Aminoacyl-tRNA synthetase ribozyme Deposited 2008-04-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain B
1–98（98 aa）
Fragment：UNP residues 1-98
|
Mutation：Y31H, Q36R Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；295 K；100 mM magnesium formate, 15% PEG 3000, 1 M lithium chloride, pH 7.0, VAPOR DIFFUSION, temperature 295K
|
Resolution 2.80 Å R-free 0.283 |
| 3CUN Aminoacyl-tRNA synthetase ribozyme Deposited 2008-04-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
1–98（98 aa）
Fragment：UNP residues 1-98
|
Mutation：Y31H, Q36R Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 5 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；295 K；100 mM magenesium formate pH 7.0, 15% PEG 3000, 1 M lithium chloride, VAPOR DIFFUSION, temperature 295K
|
Resolution 3.00 Å R-free 0.303 |
| 3CUN Aminoacyl-tRNA synthetase ribozyme Deposited 2008-04-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain B
1–98（98 aa）
Fragment：UNP residues 1-98
|
Mutation：Y31H, Q36R Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 4 CO COBALT (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；295 K；100 mM magenesium formate pH 7.0, 15% PEG 3000, 1 M lithium chloride, VAPOR DIFFUSION, temperature 295K
|
Resolution 3.00 Å R-free 0.303 |
| 3EGZ Crystal structure of an in vitro evolved tetracycline aptamer and artificial riboswitch Deposited 2008-09-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 4 PDB declaration: octameric |
Chain A
1–98（98 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 48 CTC 7-CHLOROTETRACYCLINE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；296 K；0.3 mM RNA, 0.33 mM selenomethionine labeled U1A-RBD double mutant, 0.5 mM chlorotetracycline, 50 mM Tris pH 7.5, 5 mM MgCl2, 0.25 mM spermine; 1uL macromolecular complex:1 uL reservoir; 50 mM HEPES-KOH pH 7.0, 20 mM MGCl2, 12.5-15% PEG 8000; cryo 30% glycerol, 50 mM HEPES-KOH pH 7.0, 20 mM MGCl2, 15% PEG 8000, 0.5 mM spermine, 0.5 mM chlorotetracycline, VAPOR DIFFUSION, SITTING DROP, temperature 296K
|
Resolution 2.20 Å R-free 0.260 |
| 3G8S Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme Deposited 2009-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–98（98 aa）
Fragment：RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K, VAPOR DIFFUSION, SITTING DROP
|
Resolution 3.10 Å R-free 0.306 |
| 3G8S Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme Deposited 2009-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain B
1–98（98 aa）
Fragment：RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K, VAPOR DIFFUSION, SITTING DROP
|
Resolution 3.10 Å R-free 0.306 |
| 3G8S Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme Deposited 2009-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain C
1–98（98 aa）
Fragment：RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K, VAPOR DIFFUSION, SITTING DROP
|
Resolution 3.10 Å R-free 0.306 |
| 3G8S Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme Deposited 2009-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain D
1–98（98 aa）
Fragment：RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K, VAPOR DIFFUSION, SITTING DROP
|
Resolution 3.10 Å R-free 0.306 |
| 3G8T Crystal structure of the G33A mutant Bacillus anthracis glmS ribozyme bound to GlcN6P Deposited 2009-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–98（98 aa）
Fragment：RNA BINDING DOMAIN (UNP residues 1 to 98)
|
Mutation：Y31H,Q36R | GLP 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 3.00 Å R-free 0.318 |
| 3G8T Crystal structure of the G33A mutant Bacillus anthracis glmS ribozyme bound to GlcN6P Deposited 2009-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain B
1–98（98 aa）
Fragment：RNA BINDING DOMAIN (UNP residues 1 to 98)
|
Mutation：Y31H,Q36R | GLP 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 1 MG MAGNESIUM ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 3.00 Å R-free 0.318 |
| 3G8T Crystal structure of the G33A mutant Bacillus anthracis glmS ribozyme bound to GlcN6P Deposited 2009-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain C
1–98（98 aa）
Fragment：RNA BINDING DOMAIN (UNP residues 1 to 98)
|
Mutation：Y31H,Q36R | GLP 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 1 MG MAGNESIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 3.00 Å R-free 0.318 |
| 3G8T Crystal structure of the G33A mutant Bacillus anthracis glmS ribozyme bound to GlcN6P Deposited 2009-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain D
1–98（98 aa）
Fragment：RNA BINDING DOMAIN (UNP residues 1 to 98)
|
Mutation：Y31H,Q36R | GLP 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 3.00 Å R-free 0.318 |
| 3G96 Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P Deposited 2009-02-12 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–98（98 aa）
Fragment：RNA BINDING DOMAIN (UNP residues 1 to 98)
|
