487d

SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION

Method: ELECTRON MICROSCOPY D_max: 308.0 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

50S ribosomal protein L1

OrganismNot specified

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain H； UniProt 6–229	Not recorded	50S ribosomal protein L2 × 1 （P04257） 50S ribosomal protein L6 × 1 （P02391） 50S ribosomal protein L9 × 1 （P02417） 50S ribosomal protein L11 × 1 （P29395） 50S ribosomal protein L14 × 1 （P04450） 50S ribosomal protein L25 × 1 （C3T3H7）	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 7.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 487D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AD2 RIBOSOMAL PROTEIN L1 MUTANT WITH SERINE 179 REPLACED BY CYSTEINE Deposited 1997-02-20	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 1–228（228 aa）	Mutation：S179C	SO4 SULFATE ION × 3 HG MERCURY (II) ION × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions DROPS CONTAINING: APPR. 15 MG/ML L1 50 MM GLYCINE, INITIALLY AT PH 10 5% (V/V) METHANE PENTANEDIOL 1.2 M AMMONIUM SULFATE EQUILIBRATED AGAINST 2.4 M AMMONIUM SULFATE 7% (V/V) METHANE PENTANEDIOL	Resolution 1.90 Å R-free 0.270
1EG0 FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME Deposited 2000-02-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: pentadecameric	Chain N 1–229（229 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM Hepes, 6 mM Mg(CH3COO)2 150 mM NH4Cl, 4 mM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.50 Å
1ZHO The structure of a ribosomal protein L1 in complex with mRNA Deposited 2005-04-26	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 A 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；KCl, MgCl2, HgCl2, PEG 10000, cacodylate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.281
1ZHO The structure of a ribosomal protein L1 in complex with mRNA Deposited 2005-04-26	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 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；KCl, MgCl2, HgCl2, PEG 10000, cacodylate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.281
1ZHO The structure of a ribosomal protein L1 in complex with mRNA Deposited 2005-04-26	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 E 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；KCl, MgCl2, HgCl2, PEG 10000, cacodylate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.281
1ZHO The structure of a ribosomal protein L1 in complex with mRNA Deposited 2005-04-26	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: dimeric	Chain G 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；KCl, MgCl2, HgCl2, PEG 10000, cacodylate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.281
2HW8 Structure of ribosomal protein L1-mRNA complex at 2.1 resolution. Deposited 2006-08-01	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 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 BU1 1,4-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG1000, sodium cacodylate,0.5% glycerol, 0.2 mM HgCl2 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.247
2OUM The first domain of L1 from Thermus thermophilus Deposited 2007-02-12	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 2–68（67 aa） Chain A 160–229（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；30% v/v polyethylenglycol 4K, 100 mM Tris-HCl, 200 mM acetate Na, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.55 Å R-free 0.270
2OV7 The first domain of the ribosomal protein L1 from Thermus thermophilus Deposited 2007-02-13	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 2–68（67 aa） Chain A 160–229（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；30% v/v polyethylenglycol 4K, 100 mM Tris-HCl, 200 mM LiSO4, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.30 Å R-free 0.233
2OV7 The first domain of the ribosomal protein L1 from Thermus thermophilus Deposited 2007-02-13	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 B 2–68（67 aa） Chain B 160–229（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；30% v/v polyethylenglycol 4K, 100 mM Tris-HCl, 200 mM LiSO4, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.30 Å R-free 0.233
2OV7 The first domain of the ribosomal protein L1 from Thermus thermophilus Deposited 2007-02-13	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 C 2–68（67 aa） Chain C 160–229（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；30% v/v polyethylenglycol 4K, 100 mM Tris-HCl, 200 mM LiSO4, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.30 Å R-free 0.233
2VPL The structure of the complex between the first domain of L1 protein from Thermus thermophilus and mRNA from Methanococcus jannaschii Deposited 2008-03-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 2–68（67 aa） Fragment：FIRST DOMAIN, RESIDUES 2-68,160-229 Chain A 160–229（70 aa） Fragment：FIRST DOMAIN, RESIDUES 2-68,160-229	Not recorded	K POTASSIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.274
2VPL The structure of the complex between the first domain of L1 protein from Thermus thermophilus and mRNA from Methanococcus jannaschii Deposited 2008-03-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain C 2–68（67 aa） Fragment：FIRST DOMAIN, RESIDUES 2-68,160-229 Chain C 160–229（70 aa） Fragment：FIRST DOMAIN, RESIDUES 2-68,160-229	Not recorded	K POTASSIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.274
3TG8 Mutant ribosomal protein L1 lacking ala158 from thermus thermophilus Deposited 2011-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–229（229 aa）	Mutation：lacking A158	PG4 TETRAETHYLENE GLYCOL × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；30 mM Tris-HCl, 75 mM NaCl with of 15% PEG 4K, 50 mM Tris-HCl, 0.2 M KBr (# 10 of Clear Strategy Screen I (MDL)) and 14% 2-methyl-2,4-pentandiol, 0.25 M MgCl2 in a 4:1:1, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.5	Resolution 1.95 Å R-free 0.226
3U4M Crystal structure of ribosomal protein tthl1 in complex with 80nt 23s rna from thermus thermophilus Deposited 2011-10-10	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: dimeric	Chain A 1–229（229 aa）	Mutation：V218R	SO4 SULFATE ION × 2 MLI MALONATE ION × 7 MG MAGNESIUM ION × 5 CL CHLORIDE ION × 2 NA SODIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；50mM NaCl, 2.5M Ammonium sulfate, 50mM MES, 10mM Magnesium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.208
3U56 Crystal structure of mutant ribosomal protein T217V TthL1 in complex with 80nt 23S RNA from Thermus thermophilus Deposited 2011-10-11	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 1–229（229 aa）	Mutation：V218R	MG MAGNESIUM ION × 11 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；295 K；50mM NaCl, 2.5M Ammonium sulfate, 50mM MES, 10mM Magnesium acetate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.10 Å R-free 0.238
