Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U-G wobble pairing during decoding

PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E

5-{[(2-sulfoethyl)amino]methyl}uridine 5'-(dihydrogen phosphate)

Modified Uridines with C5-Methylene Substituents at the First Position of the tRNA Anticodon Stabilize U.G Wobble Pairing During Decoding.

CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E.COLI STRUCTURE IN 2AVY

5'-R(*GP*CP*AP*UP*GP*CP*U*TM2P*AP*AP*AP *AP*CP*AP*UP*GP*C)-3'

SEE WIMBERLY ET AL.,NATURE, 2000, pH 6.5

CRYSTAL STRUCTURE OF INITIATION FACTOR IF1 BOUND TO THE 30SRIBOSOMAL SUBUNIT
STRUCTURE OF THE RIBOSOME RECYCLING FACTOR BOUND TO THE THERMUS THERMOPHILUS 70S RIBOSOME WITH MRNA, ASL-PHE AND TRNA-FMET (PART 3 OF 4). THIS FILE CONTAINS THE 30S SUBUNIT, MRNA, P-SITE ASL, E-SITE TRNA AND RRF FOR MOLECULE 2.
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH THE ANTIBIOTIC PAROMOMYCIN
CRYSTAL STRUCTURE OF T6A37-ASLLYSUUU AAA- MRNA BOUND TO THEDECODING CENTER
30S RIBOSOMAL SUBUNIT, TRNAS, MRNA AND RELEASE FACTOR RF1FROM A CRYSTAL STRUCTURE OF THE WHOLE RIBOSOMAL COMPLEX.THIS FILE CONTAINS THE 30S SUBUNIT, TRNAS, MRNA ANDRELEASE FACTOR RF1 FROM A CRYSTAL STRUCTURE OF THE WHOLERIBOSOMAL COMPLEX". THE ENTIRE CRYSTAL STRUCTURE CONTAINSONE 70S RIBOSOME, TRNAS, MRNA AND RELEASE FACTOR RF1 ANDIS DESCRIBED IN REMARK 400.
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATETRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE ANDWITH THE ANTIBIOTIC PAROMOMYCIN
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE- ASL WITH CMO5U IN POSITION 34 BOUND TO AN MRNA WITH A GUA-CODON IN THE A-SITE AND PAROMOMYCIN.
30S RIBOSOMAL SUBUNIT, TRNAS, MRNA AND RELEASE FACTOR RF2FROM A CRYSTAL STRUCTURE OF THE WHOLE RIBOSOMAL COMPLEX.THIS FILE CONTAINS THE 30S RIBOSOMAL SUBUNIT, TRNAS, MRNAAND RELEASE FACTOR RF2 FROM A CRYSTAL STRUCTURE OF THEWHOLE RIBOSOMAL COMPLEX". THE ENTIRE CRYSTAL STRUCTURECONTAINS ONE 70S RIBOSOME, TRNAS, MRNA AND RELEASE FACTORRF2 AND IS DESCRIBED IN REMARK 400.
COORDINATES OF S12, L11 PROTEINS AND E- SITE TRNA FROM 70SCRYSTAL STRUCTURE SEPARATELY FITTED INTO THE CRYO-EM MAPOF E.COLI 70S.EF-G.GDPNP COMPLEX. THE ATOMIC COORDINATESORIGINALLY FROM THE E-SITE TRNA WERE FITTED IN THEPOSITION OF THE HYBRID P /E-SITE TRNA.
CRYSTAL STRUCTURE OF AN INOSINE-CYTOSINE WOBBLE BASE PAIRIN THE CONTEXT OF THE DECODING CENTER
PARTIAL STRUCTURE OF 16S RIBONUCLEIC ACID OF THE SMALL RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH HYGROMYCIN B
RIBOSOMAL PROTEIN S7 FROM THERMUS THERMOPHILUS
STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT
THE PATH OF MESSENGER RNA THROUGH THE RIBOSOME. THIS FILE,1JGQ, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, ANDMRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY
30S RIBOSOMAL SUBUNIT, TRNAS AND MRNA FROM A CRYSTALSTRUCTURE OF THE WHOLE RIBOSOMAL COMPLEX WITH A STOP CODONIN THE A-SITE. THIS FILE CONTAINS THE 30S SUBUNIT, TRNASAND MRNA FROM A CRYSTAL STRUCTURE OF THE WHOLE RIBOSOMALCOMPLEX WITH A STOP CODON IN THE A-SITE AND IS DESCRIBEDIN REMARK 400.
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH PACTAMYCIN
CRYSTAL STRUCTURES OF THE SMALL RIBOSOMAL SUBUNIT WITHTETRACYCLINE, EDEINE AND IF3
CRYSTAL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT FROM THERMUSTHERMOPHILUS IN COMPLEX WITH THE TRANSLATION INITIATIONFACTOR IF3 (C- TERMINAL DOMAIN)
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE- ASL WITH CMO5U IN POSITION 34 BOUND TO AN MRNA WITH A GUG-CODON IN THE A-SITE AND PAROMOMYCIN.
COORDINATES OF S12, L11 PROTEINS AND P- TRNA, FROM THE 70S X-RAY STRUCTURE ALIGNED TO THE 70S CRYO-EM MAP OF E. COLIRIBOSOME
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE- ASL WITH CMO5U IN POSITION 34 BOUND TO AN MRNA WITH A GUU-CODON IN THE A-SITE AND PAROMOMYCIN.
FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E .COLI 70S RIBOSOME
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATETRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE
STRUCTURE OF 16S RRNA IN THE REGION AROUND RIBOSOMALPROTEIN S8.
CRYSTAL STRUCTURE OF AN EXTENDED TRNA ANTICODON STEM LOOP IN COMPLEX WITH ITS COGNATE MRNA GGGU IN THE CONTEXT OF THE THERMUS THERMOPHILUS 30S SUBUNIT.
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 70SRIBOSOME
STRUCTURE OF RIBOSOMAL PROTEINS S15, S6, S18 , AND 16SRIBOSOMAL RNA
STRUCTURE OF THE RIBOSOME RECYCLING FACTOR BOUND TO THE THERMUS THERMOPHILUS 70S RIBOSOME WITH MRNA, ASL-PHE AND TRNA-FMET (PART 1 OF 4). THIS FILE CONTAINS THE 30S SUBUNIT, MRNA, P-SITE ASL, E-SITE TRNA AND RRF FOR MOLECULE 1.
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT COMPLEXED WITH A VALINE- ASL WITH CMO5U IN POSITION 34 BOUND TO AN MRNA WITH A GUC-CODON IN THE A-SITE AND PAROMOMYCIN.
CRYSTAL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT FROM THERMUSTHERMOPHILUS IN COMPLEX WITH EDEINE
CRYSTAL STRUCTURE OF THE WILD TYPE RIBOSOME FROM E. COLI,30S SUBUNIT OF 70S RIBOSOME . THIS FILE, 1PNX, CONTAINSONLY MOLECULES OF THE 30S RIBOSOMAL SUBUNIT. THE 50SSUBUNIT IS IN THE PDB FILE 1PNY.
STRUCTURE OF AN INOSINE-ADENINE WOBBLE BASE PAIR COMPLEX INTHE CONTEXT OF THE DECODING CENTER
CRYSTAL STRUCTURE OF THE RIBOSOME AT 5.5 A RESOLUTION. THISFILE, 1GIX, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA,AND MRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY
THE PATH OF MESSENGER RNA THROUGH THE RIBOSOME. THIS FILE,1JGO, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, ANDMRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY
THE PATH OF MESSENGER RNA THROUGH THE RIBOSOME. THIS FILE,1JGP, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, ANDMRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITBOUND TO CODON AND NEAR- COGNATE TRANSFER RNA ANTICODONSTEM-LOOP MISMATCHED AT THE FIRST CODON POSITION AT THE ASITE WITH PAROMOMYCIN
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN THE PRESENCE OF CODON AND CRYSTALLOGRAPHICALLYDISORDERED NEAR-COGNATE TRANSFER RNA ANTICODON STEM-LOOPMISMATCHED AT THE FIRST CODON POSITION
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITBOUND TO CODON AND NEAR- COGNATE TRANSFER RNA ANTICODONSTEM-LOOP MISMATCHED AT THE SECOND CODON POSITION AT THE ASITE WITH PAROMOMYCIN
MODEL STRUCTURE OF THE T. THERMOPHILUS 70S RIBOSOME, 30SSUBUNIT OF 70S ROBOSOME. THIS FILE, 1TWT, CONTAINS ONLYMOLECULES OF THE 30S RIBOSOMAL SUBUNIT. THE 50S SUBUNIT ISIN THE PDB FILE 1TWV.
CRYSTAL STRUCTURE OF A STREPTOMYCIN DEPENDENT RIBOSOME FROME. COLI, 30S SUBUNIT OF 70S RIBOSOME. THIS FILE, 1PNS,CONTAINS THE 30S SUBUNIT, TWO TRNAS, AND ONE MRNAMOLECULE. THE 50S RIBOSOMAL SUBUNIT IS IN FILE 1PNU.
COORDINATES OF S12, SH44, LH69 AND SRL SEPARATELY FITTEDINTO THE CRYO-EM MAP OF EF-TU TERNARY COMPLEX(GDP.KIRROMYCIN) BOUND 70S RIBOSOME
CRYSTAL STRUCTURE OF AN EXTENDED TRNA ANTICODON STEM LOOP IN COMPLEX WITH ITS COGNATE MRNA CGGG IN THE CONTEXT OF THE THERMUS THERMOPHILUS 30S SUBUNIT.
STRUCTURE OF FUNCTIONALLY ACTIVATED SMALL RIBOSOMAL SUBUNITAT 3.3 A RESOLUTION
CRYSTAL STRUCTURE OF 70S RIBOSOME WITH THRS OPERATOR ANDTRNAS. 30S SUBUNIT. THE COORDINATES FOR THE 50S SUBUNITARE IN THE PDB ENTRY 1YL3
CRYSTAL STRUCTURE OF AN EXTENDED TRNA ANTICODON STEM LOOP IN COMPLEX WITH ITS COGNATE MRNA UCGU IN THE CONTEXT OF THE THERMUS THERMOPHILUS 30S SUBUNIT.
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH THE ANTIBIOTICS STREPTOMYCIN, SPECTINOMYCIN,AND PAROMOMYCIN
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN THE PRESENCE OF CRYSTALLOGRAPHICALLY DISORDERED CODONAND NEAR- COGNATE TRANSFER RNA ANTICODON STEM- LOOPMISMATCHED AT THE SECOND CODON POSITION
CRYSTAL STRUCTURE OF MNM5U34T6A37-TRNALYSUUU COMPLEXED WITHAAG-MRNA IN THE DECODING CENTER
STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNITIN COMPLEX WITH TETRACYCLINE
CRYSTAL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT FROM THERMUSTHERMOPHILUS IN COMPLEX WITH TETRACYCLINE
TERNARY COMPLEX DOCKED IN THE DECODING SITE OF THE 30SRIBOSOMAL SUBUNIT

