FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME

Solution structure of the E. coli 70S ribosome at 11.5 A resolution.

The Crystal Structure of Ribosomal Protein S4 Reveals a Two-Domain Molecule with an Extensive RNA-Binding Surface: One Domain Shows Structural Homology to the Ets DNA-Binding Motif

The Structure of Ribosomal Protein S5 Reveals Sites of Interaction with 16S Rrna

Crystal Structure of the Ribosomal Protein S6 from Thermus Thermophilus

The Structure of Ribosomal Protein S7 at 1.9 A Resolution Reveals a Beta- Hairpin Motif that Binds Double-Stranded Nucleic Acids

Crystal Structure of Ribosomal Protein S8 from Thermus Thermophilus Reveals a High Degree of Structural Conservation of a Specific RNA Binding Site

Conformational Variability of the N-Terminal Helix in the Structure of Ribosomal Protein S15

Solution Structure of Prokaryotic Ribosomal Protein S17 by High-Resolution NMR Spectroscopy

Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution

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

A Detailed View of a Ribosomal Active Site: The Structure of the L11-RNA Complex

The Two Faces of the Escherichia Coli 23 S Rrna Sarcin/Ricin Domain: The Structure at 1.11 A Resolution

Crystal Structure of the RNA Binding Ribosomal Prot L1 from Thermus Thermophilus

Crystal Structure of Methionyl-Trnafmet Transformylase Complexed with the Initiator Formyl-Methionyl-Trnafmet

REFINEMENT PROTOCOL--RIGID BODY REFINEMENT DETAILS--ALL COMPONENTS WERE FIT INTO MAP AS RIGID BODIES USING COORDINATES FROM THE REFERRED SOURCES EXCEPT FOR L1, FOR WHICH ABOUT 15-DEGREE ROTATION WAS INTRODUCED BETWEEN THE TWO DOMAINS; FITTING OF PROTEIN S17 IS RELATIVELY UNCERTAIN; CONFORMATIONAL CHANGES OF ANTICODON AND ACCEPTOR REGIONS OF TRNAFMET UPON BINDING TO THE RIBOSOME WERE NOT MODELED.

20 mM Hepes, 6 mM Mg(CH3COO)2 150 mM NH4Cl, 4 mM

MODELED AS ANALOGOUS FRAGMENT OF T. THERMOPHILUS TAKEN FROM PDB ENTRY 1QD7

T. MARITIMA RNA SEQUENCE AND MODEL TAKEN FROM PDB ENTRY 1MMS

E.COLI RNA SEQUENCE AND MODEL TAKEN FROM PDB ENTRY 480D

E.COLI FMET-TRNA SEQUENCE AND MODEL TAKEN FROM PDB ENTRY 2FMT

MODELED BY ANALOGOUS PROTEIN OF B. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRY 1C06

MODELED BY ANALOGOUS PROTEIN OF B. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRY 1PKP

MODELED BY ANALOGOUS PROTEIN OF T.THERMOPHILUS TAKEN FROM PDB ENTRY 1RIS

MODELED BY ANALOGOUS PROTEIN OF T. THERMOPHILUS TAKEN FROM PDB ENTRY 1RSS

MODELED BY ANALOGOUS PROTEIN OF T. THERMOPHILUS TAKEN FROM PDB ENTRY 1AN7

MODELED BY ANALOGOUS PROTEIN OF B. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRY 1A32

MODELED BY ANALOGOUS PROTEIN OF B. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRIES 1RIP AND 1QD7

MODELED BY ANALOGOUS PROTEIN OF T. THERMOPHILUS TAKEN FROM PDB ENTRY 1QD7

MODELED BY ANALOGOUS PROTEIN OF T. THERMOPHILUS TAKEN FROM PDB ENTRY 1AD2

MODELED BY ANALOGOUS PROTEIN OF T. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRY 1RL6
B. STEAROTHERMOPHILUS SEQUENCE AND MODEL

MODELED BY ANALOGOUS PROTEIN OF T. MARITIMA TAKEN FROM PDB ENTRY 1MMS

CGCGGGG(4SU)GGAGCAGCCGG(H2U)AGCUCGUCGGG(OMC)UCAUAACCCGAAGAUCGUCGG(5MU)(PSU)CAAAU
CCGGCCCCCGCAACCA

MKLSEYGLQLQEKQKLRHMYGVNERQFRKTFEEAGKMPGKHGENFMILLESRLDNLVYRLGLARTRRQARQLVTHGHILV
DGSRVNIPSYRVKPGQTIAVREKSRNLQVIKEALEANNYIPDYLSFDPEKMEGTYTRLPERSELPAEINEALIVEFYSR

MRRINPNKLELEERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIRKAIEDAKKNLIEVPIVGTT
IPHEVIGHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSKSIGSNTPINMVRATFDGLKQLK

MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELR
IRDNVRRVMVVKSQEPF

MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRV
GGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAE

MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVI
HHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW

MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRA
LIEKLGIRG

SERNQRKVYVGRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMETRPLSATKRFRLVEIV
EKAVRAGAGAGAA

(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)
(UNK)(UNK)(UNK)(UNK)

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXX

MPKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAK
GEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAG
RIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS

MSRVGKKPIEIPAGVTVTVNGNTVTVKGPKGELTRTFHPDMTITVEGNVITVTRPSDEKHHRALHGTTRSLLANMVEGVS
KGYEKALELVGVGYRASKQGKKLVLSVGYSHPVEIEPEEGLEIEVPSQTKIIVKGADKQRVGELAANIRAVRPPEPYKGK
GIRYEGELVRL

MAKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLK
KAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV

ONLY COORDINATES OF PHOSPHATE AND CA-ATOMS ARE DEPOSITED

ALL COMPONENTS WERE FIT INTO MAP AS RIGID BODIES USING COORDINATES FROM THE REFERRED SOURCES EXCEPT FOR L1, FOR WHICH ABOUT 15-DEGREE ROTATION WAS INTRODUCED BETWEEN THE TWO DOMAINS; FITTING OF PROTEIN S17 IS RELATIVELY UNCERTAIN; CONFORMATIONAL CHANGES OF ANTICODON AND ACCEPTOR REGIONS OF TRNAFMET UPON BINDING TO THE RIBOSOME WERE NOT MODELED.
REFINEMENT DONE BY PROGRAMS O AND SPIDER. ALL COMPONENTS WERE FIT INTO MAP AS RIGID BODIES USING COORDINATES FROM THE REFERRED SOURCES EXCEPT FOR L1, FOR WHICH ABOUT 15-DEGREE ROTATION WAS INTRODUCED BETWEEN THE TWO DOMAINS; FITTING OF PROTEIN S17 IS RELATIVELY UNCERTAIN; CONFORMATIONAL CHANGES OF ANTICODON AND ACCEPTOR REGIONS OF TRNAFMET UPON BINDING TO THE RIBOSOME WERE NOT MODELED.
70S RIBOSOME, LOW RESOLUTION MODEL, RIBOSOME

RKLSEYGLQLQEKQKLRHMYGVNERQFRKTFEEAGKMPGKHGENFMILLESRLDNLVYRLGLARTRRQARQLVTHGHIIV
DGSRVNIPSYRVKPGQTIAVREKSRNLQVIKEALEANNYIPDYLSFDPEKMEGTYTRLPERSELPAEINEALIVEFYSR