HEADER RNA BINDING PROTEIN/RNA 11-APR-05 1ZC8 TITLE COORDINATES OF TMRNA, SMPB, EF-TU AND H44 FITTED INTO CRYO-EM MAP OF TITLE 2 THE 70S RIBOSOME AND TMRNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TLD 16S RIBOSOMAL RNA; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: H2 16S RRNA; COMPND 6 CHAIN: B; COMPND 7 MOL_ID: 3; COMPND 8 MOLECULE: H2B D MRNA; COMPND 9 CHAIN: C; COMPND 10 MOL_ID: 4; COMPND 11 MOLECULE: PROTEIN KINASE 4 MRNA; COMPND 12 CHAIN: G; COMPND 13 OTHER_DETAILS: PK1; COMPND 14 MOL_ID: 5; COMPND 15 MOLECULE: H5 16S RIBOSOMAL RNA; COMPND 16 CHAIN: F; COMPND 17 MOL_ID: 6; COMPND 18 MOLECULE: PROTEIN KINASE 2 MRNA; COMPND 19 CHAIN: H; COMPND 20 OTHER_DETAILS: PK2; COMPND 21 MOL_ID: 7; COMPND 22 MOLECULE: PROTEIN KINASE 3; COMPND 23 CHAIN: I; COMPND 24 OTHER_DETAILS: PK3; COMPND 25 MOL_ID: 8; COMPND 26 MOLECULE: PROTEIN KINASE 4 MRNA; COMPND 27 CHAIN: J; COMPND 28 OTHER_DETAILS: PK4; COMPND 29 MOL_ID: 9; COMPND 30 MOLECULE: H44 16S RIBOSOMAL RNA; COMPND 31 CHAIN: Z; COMPND 32 MOL_ID: 10; COMPND 33 MOLECULE: SSRA-BINDING PROTEIN; COMPND 34 CHAIN: K; COMPND 35 MOL_ID: 11; COMPND 36 MOLECULE: ELONGATION FACTOR TU; COMPND 37 CHAIN: Y; COMPND 38 SYNONYM: EF-TU SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 6 ORGANISM_TAXID: 274; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 9 ORGANISM_TAXID: 274; SOURCE 10 MOL_ID: 4; SOURCE 11 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 12 ORGANISM_TAXID: 274; SOURCE 13 MOL_ID: 5; SOURCE 14 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 15 ORGANISM_TAXID: 274; SOURCE 16 MOL_ID: 6; SOURCE 17 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 18 ORGANISM_TAXID: 274; SOURCE 19 MOL_ID: 7; SOURCE 20 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 21 ORGANISM_TAXID: 274; SOURCE 22 MOL_ID: 8; SOURCE 23 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 24 ORGANISM_TAXID: 274; SOURCE 25 MOL_ID: 9; SOURCE 26 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 27 ORGANISM_TAXID: 274; SOURCE 28 MOL_ID: 10; SOURCE 29 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 30 ORGANISM_TAXID: 274; SOURCE 31 MOL_ID: 11; SOURCE 32 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 33 ORGANISM_TAXID: 274 KEYWDS SMPB, TMRNA, EF-TU, H44, 30S, 16S RRNA, CRYO-EM, TRANS-TRANSLATION, KEYWDS 2 70S, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN K, Y; P ATOMS ONLY, CHAIN A, B, C, G, F, H, I, J, MDLTYP 2Z AUTHOR M.VALLE,R.GILLET,S.KAUR,A.HENNE,V.RAMAKRISHNAN,J.FRANK REVDAT 4 14-FEB-24 1ZC8 1 REMARK REVDAT 3 11-DEC-13 1ZC8 1 ATOM VERSN REVDAT 2 24-FEB-09 1ZC8 1 VERSN REVDAT 1 19-APR-05 1ZC8 0 JRNL AUTH M.VALLE,R.GILLET,S.KAUR,A.HENNE,V.RAMAKRISHNAN,J.FRANK JRNL TITL