HEADER RIBOSOME 10-DEC-13 3J66 OBSLTE 10-DEC-14 3J66 4V7F TITLE ARX1 PRE-60S PARTICLE. THIS ENTRY CONTAINS THE ALTERNATIVE POSITION TITLE 2 FOR RLP7. SPLIT 3J64 3J65 3J66 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME BIOGENESIS PROTEIN RLP7; COMPND 3 CHAIN: s; COMPND 4 SYNONYM: RIBOSOMAL PROTEIN L7-LIKE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS 60S BIOGENESIS, RLP7, RIBOSOME EXPDTA ELECTRON MICROSCOPY AUTHOR C.LEIDIG,M.THOMS,I.HOLDERMANN,B.BRADATSCH,O.BERNINGHAUSEN,G.BANGE, AUTHOR 2 I.SINNING,E.HURT,R.BECKMANN REVDAT 3 10-DEC-14 3J66 1 OBSLTE REVDAT 2 09-APR-14 3J66 1 JRNL REVDAT 1 26-MAR-14 3J66 0 JRNL AUTH C.LEIDIG,M.THOMS,I.HOLDERMANN,B.BRADATSCH,O.BERNINGHAUSEN, JRNL AUTH 2 G.BANGE,I.SINNING,E.HURT,R.BECKMANN JRNL TITL 60S RIBOSOME BIOGENESIS REQUIRES ROTATION OF THE 5S JRNL TITL 2 RIBONUCLEOPROTEIN PARTICLE. JRNL REF NAT COMMUN V. 5 3491 2014 JRNL REFN ESSN 2041-1723 JRNL PMID 24662372 JRNL DOI 10.1038/NCOMMS4491 REMARK 2 REMARK 2 RESOLUTION. 8.70 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 : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 1.060 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : 1.060 REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 8.700 REMARK 3 NUMBER OF PARTICLES : NULL REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 3J66 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 5 REMARK 5 THIS ENTRY WITH OTHER SPLIT ENTRIES HAVE BEEN CONSOLIDATED INTO A REMARK 5 COMBINED FILE FOR COMPLETE REPRESENTATION. NO COORDINATES HAVE BEEN REMARK 5 CHANGED. REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-14. REMARK 100 THE RCSB ID CODE IS RCSB160300. 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 : ASYMMETRIC REMARK 245 NAME OF SAMPLE : ARX1 PRE-60S PARTICLE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : NULL REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : NULL REMARK 245 DETECTOR TYPE : NULL REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : NULL REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : NULL REMARK 245 ILLUMINATION MODE : NULL REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : NULL REMARK 245 ACCELERATION VOLTAGE (KV) : NULL 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 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: s 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO s 308 N - CA - C ANGL. DEV. = 22.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN s 10 152.98 172.13 REMARK 500 ARG s 41 143.20 -37.60 REMARK 500 ILE s 45 -125.14 -145.93 REMARK 500 LEU s 81 154.39 132.54 REMARK 500 LYS s 87 150.70 62.75 REMARK 500 ASP s 98 -136.58 -125.75 REMARK 500 PHE s 99 -12.24 77.40 REMARK 500 ALA s 107 -157.88 138.61 REMARK 500 ASN s 108 160.17 160.00 REMARK 500 GLU s 112 -178.14 -173.84 REMARK 500 GLU s 118 149.59 -171.31 REMARK 500 THR s 133 -103.12 159.74 REMARK 