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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

Method: SOLUTION NMR Dmax: 71.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A

HOMO SAPIENS

UniProt P09012

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 × 2 RNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain A； UniProt 2–102 Chain B； UniProt 2–102 Fragment：RESIDUES 2-102 Mutation：YES ;PIE, RNA (5'-R(*GP*AP*GP*AP*CP*AP*UP*UP*GP*CP*AP*CP*CP* CP*GP*GP*AP*GP*UP*CP*UP*C)-3') ; × 2 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

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 1DZ5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AUD U1A-UTRRNA, NMR, 31 STRUCTURES Deposited 1997-08-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions 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 method 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
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 experimental conditions 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 experimental method 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 experimental method 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain P 1–100（100 aa） Fragment：RNA binding domain
Mutation：Y31H, Q36R MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；NaCl, MgCl2, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.282
1SJ4 Crystal structure of a C75U mutant Hepatitis Delta Virus ribozyme precursor, in Cu2+ solution Deposited 2004-03-02 Different construct Different mutation/modification Different oligomeric state Different experimental method 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 method 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 method 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 experimental method 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 method 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 method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain C 2–98（97 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP CRYSTALLIZATION CONDITIONS: 1.8M (NH4)2 SO4, 40MM TRIS-HCL PH 7.0, 5MM SPERMINE TRANSFERRED TO 1.9M (NH4)2 SO4, 40MM TRIS-HCL PH 7.0, 5MM SPERMINE, 25% GLYCEROL FOR 15 MINUTES BEFORE FREEZING.
Resolution 1.92 Å
1VBX Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in EDTA solution Deposited 2004-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 experimental conditions 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 method 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 method 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 method 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 method 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 method 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 method 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 experimental conditions 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–98（98 aa） Fragment：RNA BINDING DOMAIN (UNP residues 1 to 98)
Mutation：Y31H,Q36R GLP 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
Resolution 3.00 Å R-free 0.318
3G96 Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P Deposited 2009-02-12 Different construct Different mutation/modification Different oligomeric state Different experimental method 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 method 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 method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–98（98 aa） Fragment：RNA BINDING DOMAIN (UNP residues 1 to 98)
Mutation：Y31H,Q36R MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
Resolution 3.01 Å R-free 0.311
3G96 Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P Deposited 2009-02-12 Different construct Different mutation/modification Different oligomeric state Different experimental method 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 method 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 method 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 method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–98（98 aa） Fragment：RNA BINDING DOMAIN
Mutation：Y31H,Q36R MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions vapor diffusion, sitting drops；pH 6.8；298 K；11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K
Resolution 2.90 Å R-free 0.307
3G9C Crystal structure of the product Bacillus anthracis glmS ribozyme Deposited 2009-02-13 Different construct Different mutation/modification Different oligomeric state Different experimental method 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 ligand/ion Different experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 experimental method 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 experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 experimental method 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 experimental method 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 method 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 method 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 method 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 method 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 method 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 method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain C 2–98（97 aa）
Not recorded GLN GLUTAMINE × 1 K POTASSIUM ION × 3 MG MAGNESIUM ION × 5 CS CESIUM ION × 4 NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；.1 M HEPES-sodium, pH 7.0, 40% (v/v) 2-methyl-2,4-pentanediol, 20 mM CsCl
Resolution 2.60 Å R-free 0.271
5FJ4 Structure of the standard kink turn HmKt-7 as stem loop bound with U1A and L7Ae proteins Deposited 2015-10-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain A 1–102（102 aa） Fragment：RRM 1 DOMAIN, UNP RESIDUES 1-102
Chain B 1–102（102 aa） Fragment：RRM 1 DOMAIN, UNP RESIDUES 1-102
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M TRIS HYDROCHLORIDE PH 8.5, 2.0 M MONO-AMMONIUM DIHYDROGEN PHOSPHATE
Resolution 2.95 Å R-free 0.237
5FJ4 Structure of the standard kink turn HmKt-7 as stem loop bound with U1A and L7Ae proteins Deposited 2015-10-06 Different construct Different mutation/modification Different oligomeric state Different experimental method 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 method 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 method 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 experimental method 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 method 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 method 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 experimental method 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 method 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 experimental method 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 method 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 method 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 method 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 experimental method 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 experimental method 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 3 PDB declaration: hexameric
Chain AAA 1–98（98 aa）
Chain BBB 1–98（98 aa）
Chain CCC 1–98（98 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；2.2 M ammonium sulfate, 0.2 M tri-potassium citrate
Resolution 2.37 Å R-free 0.294
6SQT Structure of the U1A variant A1-98 Y31H/Q36R/F56W triple mutant Deposited 2019-09-04 Different construct Different mutation/modification Different oligomeric state Different experimental method 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 method 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 experimental method 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 method 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 experimental method 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 experimental method 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 experimental method 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 method 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 experimental method 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 experimental conditions 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain C 5–96（92 aa）
Mutation：Y27H, Q32R GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 8 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Mg(OAc)2, 0.1 M C2H6AsNaO2, pH 6.5, 30% MPD
Resolution 2.80 Å R-free 0.308
7DLZ Crystal Structure of Methyltransferase Ribozyme Deposited 2020-11-30 Different construct Different mutation/modification Different oligomeric state Different experimental method 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 method 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 method 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 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 × 5 PDB declaration: heptameric
Chain C 2–98（97 aa）
Chain D 2–98（97 aa）
Chain E 2–98（97 aa）
Chain F 2–98（97 aa）
Chain G 2–98（97 aa）
Mutation：Y31H, Q36R Mutation：Y31H, Q36R Mutation：Y31H, Q36R Mutation：Y31H, Q36R Mutation：Y31H, Q36R NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 MG MAGNESIUM ION × 19 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M KCl, 0.01M MgCl2, 0.05M MES pH 5.6, 5% PEG8000
Resolution 2.15 Å R-free 0.269
8GXC Crystal structure of NAD+ -II riboswitch in complex with NMN Deposited 2022-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 5 PDB declaration: heptameric
Chain C 2–98（97 aa）
Chain D 2–98（97 aa）
Chain E 2–98（97 aa）
Chain F 2–98（97 aa）
Chain G 2–98（97 aa）
Mutation：Y31H, Q36R Mutation：Y31H, Q36R Mutation：Y31H, Q36R Mutation：Y31H, Q36R Mutation：Y31H, Q36R NMN BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE × 2 MG MAGNESIUM ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M KCl, 0.01M MgCl2, 0.05M MES pH 5.6, 5% PEG8000
Resolution 2.50 Å R-free 0.269
9QEQ Structure of the transcribing Pol II-DSIF-SPT6-U1 snRNP complex Deposited 2025-03-10 Different construct Different 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 RU1A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–101； UniProt 2–102 Author chain B； PDBConstruct 1–101； UniProt 2–102