VISUALIZING TMRNA ENTRY INTO A STALLED RIBOSOME JRNL REF SCIENCE V. 300 127 2003 JRNL REFN ISSN 0036-8075 JRNL PMID 12677067 JRNL DOI 10.1126/SCIENCE.1081798 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.DONG,J.NOWAKOWSKI,D.W.HOFFMAN REMARK 1 TITL STRUCTURE OF SMALL PROTEIN B: THE PROTEIN COMPONENT OF THE REMARK 1 TITL 2 TMRNA SMPB SYSTEM FOR RIBOSOME RESCUE REMARK 1 REF EMBO J. V. 21 1845 2002 REMARK 1 REFN ISSN 0261-4189 REMARK 1 REFERENCE 2 REMARK 1 AUTH B.KNUDSEN,J.WOWER,C.ZWIEB,J.GORODKIN REMARK 1 TITL TMRDB (TMRNA DATABASE) REMARK 1 REF NUCLEIC ACIDS RES. V. 29 171 2001 REMARK 1 REFN ISSN 0305-1048 REMARK 1 REFERENCE 3 REMARK 1 AUTH M.VALLE,J.SENGUPTA,N.K.SWAMI,R.A.GRASSUCCI,N.BURKHARDT, REMARK 1 AUTH 2 K.H.NIERHAUS,R.K.AGRAWAL,J.FRANK REMARK 1 TITL CRYO-EM REVEALS AN ACTIVE ROLE FOR AMINOACYL-TRNA IN THE REMARK 1 TITL 2 ACCOMMODATION PROCESS REMARK 1 REF EMBO J. V. 21 3557 2002 REMARK 1 REFN ISSN 0261-4189 REMARK 1 REFERENCE 4 REMARK 1 AUTH P.NISSEN,M.KJELDGAARD,S.THIRUP,J.NYBORG REMARK 1 TITL E. COLI CYSTEINYL-TRNA AND T. AQUATICUS ELONGATION FACTOR REMARK 1 TITL 2 EF-TU: GTP TERNARY COMPLEX REMARK 1 REF STRUCTURE FOLD.DES. V. 7 143 1999 REMARK 1 REFN ISSN 0969-2126 REMARK 1 REFERENCE 5 REMARK 1 AUTH J.M.OGLE,F.V.MURPHY IV,M.J.TARRY,V.RAMAKRISHNAN REMARK 1 TITL SELECTION OF TRNA BY THE RIBOSOME REQUIRES A TRANSITION FROM REMARK 1 TITL 2 AN OPEN TO A CLOSED FORM REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 111 721 2002 REMARK 1 REFN ISSN 0092-8674 REMARK 2 REMARK 2 RESOLUTION. 13.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1K8H REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--MANUAL FITTING IN O REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 13.00 REMARK 3 NUMBER OF PARTICLES : 27644 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV REMARK 3 REMARK 3 OTHER DETAILS: SPIDER PACKAGE, THIS ENTRY CONTAINS ONLY C ALPHA REMARK 3 AND P ATOMS. REMARK 4 REMARK 4 1ZC8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032557. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : 70S RIBOSOME REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.03 REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOIL HOLLEY-CARBON FILM REMARK 245 GRIDS REMARK 245 SAMPLE VITRIFICATION DETAILS : RAPID-FREEZING IN LIQUID ETHANE REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 01-AUG-03 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 93.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 3700.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1450.