3UMY Crystal structure of mutant ribosomal protein T217A TthL1 in complex with 80nt 23S RNA from Thermus thermophilus Deposited 2011-11-15	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 2–229（228 aa）	Mutation：T217A	CL CHLORIDE ION × 2 SO4 SULFATE ION × 5 NA SODIUM ION × 1 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；295 K；2.0 M Ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.90 Å R-free 0.246
4F9T Ribosomal protein L1 from Thermus thermophilus with substitution Thr217Ala Deposited 2012-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–229（229 aa）	Mutation：T217A	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；295 K；15 MG/ML L1 50 MM GLYCINE,INITIALLY AT PH 10 5% (V/V)METHANE PENTANEDIOL 1.2 M AMMONIUM SULFATE EQUILIBRATED AGAINST 2.4 M AMMONIUM SULFATE 7% (V/V) METHANE PENTANEDIOL , VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.46 Å R-free 0.202
4QG3 Crystal structure of mutant ribosomal protein G219V TthL1 in complex with 80nt 23S RNA from Thermus thermophilus Deposited 2014-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 2–229（228 aa）	Mutation：G219V	SO4 SULFATE ION × 5 IPA ISOPROPYL ALCOHOL × 8 BME BETA-MERCAPTOETHANOL × 4 URE UREA × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；1.8 M Ammonium sulfate, 0.05 M Bis-Tris,pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.226
4QGB Crystal structure of mutant ribosomal protein G219V TthL1 Deposited 2014-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–229（216 aa）	Mutation：G219V	CL CHLORIDE ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2 M ammonium sulfate, 0.1 M sodium acetate, 0.5 l 0.65% polyacrylic acid 5100 sodium salt, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.251
4QGB Crystal structure of mutant ribosomal protein G219V TthL1 Deposited 2014-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–229（216 aa）	Mutation：G219V	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2 M ammonium sulfate, 0.1 M sodium acetate, 0.5 l 0.65% polyacrylic acid 5100 sodium salt, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.251
4QGB Crystal structure of mutant ribosomal protein G219V TthL1 Deposited 2014-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–229（216 aa） Chain B 14–229（216 aa）	Mutation：G219V Mutation：G219V	CL CHLORIDE ION × 3 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2 M ammonium sulfate, 0.1 M sodium acetate, 0.5 l 0.65% polyacrylic acid 5100 sodium salt, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.251
4QVI Crystal structure of mutant ribosomal protein M218L TthL1 in complex with 80nt 23S RNA from Thermus thermophilus Deposited 2014-07-15	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 1–229（229 aa）	Mutation：M218L	SO4 SULFATE ION × 4 ACT ACETATE ION × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；2.5 M ammonium sulfate, 0.05M MES , 0.01M Magnesium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.217
4REO Mutant ribosomal protein l1 from thermus thermophilus with threonine 217 replaced by valine Deposited 2014-09-23	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 1–229（229 aa）	Mutation：T217V	SO4 SULFATE ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 GLY GLYCINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；295 K；15 MG/ML L1 50 MM GLYCINE, INITIALLY AT PH 10 5% (V/V) METHANE PENTANEDIOL 1.2 M AMMONIUM SULFATE EQUILIBRATED AGAINST 2.4 M AMMONIUM SULFATE 7% (V/V) METHANE PENTANEDIOL, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.35 Å R-free 0.209
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different construct Different oligomeric state Different experimental method Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BC 1–228（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å
4V4P Crystal structure of 70S ribosome with thrS operator and tRNAs. Deposited 2005-01-19	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric	Chain AC 1–228（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 5.50 Å R-free 0.356
4V4X Crystal structure of the 70S Thermus thermophilus ribosome showing how the 16S 3'-end mimicks mRNA E and P codons. Deposited 2006-06-27	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric	Chain BC 0–228（229 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 5.00 Å R-free 0.323
4V4Y Crystal structure of the 70S Thermus thermophilus ribosome with translocated and rotated Shine-Dalgarno Duplex. Deposited 2006-06-27	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 57-meric	Chain BC 0–228（229 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 5.50 Å R-free 0.326
4V4Z 70S Thermus thermophilous ribosome functional complex with mRNA and E- and P-site tRNAs at 4.5A. Deposited 2006-06-27	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric	Chain BC 0–228（229 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 4.51 Å R-free 0.345
4WU1 Complex of 70S ribosome with tRNA-Tyr and mRNA with G-U mismatch in the second position in the P-site Deposited 2014-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 54-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 708 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Tris-acetate, KSCN, PEG 550MME, PEG 20K	Resolution 3.20 Å R-free 0.238
4WU1 Complex of 70S ribosome with tRNA-Tyr and mRNA with G-U mismatch in the second position in the P-site Deposited 2014-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 48 PDB declaration: 54-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 673 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Tris-acetate, KSCN, PEG 550MME, PEG 20K	Resolution 3.20 Å R-free 0.238
4WZD Complex of 70S ribosome with cognate tRNA-Tyr in the P-site Deposited 2014-11-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 55-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 699 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Tris-acetate, KSCN, PEG 550MME, PEG 20K	Resolution 3.10 Å R-free 0.193
4WZD Complex of 70S ribosome with cognate tRNA-Tyr in the P-site Deposited 2014-11-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 55-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 646 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Tris-acetate, KSCN, PEG 550MME, PEG 20K	Resolution 3.10 Å R-free 0.193
