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–RNA Homooligomer Protein × 5 RNA 2 PDB declaration: heptameric（7） Consistent with all polymer counts | Chain C； UniProt 2–98 Chain D； UniProt 2–98 Chain E； UniProt 2–98 Chain F； UniProt 2–98 Chain G； UniProt 2–98 | Mutation：Y31H, Q36R | 61-mer RNA × 2 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 |
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 8GXC | 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 ligand/ion 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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 oligomeric state 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 oligomeric state 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 |
| 1OIA U1A rnp domain 1-95 Deposited 2003-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–95（95 aa）
Fragment：RNP DOMAIN RESIDUES 1-95
|
Not recorded | No recorded non-water small molecule |
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 |
| 1OIA U1A rnp domain 1-95 Deposited 2003-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–95（95 aa）
Fragment：RNP DOMAIN RESIDUES 1-95
|
Not recorded | No recorded non-water small molecule |
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 |
| 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 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 | 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 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）
|
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 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
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 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
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 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 | 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 mutation/modification Different oligomeric state Different ligand/ion 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 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
1–99（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 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
1–99（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 oligomeric state Different ligand/ion 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 mutation/modification 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 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
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 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：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 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 | 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 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 | 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 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 | 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 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
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 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 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 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
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 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 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 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
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 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 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 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
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 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 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 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
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 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, 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 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, 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 mutation/modification 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 ligand/ion 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 ligand/ion 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification 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 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 | 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 oligomeric state 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 mutation/modification 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 ligand/ion 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 |
| 9QEQ Structure of the transcribing Pol II-DSIF-SPT6-U1 snRNP complex Deposited 2025-03-10 | Different construct Different mutation/modification 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 145 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | SNRPA_HUMAN |
| Isoform | — |
| PDB entities | 2 |
| Chains and sequence ranges | Author chain C； PDBConstruct 1–97； UniProt 2–98 Author chain D； PDBConstruct 1–97； UniProt 2–98 Author chain E； PDBConstruct 1–97； UniProt 2–98 Author chain F； PDBConstruct 1–97； UniProt 2–98 Author chain G； PDBConstruct 1–97； UniProt 2–98 |