Mutation：Y31H,Q36R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 3.01 Å R-free 0.311 |
| 3G96 Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P Deposited 2009-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain B
1–98（98 aa）
Fragment：RNA BINDING DOMAIN (UNP residues 1 to 98)
|
Mutation：Y31H,Q36R | 6MN 2-amino-2-deoxy-6-O-phosphono-alpha-D-mannopyranose × 1 MG MAGNESIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 3.01 Å R-free 0.311 |
| 3G96 Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P Deposited 2009-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain C
1–98（98 aa）
Fragment：RNA BINDING DOMAIN (UNP residues 1 to 98)
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 3.01 Å R-free 0.311 |
| 3G96 Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P Deposited 2009-02-12 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain D
1–98（98 aa）
Fragment：RNA BINDING DOMAIN (UNP residues 1 to 98)
|
Mutation：Y31H,Q36R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 3.01 Å R-free 0.311 |
| 3G9C Crystal structure of the product Bacillus anthracis glmS ribozyme Deposited 2009-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–98（98 aa）
Fragment：RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | GLP 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 2.90 Å R-free 0.307 |
| 3G9C Crystal structure of the product Bacillus anthracis glmS ribozyme Deposited 2009-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain B
1–98（98 aa）
Fragment：RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 2.90 Å R-free 0.307 |
| 3G9C Crystal structure of the product Bacillus anthracis glmS ribozyme Deposited 2009-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain C
1–98（98 aa）
Fragment：RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 2.90 Å R-free 0.307 |
| 3G9C Crystal structure of the product Bacillus anthracis glmS ribozyme Deposited 2009-02-13 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain D
1–98（98 aa）
Fragment：RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 2.90 Å R-free 0.307 |
| 3HHN Crystal structure of class I ligase ribozyme self-ligation product, in complex with U1A RBD Deposited 2009-05-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain B
2–98（97 aa）
Fragment：RNA binding domain: UNP residues 1-100
Chain D
2–98（97 aa）
Fragment：RNA binding domain: UNP residues 1-100
|
Mutation：Y31H, Q31R Mutation：Y31H, Q31R | MG MAGNESIUM ION × 34 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；50mM Sodium cacodylate pH 6.0, 40mM Magnesium acetate, 26% 2-methyl-2,4-pentane diol (MPD), 1mM Spermine HCl. Diffraction-quality crystals grown by microseeding., VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.99 Å R-free 0.234 |
| 3IIN Plasticity of the kink turn structural motif Deposited 2009-08-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
4–98（95 aa）
Fragment：UNP residues 4-98, RRM 1, U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A RNA BINDING DOMAIN
|
Mutation：Y31H, Q36R | K POTASSIUM ION × 5 MG MAGNESIUM ION × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；MPD, Sodium Cacodylate, Magnesium Acetate, Potassium Acetate, Cobalt Hexamine, pH 6.8, vapor diffusion, hanging drop, temperature 298K
|
Resolution 4.18 Å R-free 0.323 |
| 3IRW Structure of a c-di-GMP riboswitch from V. cholerae Deposited 2009-08-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain P
1–98（98 aa）
Fragment：RNA Binding Domain
|
Mutation：Y31H, Q36R | C2E 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) × 1 IRI IRIDIUM HEXAMMINE ION × 9 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；298 K；22% PEG550mme, 50 mM MES, pH 6.0, 5 mM MgSO4, 300 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.70 Å R-free 0.251 |
| 3IWN Co-crystal structure of a bacterial c-di-GMP riboswitch Deposited 2009-09-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain C
6–96（91 aa）
Fragment：UNP residues 6-96, RRM 1 domain
|
Mutation：Y31H, Q36R | C2E 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；303 K；30% PEG3350
0.1M Tris pH8.5
0.3M ammonium acetate pH7.0
3mM MgCl2
1 mM spermine
, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
|
Resolution 3.20 Å R-free 0.292 |
| 3IWN Co-crystal structure of a bacterial c-di-GMP riboswitch Deposited 2009-09-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain D
6–96（91 aa）
Fragment：UNP residues 6-96, RRM 1 domain
|
Mutation：Y31H, Q36R | C2E 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；303 K；30% PEG3350
0.1M Tris pH8.5
0.3M ammonium acetate pH7.0
3mM MgCl2
1 mM spermine
, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
|
Resolution 3.20 Å R-free 0.292 |
| 3K0J Crystal structure of the E. coli ThiM riboswitch in complex with thiamine pyrophosphate and the U1A crystallization module Deposited 2009-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain A
2–97（96 aa）