SHEET
DETERMINATION METHOD: DSSP
THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS
BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY
A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS
ARE IDENTICAL.

THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN
ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW,
TWO SHEETS ARE DEFINED.

THIS FILE, 2VQF, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME.

PAROMOMYCIN (PAR): SEE 2UUA
5-TAURINOMETHYLURIDINE (TM2)

30S RIBOSOMAL PROTEIN S2, 30S RIBOSOMAL PROTEIN S3, 30S RIBOSOMAL PROTEIN S4, 30S RIBOSOMAL PROTEIN S5, 30S RIBOSOMAL PROTEIN S6, 30S RIBOSOMAL PROTEIN S7, 30S RIBOSOMAL PROTEIN S8, 30S RIBOSOMAL PROTEIN S9, 30S RIBOSOMAL PROTEIN S10, 30S RIBOSOMAL PROTEIN S11, 30S RIBOSOMAL PROTEIN S12, 30S RIBOSOMAL PROTEIN S13, 30S RIBOSOMAL PROTEIN S14 TYPE Z, 30S RIBOSOMAL PROTEIN S15, 30S RIBOSOMAL PROTEIN S16, 30S RIBOSOMAL PROTEIN S17, 30S RIBOSOMAL PROTEIN S18, 30S RIBOSOMAL PROTEIN S19, 30S RIBOSOMAL PROTEIN S20, 30S RIBOSOMAL PROTEIN THX/RNA Complex, PAROMOMYCIN
TRNA-BINDING, RRNA-BINDING, METAL-BINDING, ZINC-FINGER, TRANSLATION, COILED COIL, PAROMOMYCIN, TRNA, ZINC, MRNA, CMO5U, RIBOSOME, RNA-BINDING, MODIFIACTIONS, RIBOSOMAL PROTEIN, RIBONUCLEOPROTEIN