4WZO Complex of 70S ribosome with tRNA-fMet and mRNA Deposited 2014-11-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 56-MERIC	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 576 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；Tris-acetate, KSCN, PEG 550MME, PEG 20K	Resolution 3.30 Å R-free 0.258
5E7K Structure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-site Deposited 2015-10-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 628 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.20 Å R-free 0.258
5E7K Structure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-site Deposited 2015-10-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 47 PDB declaration: 54-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 510 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.20 Å R-free 0.258
5EL5 Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position Deposited 2015-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-MERIC	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 660 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.15 Å R-free 0.254
5EL6 Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycin Deposited 2015-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 593 PAR PAROMOMYCIN × 1 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.10 Å R-free 0.249
5EL6 Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycin Deposited 2015-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 47 PDB declaration: 54-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 480 PAR PAROMOMYCIN × 1 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.10 Å R-free 0.249
5EL7 Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycin Deposited 2015-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 687 PAR PAROMOMYCIN × 1 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.15 Å R-free 0.247
5EL7 Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycin Deposited 2015-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 47 PDB declaration: 54-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 574 PAR PAROMOMYCIN × 1 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.15 Å R-free 0.247
5IB7 Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycin Deposited 2016-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 56-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 695 PAR PAROMOMYCIN × 1 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 2.99 Å R-free 0.241
5IB8 Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and near-cognate tRNALys with U-G mismatch in the A-site Deposited 2016-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 723 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.13 Å R-free 0.244
5IBB Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-site Deposited 2016-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 736 SPE THERMINE × 1 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 2.96 Å R-free 0.243
5IBB Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-site Deposited 2016-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 608 SPE THERMINE × 4 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 2.96 Å R-free 0.243
5IMQ Structure of ribosome bound to cofactor at 3.8 angstrom resolution Deposited 2016-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric	Chain Z 1–229（229 aa）	Not recorded	GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Buffer G 5 mM HEPES pH 7.5, 10 mM MgAc, 50 mM KCl, 10 mM NH4Cl, and 6 mM 2-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
5IMR Structure of ribosome bound to cofactor at 5.7 angstrom resolution Deposited 2016-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric	Chain Z 1–229（229 aa）	Not recorded	GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Buffer G 5 mM HEPES pH 7.5, 10 mM MgAc, 50 mM KCl, 10 mM NH4Cl, and 6 mM 2-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.70 Å
5J8B Crystal structure of Elongation Factor 4 (EF-4/LepA) in complex with GDPCP bound to the Thermus thermophilus 70S ribosome Deposited 2016-04-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 52 PDB declaration: 59-meric	Chain C 2–229（228 aa）	Not recorded	MG MAGNESIUM ION × 919 ZN ZINC ION × 6 SF4 IRON/SULFUR CLUSTER × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.6；292 K；0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.6-3.0% PEG-20K, 7-10% MPD, 0.5mM BME	Resolution 2.60 Å R-free 0.261
5NPM CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN TTHL1 LACKING 8 N-TERMINAL RESIDUES IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS Deposited 2017-04-17	Different construct 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 10–229（220 aa）	Not recorded	MLI MALONATE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；2.4 M sodium malonate	Resolution 2.70 Å R-free 0.249
5ZLU Ribosome Structure bound to ABC-F protein. Deposited 2018-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric	Chain Y 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6GSL Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAArg in the A-site Deposited 2018-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 60-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 954 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Tris-OAc, KSCN, PEG-20000, PEG-550mme	Resolution 3.16 Å
6GSL Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAArg in the A-site Deposited 2018-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 47 PDB declaration: 54-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 810 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Tris-OAc, KSCN, PEG-20000, PEG-550mme	Resolution 3.16 Å
6QNQ 70S ribosome initiation complex (IC) with experimentally assigned potassium ions Deposited 2019-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 57-meric	Chain 71 1–229（229 aa）	Not recorded	K POTASSIUM ION × 169 MG MAGNESIUM ION × 543 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Tris-OAc, KSCN, PEG-20K, PEG-550mme	Resolution 3.50 Å R-free 0.251
6QNR 70S ribosome elongation complex (EC) with experimentally assigned potassium ions Deposited 2019-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 57-meric	Chain 71 1–229（229 aa）	Not recorded	K POTASSIUM ION × 211 MG MAGNESIUM ION × 585 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Tris-OAc, KSCN, PEG-20k, PEG-550mme	Resolution 3.10 Å R-free 0.253
6QNR 70S ribosome elongation complex (EC) with experimentally assigned potassium ions Deposited 2019-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 56-meric	Chain 79 1–229（229 aa）	Not recorded	K POTASSIUM ION × 155 MG MAGNESIUM ION × 409 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Tris-OAc, KSCN, PEG-20k, PEG-550mme	Resolution 3.10 Å R-free 0.253