Fragment：UNP residues 2-97, RRM 1 domain
Chain C
2–97（96 aa）
Fragment：UNP residues 2-97, RRM 1 domain
|
Mutation：Y231H,Q236R Mutation：Y231H,Q236R | TPP THIAMINE DIPHOSPHATE × 1 MG MAGNESIUM ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.6；298 K；20% (v/v) PEG 550 MME, 20% MPD, and 80 mM sodium citrate (pH 5.6), VAPOR DIFFUSION, temperature 298K
|
Resolution 3.10 Å R-free 0.279 |
| 3K0J Crystal structure of the E. coli ThiM riboswitch in complex with thiamine pyrophosphate and the U1A crystallization module Deposited 2009-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain B
2–97（96 aa）
Fragment：UNP residues 2-97, RRM 1 domain
Chain D
2–97（96 aa）
Fragment：UNP residues 2-97, RRM 1 domain
|
Mutation：Y231H,Q236R Mutation：Y231H,Q236R | TPP THIAMINE DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.6；298 K；20% (v/v) PEG 550 MME, 20% MPD, and 80 mM sodium citrate (pH 5.6), VAPOR DIFFUSION, temperature 298K
|
Resolution 3.10 Å R-free 0.279 |
| 3L3C Crystal structure of the Bacillus anthracis glmS ribozyme bound to Glc6P Deposited 2009-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
7–96（90 aa）
Fragment：RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 4 G6P 6-O-phosphono-alpha-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 2.85 Å R-free 0.303 |
| 3L3C Crystal structure of the Bacillus anthracis glmS ribozyme bound to Glc6P Deposited 2009-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain B
7–96（90 aa）
Fragment：RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 4 G6P 6-O-phosphono-alpha-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 2.85 Å R-free 0.303 |
| 3L3C Crystal structure of the Bacillus anthracis glmS ribozyme bound to Glc6P Deposited 2009-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain C
7–96（90 aa）
Fragment：RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 4 G6P 6-O-phosphono-alpha-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 2.85 Å R-free 0.303 |
| 3L3C Crystal structure of the Bacillus anthracis glmS ribozyme bound to Glc6P Deposited 2009-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain D
7–96（90 aa）
Fragment：RNA BINDING DOMAIN
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 4 G6P 6-O-phosphono-alpha-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
|
Resolution 2.85 Å R-free 0.303 |
| 3MUM Crystal Structure of the G20A mutant c-di-GMP riboswith bound to c-di-GMP Deposited 2010-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain P
1–98（98 aa）
Fragment：UNP residues 1-98
|
Mutation：Y31H, Q36R | C2E 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；22% PEG 550 MME, 5 mM MgSO4, 50 mM MES, pH 6.0, 300 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.90 Å R-free 0.265 |
| 3MUR Crystal Structure of the C92U mutant c-di-GMP riboswith bound to c-di-GMP Deposited 2010-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain P
1–98（98 aa）
Fragment：UNP residues 1-98
|
Mutation：Y31H, Q36R | C2E 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；25% PEG 550 MME, 5 mM MgSO4, 50 mM MES, pH 6.0, 300 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.00 Å R-free 0.252 |
| 3MUT Crystal Structure of the G20A/C92U mutant c-di-GMP riboswith bound to c-di-GMP Deposited 2010-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain P
1–98（98 aa）
Fragment：UNP residues 1-98
|
Mutation：Y31H, Q36R | C2E 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；25% PEG 550 MME, 5 mM MgSO4, 50 mM MES, pH 6.0, 300 mM NaCl. Streak seeding after 3-6 hours, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.00 Å R-free 0.268 |
| 3MUV Crystal Structure of the G20A/C92U mutant c-di-GMP riboswith bound to c-di-AMP Deposited 2010-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain P
1–98（98 aa）
Fragment：UNP residues 1-98
|
Mutation：Y31H, Q36R | 2BA (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；298 K；25% PEG 550 MME, 5 mM MgSO4, 50 mM MES, pH 6.0, 300 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.20 Å R-free 0.260 |
| 3MXH Native structure of a c-di-GMP riboswitch from V. cholerae Deposited 2010-05-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain P
1–98（98 aa）
Fragment：UNP residues 1-98
|
Mutation：Y31H, Q36R | MG MAGNESIUM ION × 5 C2E 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；22% PEG550mme, 50 mM MES, pH 6.0, 5 mM MgSO4, 300 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.239 |
| 3P49 Crystal Structure of a Glycine Riboswitch from Fusobacterium nucleatum Deposited 2010-10-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain B
1–98（98 aa）
Fragment：RNA BINDING DOMAIN (UNP RESIDUES 1-98)
|
Mutation：Y31H Q36R | MG MAGNESIUM ION × 13 GLY GLYCINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% PEGmme550, 0.05M HEPES PH 7.0, 0.01M MgCL2, 0.025M NaOAC pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.55 Å R-free 0.310 |