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1dz5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dz5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dz5
Deposition date deposition_date2000-02-16
Structure title titleThe NMR structure of the 38KDa U1A protein-PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein
Keywords keywordsRIBONUCLEOPROTEIN-RNA COMPLEX, POLYADENYLATION, PROTEIN PROTEIN INTERACTION, RNA PROTEIN INTERACTION; RIBONUCLEOPROTEIN/RNA
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.88 Å
Radius of gyration Rg (electron density) rg_electron22.95 Å
Forward intensity I(0) i05126220000.00
Molecular weight molecular_weight484220.0 kDa
Excluded volume excluded_volume555100 ų
Envelope volume envelope_volume95029 ų
Hydration-shell volume shell_volume30836 ų
Envelope diameter envelope_diameter80.0 Å
Shell Rg shell_rg33.23 Å
Envelope Rg envelope_rg25.23 Å
Shape Rg shape_rg22.94 Å
Total Rg total_rg23.13 Å
Total atoms total_atoms61644
Residues n_residues3197
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax71.5 Å
Rg (real space) rg_real22.84 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real5.1260e+09
I(0) uncertainty (real space) i0_real_error6.8890e+07
Rg (reciprocal space) rg_reciprocal22.85 Å
I(0) (reciprocal space) i0_reciprocal5126000000.0000
Solution quality estimate total_estimate0.7529
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary69.3 Å
Skewness Skewness skewness0.202
Kurtosis Kurtosis kurtosis-0.666
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3061000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 0.307; Positv: 1.000; Valcen: 0.992; Smooth: 0.997
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1dz5a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family familyd.58.7.1 — Canonical RBD
Domain ID domain_idd1dz5b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family familyd.58.7.1 — Canonical RBD

CATH v4.4 (2 domains)

Domain ID domain_id1dz5A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id1dz5B00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
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8. Citations (1)

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9. Files and Curves (10)