39 other PDB entries and 55 assemblies. Open the comparison page and filter oligomeric states

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UniProt name	RL1_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–224； UniProt 6–229

50S ribosomal protein L2

OrganismNot specified

UniProt P04257

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain I； UniProt 61–195	Non-standard monomer：Yes (specific site not provided by mmCIF)	50S ribosomal protein L1 × 1 （P27150） 50S ribosomal protein L6 × 1 （P02391） 50S ribosomal protein L9 × 1 （P02417） 50S ribosomal protein L11 × 1 （P29395） 50S ribosomal protein L14 × 1 （P04450） 50S ribosomal protein L25 × 1 （C3T3H7）	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 7.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 487D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C04 IDENTIFICATION OF KNOWN PROTEIN AND RNA STRUCTURES IN A 5 A MAP OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI Deposited 1999-07-14	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 60–196（137 aa） Fragment：CENTRAL RNA-BINDING DOMAINS	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；292 K；PEG 6000, POTASSIUM CHLORIDE, AMMONIUM CHLORIDE, MAGNESIUM CHLORIDE, ACETATE, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 5.00 Å
1RL2 RIBOSOMAL PROTEIN L2 RNA-BINDING DOMAIN FROM BACILLUS STEAROTHERMOPHILUS Deposited 1999-03-25	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 60–196（137 aa）	Mutation：METHIONINES ARE SUBSTITUED BY SELONOMETHIONINE Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 15% PEK20000 IN 0.1M MES PH6, pH 6.5	Resolution 2.30 Å R-free 0.258
1RL2 RIBOSOMAL PROTEIN L2 RNA-BINDING DOMAIN FROM BACILLUS STEAROTHERMOPHILUS Deposited 1999-03-25	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 60–196（137 aa）	Mutation：METHIONINES ARE SUBSTITUED BY SELONOMETHIONINE Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 15% PEK20000 IN 0.1M MES PH6, pH 6.5	Resolution 2.30 Å R-free 0.258
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BD 60–196（137 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL2_GEOSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–135； UniProt 61–195