| 3PGW Crystal structure of human U1 snRNP Deposited 2010-11-02 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–282（282 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；8-10% PEG 4000, 0.1 M Trisodium citrate, 2 mM EDTA, 100 mM NaCl, 1-2% Anapoe X-305, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 4.40 Å R-free 0.348 |
| 3PGW Crystal structure of human U1 snRNP Deposited 2010-11-02 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 9 PDB declaration: undecameric |
Chain P
1–282（282 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；8-10% PEG 4000, 0.1 M Trisodium citrate, 2 mM EDTA, 100 mM NaCl, 1-2% Anapoe X-305, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 4.40 Å R-free 0.348 |
| 3R1H Crystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Ca2+ bound Deposited 2011-03-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–98（98 aa）
Fragment：RNA binding domain (UNP residues 1-98)
|
Mutation：Y31H,Q36R | CA CALCIUM ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；50 mM sodium cacodylate, pH 6.0, 20 mM calcium acetate, 10 mM strontium acetate, 1mM spermine, 16-20% MPD, crystals in same conditions with 30% MPD were crushed and used as microseeding stocks, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.15 Å R-free 0.255 |
| 3R1H Crystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Ca2+ bound Deposited 2011-03-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain D
1–98（98 aa）
Fragment：RNA binding domain (UNP residues 1-98)
|
Mutation：Y31H,Q36R | CA CALCIUM ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；50 mM sodium cacodylate, pH 6.0, 20 mM calcium acetate, 10 mM strontium acetate, 1mM spermine, 16-20% MPD, crystals in same conditions with 30% MPD were crushed and used as microseeding stocks, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.15 Å R-free 0.255 |
| 3R1L Crystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Mg2+ bound Deposited 2011-03-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–98（98 aa）
Fragment：RNA binding domain (UNP residues 1-98)
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 25 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；50 mM sodium cacodylate, pH 6.0, 20 mM calcium chloride, 10 mM strontium chloride, 1 mM spermine, 26% MPD, crystals were crushed and used as microseeding stocks, calcium chloride was replaced with magnesium chloride prior to freezing, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.12 Å R-free 0.240 |
| 3R1L Crystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Mg2+ bound Deposited 2011-03-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain D
1–98（98 aa）
Fragment：RNA binding domain (UNP residues 1-98)
|
Mutation：Y31H,Q36R | MG MAGNESIUM ION × 21 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；50 mM sodium cacodylate, pH 6.0, 20 mM calcium chloride, 10 mM strontium chloride, 1 mM spermine, 26% MPD, crystals were crushed and used as microseeding stocks, calcium chloride was replaced with magnesium chloride prior to freezing, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.12 Å R-free 0.240 |
| 3UCU The c-di-GMP-I riboswitch bound to pGpG Deposited 2011-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain P
1–98（98 aa）
Fragment：RNA binding domain, UNP residues 1-98
|
Mutation：Y31H, Q36R | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；24% PEG550mme, 50 mM MES, pH 6.0, 5 mM MgSO4, 300 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.80 Å R-free 0.262 |
| 3UCZ The c-di-GMP-I riboswitch bound to GpG Deposited 2011-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain P
1–98（98 aa）
Fragment：RNA binding domain, UNP residues 1-98
|
Mutation：Y31H, Q36R | MG MAGNESIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；24% PEG550mme, 50 mM MES, pH 6.0, 5 mM MgSO4, 300 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.80 Å R-free 0.269 |
| 3UD3 The C92U mutant c-di-GMP-I riboswitch bound to pGpA Deposited 2011-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain P
1–98（98 aa）
Fragment：RNA binding domain, UNP residues 1-98
|
Mutation：Y31H, Q36R | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；26% PEG550mme, 50 mM MES, pH 6.0, 5 mM MgSO4, 300 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.10 Å R-free 0.258 |
| 3UD4 The C92U mutant c-di-GMP-I riboswitch bound to GpA Deposited 2011-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain P
1–98（98 aa）
Fragment：RNA binding domain, UNP residues 1-98
|
Mutation：Y31H, Q36R | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；24% PEG550mme, 50 mM MES, pH 6.0, 5 mM MgSO4, 300 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.70 Å R-free 0.290 |
| 4C4W Structure of a rare, non-standard sequence k-turn bound by L7Ae protein Deposited 2013-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric |
Chain A
1–102（102 aa）