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 1500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 49000 REMARK 245 CALIBRATED MAGNIFICATION : 52000 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: UNDECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, G, F, H, I, J, Z, K, REMARK 350 AND CHAINS: Y REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 P C I 15 P U I 44 0.57 REMARK 500 P C G 18 P C J 19 0.79 REMARK 500 P C A 348 CA TYR K 19 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K8H RELATED DB: PDB REMARK 900 STRUCTURE OF SMPB REMARK 900 RELATED ID: 1B23 RELATED DB: PDB REMARK 900 STRUCTURE OF EF-TU REMARK 900 RELATED ID: 1N32 RELATED DB: PDB REMARK 900 STRUCTURE OF H44 REMARK 900 RELATED ID: EMD-1122 RELATED DB: EMDB REMARK 999 REMARK 999 SEQUENCE AUTHOR STATES THAT THE MAP WAS FOR THERMUS THERMOPHILUS, REMARK 999 BUT THE EF-TU MODEL WAS FROM THERMUS AQUATICUS (SWS CODE Q01698) REMARK 999 . DBREF 1ZC8 A 1 359 PDB 1ZC8 1ZC8 1 359 DBREF 1ZC8 B 1 16 PDB 1ZC8 1ZC8 1 16 DBREF 1ZC8 C 1 31 PDB 1ZC8 1ZC8 1 31 DBREF 1ZC8 G 1 30 PDB 1ZC8 1ZC8 1 30 DBREF 1ZC8 F 1 29 PDB 1ZC8 1ZC8 1 29 DBREF 1ZC8 H 1 59 PDB 1ZC8 1ZC8 1 59 DBREF 1ZC8 I 1 49 PDB 1ZC8 1ZC8 1 49 DBREF 1ZC8 J 1 52 PDB 1ZC8 1ZC8 1 52 DBREF 1ZC8 Z 1406 1496 PDB 1ZC8 1ZC8 1406 1496 DBREF 1ZC8 K 1 130 PDB 1ZC8 1ZC8 1 130 DBREF 1ZC8 Y 1 405 PDB 1ZC8 1ZC8 1 405 SEQRES 1 A 59 G G G G C U G A U U C U G SEQRES 2 A 59 G A U U C G A C G G G A U SEQRES 3 A 59 A U U U C G G A C G C G G SEQRES 4 A 59 G U U C A A C U C C C G C SEQRES 5 A 59 C A G C U C C SEQRES 1 B 16 U U G C G A A A C A U G U SEQRES 2 B 16 A G G SEQRES 1 C 31 C C C A A G G U G C A U G SEQRES 2 C 31 C G C A U G U A G U A C C SEQRES 3 C 31 G A G G A SEQRES 1 G 30 C G A G G G G C G G U U G SEQRES 2 G 30 G C C U C G U A A A A A G SEQRES 3 G 30 C C G C SEQRES 1 F 29 C U U U A G C A G C U U A SEQRES 2 F 29 A U A A C C U G C U U A G SEQRES 3 F 29 A G C SEQRES 1 H 59 C C U C U C U C C C U A G SEQRES 2 H 59 C C U C C G C U C U U A G SEQRES 3 H 59 G A C G G G G A U C A A G SEQRES 4 H 59 A G A G G U C A A A C C C SEQRES 5 H 59 A A A A G A G SEQRES 1 I 49 A U C G C G U G G A A G C SEQRES 2 I 49 C C U G C C U G G G G U U SEQRES 3 I 49 G A A G C G U U A A A A C SEQRES 4 I 49 U U A A U C A G G C SEQRES 1 J 52 G U U U G U U A G U G G C SEQRES 2 J 52 G U G U C C G U C C G C A SEQRES 3 J 52 G C U G G C A A G C G A A SEQRES 4 J 52 U G U A A A G A C U G A C SEQRES 1 Z 91 G C C C G U C A C G C C A SEQRES 2 Z 91 U G G G A G C G G G C U C SEQRES 3 Z 91 U A C C C G A A G U C G C SEQRES 4 Z 91 C G G G A G C C U A C G G SEQRES 5 Z 91 G C A G G C G C C G A G G SEQRES 6 Z 91 G U A G G G C C C G U G A SEQRES 7 Z 91 C U G G G G C G A A G U C SEQRES 1 K 130 GLY LYS SER ASP LYS ILE ILE PRO ILE ALA GLU ASN LYS SEQRES 2 K 130 GLU ALA LYS ALA LYS TYR ASP ILE LEU GLU THR TYR GLU SEQRES 3 K 130 ALA