50S ribosomal protein L6

OrganismNot specified

UniProt P02391

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain J； UniProt 8–171	Not recorded	50S ribosomal protein L1 × 1 （P27150） 50S ribosomal protein L2 × 1 （P04257） 50S ribosomal protein L9 × 1 （P02417） 50S ribosomal protein L11 × 1 （P29395） 50S ribosomal protein L14 × 1 （P04450） 50S ribosomal protein L25 × 1 （C3T3H7）	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 7.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 487D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C04 IDENTIFICATION OF KNOWN PROTEIN AND RNA STRUCTURES IN A 5 A MAP OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI Deposited 1999-07-14	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–177（177 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；292 K；PEG 6000, POTASSIUM CHLORIDE, AMMONIUM CHLORIDE, MAGNESIUM CHLORIDE, ACETATE, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 5.00 Å
1EG0 FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME Deposited 2000-02-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: pentadecameric	Chain J 1–171（171 aa）	Mutation：B. STEAROTHERMOPHILUS SEQUENCE AND MODEL	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM Hepes, 6 mM Mg(CH3COO)2 150 mM NH4Cl, 4 mM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.50 Å
1RL6 RIBOSOMAL PROTEIN L6 Deposited 1999-01-14	Different construct 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 1–177（177 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；pH 7.6	Resolution 2.00 Å R-free 0.302
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different construct Different oligomeric state Different experimental method Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BH 1–177（177 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL6_GEOSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain J； PDBConstruct 1–164； UniProt 8–171

50S ribosomal protein L9

OrganismNot specified

UniProt P02417

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain K； UniProt 1–149	Not recorded	50S ribosomal protein L1 × 1 （P27150） 50S ribosomal protein L2 × 1 （P04257） 50S ribosomal protein L6 × 1 （P02391） 50S ribosomal protein L11 × 1 （P29395） 50S ribosomal protein L14 × 1 （P04450） 50S ribosomal protein L25 × 1 （C3T3H7）	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 7.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 487D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CQU SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L9 Deposited 1999-08-11	Different construct 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 1–56（56 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Pressure AMBIENT	Resolution not provided
1DIV RIBOSOMAL PROTEIN L9 Deposited 1996-07-02	Different oligomeric state Different experimental method Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–149（149 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.276
2HBA Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9) K12M Deposited 2006-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–52（52 aa） Fragment：N-terminal domain	Mutation：K12M	ZN ZINC ION × 3 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.25 Å R-free 0.164
2HBA Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9) K12M Deposited 2006-06-14	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 1–52（52 aa） Fragment：N-terminal domain	Mutation：K12M	ZN ZINC ION × 5 CL CHLORIDE ION × 6 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.25 Å R-free 0.164
2HBA Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9) K12M Deposited 2006-06-14	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 × 4 PDB declaration: tetrameric	Chain A 1–52（52 aa） Fragment：N-terminal domain Chain B 1–52（52 aa） Fragment：N-terminal domain	Mutation：K12M Mutation：K12M	ZN ZINC ION × 16 CL CHLORIDE ION × 20 IMD IMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.25 Å R-free 0.164
2HBA Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9) K12M Deposited 2006-06-14	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 × 4 PDB declaration: tetrameric	Chain A 1–52（52 aa） Fragment：N-terminal domain Chain B 1–52（52 aa） Fragment：N-terminal domain	Mutation：K12M Mutation：K12M	ZN ZINC ION × 16 CL CHLORIDE ION × 20 IMD IMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.25 Å R-free 0.164
2HBB Crystal Structure of the N-terminal Domain of Ribosomal Protein L9 (NTL9) Deposited 2006-06-14	Different construct 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 1–51（51 aa） Fragment：N-terminal domain	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.236
2HBB Crystal Structure of the N-terminal Domain of Ribosomal Protein L9 (NTL9) Deposited 2006-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–51（51 aa） Fragment：N-terminal domain	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.236
2HBB Crystal Structure of the N-terminal Domain of Ribosomal Protein L9 (NTL9) Deposited 2006-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–51（51 aa） Fragment：N-terminal domain	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 200 mM Zn Acetate, 2.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.236
2HVF Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9), G34dA Deposited 2006-07-28	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 1–52（52 aa） Fragment：N-terminal domain	Mutation：G34(DAL) Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 4 CL CHLORIDE ION × 4 IMD IMIDAZOLE × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 300 mM Zn Acetate, 3 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.57 Å R-free 0.208
2HVF Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9), G34dA Deposited 2006-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–52（52 aa） Fragment：N-terminal domain	Mutation：G34(DAL) Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 8 CL CHLORIDE ION × 8 IMD IMIDAZOLE × 2 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Imidazole (pH 8.0), 300 mM Zn Acetate, 3 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.57 Å R-free 0.208
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different oligomeric state Different experimental method Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BK 1–149（149 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å

6 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL9_GEOSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain K； PDBConstruct 1–149； UniProt 1–149