Fragment：RRM 1 DOMAIN, RESIDUES 1-102
Chain B
1–102（102 aa）
Fragment：RRM 1 DOMAIN, RESIDUES 1-102
|
Not recorded | 2HP DIHYDROGENPHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；100 MM TRISHCL 8.5 AND 2.0 M MONO-AMMONIUM DIHYDROGEN PHOSPHATE
|
Resolution 2.95 Å R-free 0.211 |
| 4C4W Structure of a rare, non-standard sequence k-turn bound by L7Ae protein Deposited 2013-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric |
Chain E
1–102（102 aa）
Fragment：RRM 1 DOMAIN, RESIDUES 1-102
Chain F
1–102（102 aa）
Fragment：RRM 1 DOMAIN, RESIDUES 1-102
|
Not recorded | 2HP DIHYDROGENPHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；100 MM TRISHCL 8.5 AND 2.0 M MONO-AMMONIUM DIHYDROGEN PHOSPHATE
|
Resolution 2.95 Å R-free 0.211 |
| 4PR6 A Second Look at the HDV Ribozyme Structure and Dynamics. Deposited 2014-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
4–96（93 aa）
Fragment：RNA BINDING DOMAIN, UNP residues 101-244
|
Mutation：Y31H, Q36R Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 16 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG MME 2000, LITHIUM SULPHATE, SPERMINE, TRIS, COBALT HEXAMMINE, MAGNESIUM
CHLORIDE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.241 |
| 4PRF A Second Look at the HDV Ribozyme Structure and Dynamics. Deposited 2014-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
1–100（100 aa）
Fragment：U1A_RBD, UNP residues 98-173
|
Mutation：Y31H, Q36R | SR STRONTIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；SrCl2, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.40 Å R-free 0.252 |
| 4W90 Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO Deposited 2014-08-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain B
6–96（91 aa）
|
Mutation：Y31H, Q36R Non-standard monomer：Yes (specific site not provided by mmCIF) | 2BA (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide × 2 MG MAGNESIUM ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；PEG 3350
|
Resolution 3.12 Å R-free 0.288 |
| 4W92 Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO Deposited 2014-08-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain B
6–96（91 aa）
Fragment：unp residues 6-96
|
Mutation：Y31H, Q36R Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 5 K POTASSIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 2BA (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；PEG 3350
|
Resolution 3.21 Å R-free 0.289 |
| 4YB1 20A Mutant c-di-GMP Vc2 Riboswitch bound with 3',3'-cGAMP Deposited 2015-02-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain P
7–97（91 aa）
Fragment：UNP residues 7-97
|
Not recorded | MG MAGNESIUM ION × 1 4BW 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M Na-citrate pH 5.5, 5% PEG1000, 35% iso-propanol
|
Resolution 2.08 Å R-free 0.298 |
| 5DDO Structural and Dynamic Basis for Low Affinity-High Selectivity Binding of L-glutamine by the Gln-riboswitch Deposited 2015-08-25 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain G
2–98（97 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.2 M Na-formate, 21% (w/v) PEG3350
|
Resolution 3.10 Å R-free 0.289 |
| 5DDO Structural and Dynamic Basis for Low Affinity-High Selectivity Binding of L-glutamine by the Gln-riboswitch Deposited 2015-08-25 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain C
2–98（97 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.2 M Na-formate, 21% (w/v) PEG3350
|
Resolution 3.10 Å R-free 0.289 |
| 5DDP L-glutamine riboswitch bound with L-glutamine Deposited 2015-08-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain D
2–98（97 aa）
|
Not recorded | GLN GLUTAMINE × 1 MG MAGNESIUM ION × 5 NA SODIUM ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.1 M HEPES-sodium, pH 7.0, 40% (v/v) 2-methyl-2,4-pentanediol
|
Resolution 2.30 Å R-free 0.243 |
| 5DDP L-glutamine riboswitch bound with L-glutamine Deposited 2015-08-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain C
2–98（97 aa）
|
Not recorded | GLN GLUTAMINE × 1 MG MAGNESIUM ION × 4 NA SODIUM ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.1 M HEPES-sodium, pH 7.0, 40% (v/v) 2-methyl-2,4-pentanediol
|
Resolution 2.30 Å R-free 0.243 |
| 5DDQ L-glutamine riboswitch bound with L-glutamine soaked with Mn2+ Deposited 2015-08-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain D
2–98（97 aa）
|
Not recorded | GLN GLUTAMINE × 1 MN MANGANESE (II) ION × 3 MG MAGNESIUM ION × 1 NA SODIUM ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.1 M HEPES-sodium, pH 7.0, 40% (v/v) 2-methyl-2,4-pentanediol, 2 mM MnCl2
|
Resolution 2.40 Å R-free 0.257 |
| 5DDQ L-glutamine riboswitch bound with L-glutamine soaked with Mn2+ Deposited 2015-08-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain C
2–98（97 aa）
|
Not recorded | GLN GLUTAMINE × 1 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.1 M HEPES-sodium, pH 7.0, 40% (v/v) 2-methyl-2,4-pentanediol, 2 mM MnCl2