GLY ILE VAL LEU LYS GLY SER GLU VAL LYS SER LEU SEQRES 4 K 130 ARG GLU LYS GLY THR VAL SER PHE LYS ASP SER PHE VAL SEQRES 5 K 130 ARG ILE GLU ASN GLY GLU ALA TRP LEU TYR ASN LEU TYR SEQRES 6 K 130 ILE ALA PRO TYR LYS HIS ALA THR ILE GLU ASN HIS ASP SEQRES 7 K 130 PRO LEU ARG LYS ARG LYS LEU LEU LEU HIS LYS ARG GLU SEQRES 8 K 130 ILE MET ARG LEU TYR GLY LYS VAL GLN GLU LYS GLY TYR SEQRES 9 K 130 THR ILE ILE PRO LEU LYS LEU TYR TRP LYS ASN ASN LYS SEQRES 10 K 130 VAL LYS VAL LEU ILE ALA LEU ALA LYS GLY LYS LYS LEU SEQRES 1 Y 405 ALA LYS GLY GLU PHE ILE ARG THR LYS PRO HIS VAL ASN SEQRES 2 Y 405 VAL GLY THR ILE GLY HIS VAL ASP HIS GLY LYS THR THR SEQRES 3 Y 405 LEU THR ALA ALA LEU THR TYR VAL ALA ALA ALA GLU ASN SEQRES 4 Y 405 PRO ASN VAL GLU VAL LYS ASP TYR GLY ASP ILE ASP LYS SEQRES 5 Y 405 ALA PRO GLU GLU ARG ALA ARG GLY ILE THR ILE ASN THR SEQRES 6 Y 405 ALA HIS VAL GLU TYR GLU THR ALA LYS ARG HIS TYR SER SEQRES 7 Y 405 HIS VAL ASP CYS PRO GLY HIS ALA ASP TYR ILE LYS ASN SEQRES 8 Y 405 MET ILE THR GLY ALA ALA GLN MET ASP GLY ALA ILE LEU SEQRES 9 Y 405 VAL VAL SER ALA ALA ASP GLY PRO MET PRO GLN THR ARG SEQRES 10 Y 405 GLU HIS ILE LEU LEU ALA ARG GLN VAL GLY VAL PRO TYR SEQRES 11 Y 405 ILE VAL VAL PHE MET ASN LYS VAL ASP MET VAL ASP ASP SEQRES 12 Y 405 PRO GLU LEU LEU ASP LEU VAL GLU MET GLU VAL ARG ASP SEQRES 13 Y 405 LEU LEU ASN GLN TYR GLU PHE PRO GLY ASP GLU VAL PRO SEQRES 14 Y 405 VAL ILE ARG GLY SER ALA LEU LEU ALA LEU GLU GLU MET SEQRES 15 Y 405 HIS LYS ASN PRO LYS THR LYS ARG GLY GLU ASN GLU TRP SEQRES 16 Y 405 VAL ASP LYS ILE TRP GLU LEU LEU ASP ALA ILE ASP GLU SEQRES 17 Y 405 TYR ILE PRO THR PRO VAL ARG ASP VAL ASP LYS PRO PHE SEQRES 18 Y 405 LEU MET PRO VAL GLU ASP VAL PHE THR ILE THR GLY ARG SEQRES 19 Y 405 GLY THR VAL ALA THR GLY ARG ILE GLU ARG GLY LYS VAL SEQRES 20 Y 405 LYS VAL GLY ASP GLU VAL GLU ILE VAL GLY LEU ALA PRO SEQRES 21 Y 405 GLU THR ARG LYS THR VAL VAL THR GLY VAL GLU MET HIS SEQRES 22 Y 405 ARG LYS THR LEU GLN GLU GLY ILE ALA GLY ASP ASN VAL SEQRES 23 Y 405 GLY LEU LEU LEU ARG GLY VAL SER ARG GLU GLU VAL GLU SEQRES 24 Y 405 ARG GLY GLN VAL LEU ALA LYS PRO GLY SER ILE THR PRO SEQRES 25 Y 405 HIS THR LYS PHE GLU ALA SER VAL TYR ILE LEU LYS LYS SEQRES 26 Y 405 GLU GLU GLY GLY ARG HIS THR GLY PHE PHE THR GLY TYR SEQRES 27 Y 405 ARG PRO GLN PHE TYR PHE ARG THR THR ASP VAL THR GLY SEQRES 28 Y 405 VAL VAL ARG LEU PRO GLN GLY VAL GLU MET VAL MET PRO SEQRES 29 Y 405 GLY ASP ASN VAL THR PHE THR VAL GLU LEU ILE LYS PRO SEQRES 30 Y 405 VAL ALA LEU GLU GLU GLY LEU ARG PHE ALA ILE ARG GLU SEQRES 31 Y 405 GLY GLY ARG THR VAL GLY ALA GLY VAL VAL THR LYS ILE SEQRES 32 Y 405 LEU GLU CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000