50S ribosomal protein L11

OrganismNot specified

UniProt P29395

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain L； UniProt 8–140	Not recorded	50S ribosomal protein L1 × 1 （P27150） 50S ribosomal protein L2 × 1 （P04257） 50S ribosomal protein L6 × 1 （P02391） 50S ribosomal protein L9 × 1 （P02417） 50S ribosomal protein L14 × 1 （P04450） 50S ribosomal protein L25 × 1 （C3T3H7）	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 7.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 487D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EG0 FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME Deposited 2000-02-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: pentadecameric	Chain K 1–140（140 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM Hepes, 6 mM Mg(CH3COO)2 150 mM NH4Cl, 4 mM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.50 Å
1JQM Fitting of L11 protein and elongation factor G (EF-G) in the cryo-em map of e. coli 70S ribosome bound with EF-G, GDP and fusidic acid Deposited 2001-08-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–139（139 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6	Resolution 18.00 Å
1JQS Fitting of L11 protein and elongation factor G (domain G' and V) in the cryo-em map of E. coli 70S ribosome bound with EF-G and GMPPCP, a nonhydrolysable GTP analog Deposited 2001-08-07	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–139（139 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 18.00 Å
1JQT Fitting of L11 protein in the low resolution cryo-EM map of E.coli 70S ribosome Deposited 2001-08-07	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–139（139 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 18.00 Å
1MMS Crystal structure of the ribosomal PROTEIN L11-RNA complex Deposited 1999-04-14	Different construct 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 1–140（140 aa）	Not recorded	CD CADMIUM ION × 5 MG MAGNESIUM ION × 10 MMC METHYL MERCURY ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；25% GLYCEROL, 15% PEG 4000, 50 MM TRIS PH 7.5, 50 MM MGCL2, 20 MM CDCL2, 0.2 M KCL, 1 MM DITHIOTHREITOL, 4 DEGREES C, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.57 Å R-free 0.254
1MMS Crystal structure of the ribosomal PROTEIN L11-RNA complex Deposited 1999-04-14	Different construct 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 1–140（140 aa）	Not recorded	CD CADMIUM ION × 3 MG MAGNESIUM ION × 9 MMC METHYL MERCURY ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；25% GLYCEROL, 15% PEG 4000, 50 MM TRIS PH 7.5, 50 MM MGCL2, 20 MM CDCL2, 0.2 M KCL, 1 MM DITHIOTHREITOL, 4 DEGREES C, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.57 Å R-free 0.254
1MVR Decoding Center & Peptidyl transferase center from the X-ray structure of the Thermus thermophilus 70S ribosome, aligned to the low resolution Cryo-EM map of E.coli 70S Ribosome Deposited 2002-09-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: octameric	Chain L 1–140（140 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer polymix buffer；pH 7.5；polymix buffer cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane	Resolution 12.80 Å
1OLN Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA Deposited 2003-08-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain A 2–141（140 aa）	Not recorded	No recorded non-water small molecule	Experimental method not declared NMR measurement conditions pH 6.2；303 K；Ionic strength (raw mmCIF value) 100 MM NACL, 5 MM MGCL2；Pressure 1	Resolution not provided
1PN7 Coordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray structure aligned to the 70S Cryo-EM map of E.coli ribosome Deposited 2003-06-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain L 7–139（133 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane	Resolution 10.80 Å
1PN8 Coordinates of S12, L11 proteins and E-site tRNA from 70S crystal structure separately fitted into the Cryo-EM map of E.coli 70S.EF-G.GDPNP complex. The atomic coordinates originally from the E-site tRNA were fitted in the position of the hybrid P/E-site tRNA. Deposited 2003-06-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain L 7–139（133 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane	Resolution 10.80 Å
1R2W Coordinates of L11 with 58nts of 23S rRNA fitted into the cryo-EM map of the 70S ribosome Deposited 2003-09-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–140（140 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer Polymix buffer；pH 7.5；Polymix buffer cryo-EM vitrification conditions Cryogen ETHANE；Rapid freezing in liquid ethane	Resolution 9.00 Å
1R2X Coordinates of L11 with 58nts of 23S rRNA fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome Deposited 2003-09-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–140（140 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer Polymix buffer；pH 7.5；Polymix buffer cryo-EM vitrification conditions Cryogen ETHANE；Rapid freezing in liquid ethane	Resolution 9.00 Å
2BCW Coordinates of the N-terminal domain of ribosomal protein L11,C-terminal domain of ribosomal protein L7/L12 and a portion of the G' domain of elongation factor G, as fitted into cryo-em map of an Escherichia coli 70SEF-GGDP*fusidic acid complex Deposited 2005-10-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 7–71（65 aa） Fragment：N-terminal domain	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20mM HEPES-KOH (pH 7.5), 6mM MgCl2, and 150 mM NH4Cl, 2mM spermidine, 0.4 mM spermine；pH 7.5；20mM HEPES-KOH (pH 7.5), 6mM MgCl2, and 150 mM NH4Cl, 2mM spermidine, 0.4 mM spermine cryo-EM vitrification conditions RAPID-FREEZING IN LIQUID ETHANE	Resolution 11.20 Å
2JQ7 Model for thiostrepton binding to the ribosomal L11-RNA Deposited 2007-05-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain A 1–141（141 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K；Ionic strength (raw mmCIF value) 220；Pressure 1 NMR sample composition 0.3 MM [U-13C, U-15N U-2H] RIBOSOMAL PROTEIN L11, 0.3 MM RIBOSOMAL RNA, 0.3 MM THIOSTREPTON ANTIBIOTIC, 20 MM POTASSIUM PHOSPHATE, 200 MM POTASSIUM CHLORIDE, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2K3F Ribosomal protein L11 from Thermotoga maritima Deposited 2008-05-06	Different construct 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 1–141（141 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K；Ionic strength (raw mmCIF value) 70；Pressure ambient NMR sample composition 1.2 mM [U-100% 15N] L11, 20 mM potassium phosphate, 50 mM potassium chloride, 10 % [U-100% 2H] D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different construct Different oligomeric state Different experimental method Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BL 1–141（141 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL11_THEMA
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain L； PDBConstruct 1–133； UniProt 8–140