|
Resolution 2.40 Å R-free 0.257 |
| 5DDR L-glutamine riboswitch bound with L-glutamine soaked with Cs+ Deposited 2015-08-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain D
2–98（97 aa）
|
Not recorded | GLN GLUTAMINE × 1 K POTASSIUM ION × 4 MG MAGNESIUM ION × 6 CS CESIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；.1 M HEPES-sodium, pH 7.0, 40% (v/v) 2-methyl-2,4-pentanediol, 20 mM CsCl
|
Resolution 2.60 Å R-free 0.271 |
| 5DDR L-glutamine riboswitch bound with L-glutamine soaked with Cs+ Deposited 2015-08-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain C
2–98（97 aa）
|
Not recorded | GLN GLUTAMINE × 1 K POTASSIUM ION × 3 MG MAGNESIUM ION × 5 CS CESIUM ION × 4 NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；.1 M HEPES-sodium, pH 7.0, 40% (v/v) 2-methyl-2,4-pentanediol, 20 mM CsCl
|
Resolution 2.60 Å R-free 0.271 |
| 5FJ4 Structure of the standard kink turn HmKt-7 as stem loop bound with U1A and L7Ae proteins Deposited 2015-10-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric |
Chain A
1–102（102 aa）
Fragment：RRM 1 DOMAIN, UNP RESIDUES 1-102
Chain B
1–102（102 aa）
Fragment：RRM 1 DOMAIN, UNP RESIDUES 1-102
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1 M TRIS HYDROCHLORIDE PH 8.5, 2.0 M MONO-AMMONIUM DIHYDROGEN PHOSPHATE
|
Resolution 2.95 Å R-free 0.237 |
| 5FJ4 Structure of the standard kink turn HmKt-7 as stem loop bound with U1A and L7Ae proteins Deposited 2015-10-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric |
Chain E
1–102（102 aa）
Fragment：RRM 1 DOMAIN, UNP RESIDUES 1-102
Chain F
1–102（102 aa）
Fragment：RRM 1 DOMAIN, UNP RESIDUES 1-102
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1 M TRIS HYDROCHLORIDE PH 8.5, 2.0 M MONO-AMMONIUM DIHYDROGEN PHOSPHATE
|
Resolution 2.95 Å R-free 0.237 |
| 6LAS the wildtype SAM-VI riboswitch bound to SAM Deposited 2019-11-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain E
6–96（91 aa）
|
Mutation：Y31H, Q36R, S46K Non-standard monomer：Yes (specific site not provided by mmCIF) | SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M sodium acetate trihydrate pH 4.6, 10% w/v polyethylene glycol 4,000
|
Resolution 2.71 Å R-free 0.244 |
| 6LAS the wildtype SAM-VI riboswitch bound to SAM Deposited 2019-11-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain C
6–96（91 aa）
|
Mutation：Y31H, Q36R, S46K Non-standard monomer：Yes (specific site not provided by mmCIF) | SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M sodium acetate trihydrate pH 4.6, 10% w/v polyethylene glycol 4,000
|
Resolution 2.71 Å R-free 0.244 |
| 6LAS the wildtype SAM-VI riboswitch bound to SAM Deposited 2019-11-13 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
6–96（91 aa）
|
Mutation：Y31H, Q36R, S46K 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, SITTING DROP；289 K；0.1 M sodium acetate trihydrate pH 4.6, 10% w/v polyethylene glycol 4,000
|
Resolution 2.71 Å R-free 0.244 |
| 6LAU the wildtype SAM-VI riboswitch bound to SAH Deposited 2019-11-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain E
6–96（91 aa）
|
Mutation：Y31H, Q36R, S46K Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 CS CESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M sodium acetate trihydrate pH 4.6, 10% w/v polyethylene glycol 4,000
|
Resolution 3.11 Å R-free 0.252 |
| 6LAU the wildtype SAM-VI riboswitch bound to SAH Deposited 2019-11-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain C
6–96（91 aa）
|
Mutation：Y31H, Q36R, S46K Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M sodium acetate trihydrate pH 4.6, 10% w/v polyethylene glycol 4,000
|
Resolution 3.11 Å R-free 0.252 |
| 6LAU the wildtype SAM-VI riboswitch bound to SAH Deposited 2019-11-13 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
6–96（91 aa）
|
Mutation：Y31H, Q36R, S46K 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, SITTING DROP；289 K；0.1 M sodium acetate trihydrate pH 4.6, 10% w/v polyethylene glycol 4,000
|
Resolution 3.11 Å R-free 0.252 |
| 6LAX the mutant SAM-VI riboswitch (U6C) bound to SAM Deposited 2019-11-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain E
6–96（91 aa）
|
Mutation：Y31H, Q36R, S46K Non-standard monomer：Yes (specific site not provided by mmCIF) | SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；sodium acetate trihydrate, polyethylene glycol 4,000
|
Resolution 2.70 Å R-free 0.239 |
| 6LAX the mutant SAM-VI riboswitch (U6C) bound to SAM Deposited 2019-11-13 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
6–96（91 aa）
|
Mutation：Y31H, Q36R, S46K 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, SITTING DROP；289 K；sodium acetate trihydrate, polyethylene glycol 4,000
|
Resolution 2.70 Å R-free 0.239 |
| 6LAX the mutant SAM-VI riboswitch (U6C) bound to SAM Deposited 2019-11-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain C