500 THR s 134 -82.45 173.09 REMARK 500 TYR s 135 -165.95 -175.89 REMARK 500 ALA s 140 113.25 72.84 REMARK 500 LEU s 141 -150.02 -86.46 REMARK 500 VAL s 153 -159.79 72.22 REMARK 500 ARG s 167 51.85 76.94 REMARK 500 VAL s 194 144.68 123.35 REMARK 500 TYR s 216 165.00 -40.38 REMARK 500 ILE s 227 117.82 -1.00 REMARK 500 ASN s 230 161.43 -41.93 REMARK 500 GLN s 238 141.84 129.39 REMARK 500 GLU s 259 -80.84 -59.93 REMARK 500 GLN s 269 -151.27 -163.21 REMARK 500 LYS s 272 107.36 -59.65 REMARK 500 GLU s 276 127.74 166.93 REMARK 500 ASN s 284 59.00 39.71 REMARK 500 LYS s 290 -173.90 178.76 REMARK 500 ALA s 294 179.92 154.41 REMARK 500 GLU s 295 149.57 170.10 REMARK 500 SER s 296 157.49 137.52 REMARK 500 ALA s 304 47.67 77.20 REMARK 500 ALA s 307 170.96 -39.53 REMARK 500 PRO s 308 -104.47 -25.50 REMARK 500 ILE s 310 112.87 -169.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA s 307 PRO s 308 -146.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-2528 RELATED DB: EMDB REMARK 900 ASSOCIATED CRYO-EM RECONSTRUCTION REMARK 900 RELATED ID: 4V7F RELATED DB: PDB DBREF 3J66 s 1 322 UNP P40693 RLP7_YEAST 1 322 SEQRES 1 s 322 MET SER SER THR GLN ASP SER LYS ALA GLN THR LEU ASN SEQRES 2 s 322 SER ASN PRO GLU ILE LEU LEU ARG LYS ARG ARG ASN ALA SEQRES 3 s 322 ASP ARG THR ARG ILE GLU ARG GLN GLU LEU ALA LYS LYS SEQRES 4 s 322 LYS ARG GLU GLU GLN ILE LYS LYS LYS ARG SER ASN LYS SEQRES 5 s 322 ASN LYS PHE VAL ARG ALA GLU SER ILE VAL ALA LYS THR SEQRES 6 s 322 LEU ALA THR SER ARG GLU LYS GLU ARG ILE LYS ARG VAL SEQRES 7 s 322 SER ILE LEU GLU ASP LYS LYS ALA LYS ASN GLU THR GLN SEQRES 8 s 322 HIS ILE ALA SER GLY LYS ASP PHE ILE LEU LYS ILE THR SEQRES 9 s 322 GLU LYS ALA ASN GLY ALA GLU GLU ASN SER VAL ASP LEU SEQRES 10 s 322 GLU GLU THR GLU GLU GLU GLU ASP ASP GLY LEU ILE ARG SEQRES 11 s 322 GLU LYS THR THR TYR ASP GLY LYS PRO ALA LEU LEU PHE SEQRES 12 s 322 ILE VAL ARG VAL ARG GLY PRO LEU ALA VAL ASN ILE PRO SEQRES 13 s 322 ASN LYS ALA PHE LYS ILE LEU SER LEU LEU ARG LEU VAL SEQRES 14 s 322 GLU THR ASN THR GLY VAL PHE VAL LYS LEU THR LYS ASN SEQRES 15 s 322 VAL TYR PRO LEU LEU LYS VAL ILE ALA PRO TYR VAL VAL SEQRES 16 s 322 ILE GLY LYS PRO SER LEU SER SER ILE ARG SER LEU ILE SEQRES 17 s 322 GLN LYS ARG GLY ARG ILE ILE TYR LYS GLY GLU ASN GLU SEQRES 18 s 322 ALA GLU PRO HIS GLU ILE VAL LEU ASN ASP ASN ASN ILE SEQRES 19 s 322 VAL GLU GLU GLN LEU GLY ASP HIS GLY ILE ILE CYS VAL SEQRES 20 s 322 GLU ASP ILE ILE HIS GLU ILE ALA THR MET GLY GLU SER SEQRES 21 s 322 PHE SER VAL CYS ASN PHE PHE LEU GLN PRO PHE LYS LEU SEQRES 22 s 322 ASN ARG GLU VAL SER GLY PHE GLY SER LEU ASN ARG LEU SEQRES 23 s 322 ARG LYS ILE LYS GLN ARG GLU ALA GLU SER ARG THR ARG SEQRES 24 s 322 GLN PHE SER ASN ALA ALA THR ALA PRO VAL ILE GLU VAL SEQRES 25 s 322 ASP ILE ASP SER LEU LEU ALA LYS LEU ASN 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