50S ribosomal protein L14

OrganismNot specified

UniProt P04450

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain M； UniProt 1–122	Not recorded	50S ribosomal protein L1 × 1 （P27150） 50S ribosomal protein L2 × 1 （P04257） 50S ribosomal protein L6 × 1 （P02391） 50S ribosomal protein L9 × 1 （P02417） 50S ribosomal protein L11 × 1 （P29395） 50S ribosomal protein L25 × 1 （C3T3H7）	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 7.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 487D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C04 IDENTIFICATION OF KNOWN PROTEIN AND RNA STRUCTURES IN A 5 A MAP OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI Deposited 1999-07-14	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain D 1–122（122 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；292 K；PEG 6000, POTASSIUM CHLORIDE, AMMONIUM CHLORIDE, MAGNESIUM CHLORIDE, ACETATE, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 5.00 Å
1WHI RIBOSOMAL PROTEIN L14 Deposited 1996-01-10	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.50 Å R-free 0.255
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different oligomeric state Different experimental method Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BN 1–122（122 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL14_GEOSE
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain M； PDBConstruct 1–122； UniProt 1–122

50S ribosomal protein L25

OrganismNot specified

UniProt C3T3H7

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain N； UniProt 1–94	Not recorded	50S ribosomal protein L1 × 1 （P27150） 50S ribosomal protein L2 × 1 （P04257） 50S ribosomal protein L6 × 1 （P02391） 50S ribosomal protein L9 × 1 （P02417） 50S ribosomal protein L11 × 1 （P29395） 50S ribosomal protein L14 × 1 （P04450）	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 7.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 487D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4V85 Crystal Structure of Release Factor RF3 Trapped in the GTP State on a Rotated Conformation of the Ribosome. Deposited 2011-06-13	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric	Chain BZ 1–94（94 aa）	Not recorded	MG MAGNESIUM ION × 493 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；Tris Ac PH.7.0, 25-35 mM KCL, 6.1% PEG 20000, 1% glycerol, 50mM sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.20 Å R-free 0.250

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C3T3H7_ECOLX
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain N； PDBConstruct 1–94； UniProt 1–94

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	487d
Deposition date deposition_date	2000-02-23
Structure title title	SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION
Keywords keywords	;RIBOSOME, LARGE RIBOSOMAL SUBUNIT, RIBOSOMAL PROTEIN, PROTEIN BIOSYNTHESIS, EM-RECONSTRUCTION, ATOMIC STRUCTURE, 3D ARRANGEMENT, FITTING ;; RIBOSOME
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	95.46 Å
Radius of gyration Rg (electron density) rg_electron	95.86 Å
Forward intensity I(0) i0	164285000.00
Molecular weight molecular_weight	111430.0 kDa
Excluded volume excluded_volume	140930 Å³
Envelope volume envelope_volume	432190 Å³
Hydration-shell volume shell_volume	38906 Å³
Envelope diameter envelope_diameter	246.6 Å
Shell Rg shell_rg	101.50 Å
Envelope Rg envelope_rg	82.21 Å
Shape Rg shape_rg	95.89 Å
Total Rg total_rg	95.85 Å
Total atoms total_atoms	8778
Residues n_residues	1018
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	308.0 Å
Rg (real space) rg_real	95.85 Å
Rg uncertainty (real space) rg_real_error	4.96 Å
I(0) (real space) i0_real	1.6430e+08
I(0) uncertainty (real space) i0_real_error	4.5420e+06
Rg (reciprocal space) rg_reciprocal	91.40 Å
I(0) (reciprocal space) i0_reciprocal	162000000.0000
Solution quality estimate total_estimate	0.6040
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	173.2 Å
Skewness Skewness skewness	-0.071
Kurtosis Kurtosis kurtosis	-1.380
Angular range angular_range	— – 0.0800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21170000.0000
Real-space data points n_real_points	17
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.000; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.852; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	50S ribosomal protein L1
Molecular weight formula_weight	24331.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	8778

KRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKACFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS

Entity 2 Entity 2 polymer

Description description	50S ribosomal protein L2
Molecular weight formula_weight	14759.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGMEIMSGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGEVRMILGKCRATVGEV

Entity 3 Entity 3 polymer

Description description	50S ribosomal protein L6
Molecular weight formula_weight	17811.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

PIEIPAGVTVTVNGNTVTVKGPKGELTRTFHPDMTITVEGNVITVTRPSDEKHHRALHGTTRSLLANMVEGVSKGYEKALELVGVGYRASKQGKKLVLSVGYSHPVEIEPEEGLEIEVPSQTKIIVKGADKQRVGELAANIRAVRPPEPYKGKGIRYEGELVRL

Entity 4 Entity 4 polymer

Description description	50S ribosomal protein L9
Molecular weight formula_weight	16341.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQKEQRQAAEELANAKKLKEQLEKLTVTIPAKAGEGGRLFGSITSKQIAESLQAQHGLKLDKRKIELADAIRALGYTNVPVKLHPEVTATLKVHVTEQK

Entity 5 Entity 5 polymer

Description description	50S ribosomal protein L11
Molecular weight formula_weight	14294.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV

Entity 6 Entity 6 polymer

Description description	50S ribosomal protein L14
Molecular weight formula_weight	13369.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MIQQESRLKVADNSGAREVLVIKVLGGSGRRYANIGDVVVATVKDATPGGVVKKGQVVKAVVVRTKRGVRRPDGSYIRFDENACVIIRDDKSPRGTRIFGPVARELRDKDFMKIISLAPEVI

Entity 7 Entity 7 polymer

Description description	50S ribosomal protein L25
Molecular weight formula_weight	10713.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d487dh_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d487di_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d487dj_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d487dk_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d487dl_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d487dm_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

Domain ID domain_id	d487dn_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.2 — Large subunit

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8. Citations (9)

;The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution. ;

J.Mol.Biol. (2000)

PMID: 10756104 · DOI: 10.1006/jmbi.2000.3635 PRIMARY

A Detailed View of a Ribosomal Active Site: The Structure of the Gtpase Center at 2.6 Angstroms Resolution.

Cell(Cambridge,Mass.) (1999)

DOI: 10.1016/S0092-8674(00)80759-X

The NMR Structure of the 5S Rrna E-Domain-Protein C25 Complex Shows Pre-Formed and Induced Recognition.

Embo J. (1999)

DOI: 10.1093/emboj/18.22.6508

;The Three-Dimensional Structure of the RNA-Binding Domain of Ribosomal Protein L2; a Protein at the Peptidyl Transferase Center of the Ribosome. ;

Embo J. (1999)

DOI: 10.1093/emboj/18.6.1459

The Escherichia coli large ribosomal subunit at 7.5 A resolution

Structure (1999)

DOI: 10.1016/S0969-2126(00)88348-3

Ribosomal Protein L9: A Structure Determination by the Combined Use of X-Ray Crystallography and NMR Spectroscopy.

J.Mol.Biol. (1996)

DOI: 10.1006/jmbi.1996.0696

Crystal Structure of the RNA Binding Ribosomal Protein L1 from Thermus Thermophilus.

Embo J. (1996)

The Crystal Structure of Ribosomal Protein L14 Reveals an Important Organizational Component of the Translational Apparatus.

Structure (1996)

DOI: 10.1016/S0969-2126(96)00115-3

Ribosomal Protein L6: Structural Evidence of Gene Duplication from a Primitive RNA Binding Proetin.

Embo J. (1993)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	7.500 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	7.50 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	16000

fit	/app/data/saxs_computation/87/487d/487d.fit
pddf	/app/data/pr_computation/87/487d/487d.pr.out
profile	/app/data/saxs_computation/87/487d/487d.dat

SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION

1. Protein Identity and Related Structures Protein Identity & Related Structures

50S ribosomal protein L1

State in the Current Structure

Other States of the Same Protein in the Database

50S ribosomal protein L2

State in the Current Structure

Other States of the Same Protein in the Database

50S ribosomal protein L6

State in the Current Structure

Other States of the Same Protein in the Database

50S ribosomal protein L9

State in the Current Structure

Other States of the Same Protein in the Database

50S ribosomal protein L11

State in the Current Structure

Other States of the Same Protein in the Database

50S ribosomal protein L14

State in the Current Structure

Other States of the Same Protein in the Database

50S ribosomal protein L25

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (7 domains)

8. Citations (9)

9. Files and Curves (10)

Files (7)

Curves (3)