6–96（91 aa）
|
Mutation：Y31H, Q36R, S46K Non-standard monomer：Yes (specific site not provided by mmCIF) | SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；sodium acetate trihydrate, polyethylene glycol 4,000
|
Resolution 2.70 Å R-free 0.239 |
| 6LAZ the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1 Deposited 2019-11-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain E
6–96（91 aa）
|
Mutation：Y31H, Q36R, S46K | MG MAGNESIUM ION × 1 E7X (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-hydroxyethyl)amino]-2-azaniumyl-butanoate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M sodium acetate trihydrate pH 4.6, 10% w/v polyethylene glycol 4,000
|
Resolution 2.76 Å R-free 0.223 |
| 6LAZ the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1 Deposited 2019-11-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain C
6–96（91 aa）
|
Mutation：Y31H, Q36R, S46K | E7X (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-hydroxyethyl)amino]-2-azaniumyl-butanoate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M sodium acetate trihydrate pH 4.6, 10% w/v polyethylene glycol 4,000
|
Resolution 2.76 Å R-free 0.223 |
| 6LAZ the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1 Deposited 2019-11-13 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
6–96（91 aa）
|
Mutation：Y31H, Q36R, S46K | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M sodium acetate trihydrate pH 4.6, 10% w/v polyethylene glycol 4,000
|
Resolution 2.76 Å R-free 0.223 |
| 6QX9 Structure of a human fully-assembled precatalytic spliceosome (pre-B complex). Deposited 2019-03-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 65 PDB declaration: 71-meric |
Chain 1A
1–282（282 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 |
| 6SQN Structure of the U1A variant A1-98 Y31H/Q36R/F56W triple mutant co-crystallized with RNA Deposited 2019-09-04 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 3 PDB declaration: hexameric |
Chain A
2–98（97 aa）
Chain B
2–98（97 aa）
Chain C
2–98（97 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.2 M ammonium sulfate, 0.1 M tri-potassium citrate
|
Resolution 2.05 Å R-free 0.249 |
| 6SQQ Structure of the U1A variant A1-98 Y31H/Q36R/F56W triple mutant in complex with RNA obtained by soaking Deposited 2019-09-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 3 PDB declaration: hexameric |
Chain AAA
1–98（98 aa）
Chain BBB
1–98（98 aa）
Chain CCC
1–98（98 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；2.2 M ammonium sulfate, 0.2 M tri-potassium citrate
|
Resolution 2.37 Å R-free 0.294 |
| 6SQT Structure of the U1A variant A1-98 Y31H/Q36R/F56W triple mutant Deposited 2019-09-04 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain AAA
1–98（98 aa）
Chain BBB
1–98（98 aa）
Chain CCC
1–98（98 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2.2 M ammonium sulfate, 0.2 M tri-potassium citrate
|
Resolution 1.84 Å R-free 0.245 |
| 6SQV Structure of the U1A variant A1-98 Y31H/Q36R/R70W Deposited 2019-09-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain AAA
1–97（97 aa）
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2.2 M ammonium sulfate, 0.2 M tri-potassium citrate
|
Resolution 2.45 Å R-free 0.273 |
| 6SQV Structure of the U1A variant A1-98 Y31H/Q36R/R70W Deposited 2019-09-04 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain BBB
1–97（97 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2.2 M ammonium sulfate, 0.2 M tri-potassium citrate
|
Resolution 2.45 Å R-free 0.273 |
| 6SQV Structure of the U1A variant A1-98 Y31H/Q36R/R70W Deposited 2019-09-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain CCC
1–97（97 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2.2 M ammonium sulfate, 0.2 M tri-potassium citrate
|
Resolution 2.45 Å R-free 0.273 |
| 6SQV Structure of the U1A variant A1-98 Y31H/Q36R/R70W Deposited 2019-09-04 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain DDD
1–97（97 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2.2 M ammonium sulfate, 0.2 M tri-potassium citrate
|
Resolution 2.45 Å R-free 0.273 |
| 6SR7 Structure of the U1A variant A1-98 Y31H/Q36R/K98W Deposited 2019-09-05 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain AAA
1–98（98 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；2.2 M ammonium sulfate, 0.2 M tri-potassium citrate
|
Resolution 1.86 Å R-free 0.256 |
| 6SR7 Structure of the U1A variant A1-98 Y31H/Q36R/K98W Deposited 2019-09-05 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain BBB
1–98（98 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；2.2 M ammonium sulfate, 0.2 M tri-potassium citrate
|
Resolution 1.86 Å R-free 0.256 |
| 6SR7 Structure of the U1A variant A1-98 Y31H/Q36R/K98W Deposited 2019-09-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain CCC
1–98（98 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；2.2 M ammonium sulfate, 0.2 M tri-potassium citrate
|
Resolution 1.86 Å R-free 0.256 |
| 6SR7 Structure of the U1A variant A1-98 Y31H/Q36R/K98W Deposited 2019-09-05 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain DDD
1–98（98 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；2.2 M ammonium sulfate, 0.2 M tri-potassium citrate
|
Resolution 1.86 Å R-free 0.256 |
| 7AEP Solution structure of U1-A RRM2 (190-282) Deposited 2020-09-18 | Different construct Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
157–282（126 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；313 K；Ionic strength (raw mmCIF value) 60；Pressure atmospheric
NMR sample composition
10 mM NaPO4, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 7B0Y Structure of a transcribing RNA polymerase II-U1 snRNP complex Deposited 2020-11-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 25-meric |
Chain c
1–282（282 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7D7V Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+) and U1A protein Deposited 2020-10-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain C
5–96（92 aa）
|
Mutation：Y27H, Q32R | GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 8 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Mg(OAc)2, 0.1 M C2H6AsNaO2, pH 6.5, 30% MPD
|
Resolution 2.80 Å R-free 0.308 |
| 7DLZ Crystal Structure of Methyltransferase Ribozyme Deposited 2020-11-30 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–102（102 aa）
Chain B
1–102（102 aa）
Chain C
1–102（102 aa）
Chain D
1–102（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；polyethylene glycol 3350
|
Resolution 3.00 Å R-free 0.266 |
| 7DWH Complex structure of SAM-dependent methyltransferase ribozyme Deposited 2021-01-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–102（102 aa）
Chain B
1–102（102 aa）
Chain C
1–102（102 aa）
Chain D
1–102（102 aa）
|
Not recorded | CU COPPER (II) ION × 2 SAM S-ADENOSYLMETHIONINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.7；291 K；sodium phosphate monobasic monohydrate, polyethylene glycol 3350
|
Resolution 3.10 Å R-free 0.258 |
| 7LHX Human U1A protein with F37M and F77M mutations for improved phasing Deposited 2021-01-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–98（98 aa）
|
Mutation：Y31H, Q36R, F37M, F77M Non-standard monomer：Yes (specific site not provided by mmCIF) | NA SODIUM ION × 1 ACT ACETATE ION × 2 BME BETA-MERCAPTOETHANOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；2.7-3.1 M Sodium Acetate
|
Resolution 2.20 Å R-free 0.213 |
| 7VPX The cryo-EM structure of the human pre-A complex Deposited 2021-10-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 35-meric |
Chain M
1–282（282 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 |
| 8GXB Crystal structure of NAD+ -II riboswitch in complex with NAD+ Deposited 2022-09-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 5 PDB declaration: heptameric |
Chain C
2–98（97 aa）
Chain D
2–98（97 aa）
Chain E
2–98（97 aa）
Chain F
2–98（97 aa）
Chain G
2–98（97 aa）
|
Mutation：Y31H, Q36R Mutation：Y31H, Q36R Mutation：Y31H, Q36R Mutation：Y31H, Q36R Mutation：Y31H, Q36R | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 MG MAGNESIUM ION × 19 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2M KCl, 0.01M MgCl2, 0.05M MES pH 5.6, 5% PEG8000
|
Resolution 2.15 Å R-free 0.269 |
| 8GXC Crystal structure of NAD+ -II riboswitch in complex with NMN Deposited 2022-09-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 5 PDB declaration: heptameric |
Chain C
2–98（97 aa）
Chain D
2–98（97 aa）
Chain E
2–98（97 aa）
Chain F
2–98（97 aa）
Chain G
2–98（97 aa）
|
Mutation：Y31H, Q36R Mutation：Y31H, Q36R Mutation：Y31H, Q36R Mutation：Y31H, Q36R Mutation：Y31H, Q36R | NMN BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE × 2 MG MAGNESIUM ION × 16 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2M KCl, 0.01M MgCl2, 0.05M MES pH 5.6, 5% PEG8000
|
Resolution 2.50 Å R-free 0.269 |
| 9QEQ Structure of the transcribing Pol II-DSIF-SPT6-U1 snRNP complex Deposited 2025-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 28-meric |
Chain c
1–282（282 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, 100 mM NaCl, 3 mM MgCl2, 0.5 mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9YXV Cryo-EM structure of the core region of cIL-U1A-Fab1R-PGA1-sfFab quaternary complex at 2.9 A resolution Deposited 2025-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: heptameric |
Chain A
2–98（97 aa）
|
Mutation：Y31H, Q36R | DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；10 mM HEPES, 75 mM NaCl, 5 mM MgCl2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
87 other PDB entries and 144 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | RU1A_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–95； UniProt 1–95 Author chain B； PDBConstruct 1–95； UniProt 1–95 |
