HEADER RIBOSOME 28-APR-22 7UUI TITLE NUCLEOPLASMIC PRE-60S INTERMEDIATE OF THE NOG2 CONTAINING POST- TITLE 2 ROTATION STATE FROM A SPB1 D52A STRAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOLAR GTP-BINDING PROTEIN 2; COMPND 3 CHAIN: m SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE BY4741; SOURCE 3 ORGANISM_TAXID: 1247190 KEYWDS RIBOSOME BIOGENESIS, K-LOOP GTPASE, GTPASE, RIBOSOME, 5S RRNP EXPDTA ELECTRON MICROSCOPY AUTHOR K.SEKULSKI,V.E.CRUZ,C.S.WEIRICH,J.P.ERZBERGER REVDAT 1 15-MAR-23 7UUI 0 JRNL AUTH K.SEKULSKI,V.E.CRUZ,C.S.WEIRICH,J.P.ERZBERGER JRNL TITL RRNA METHYLATION BY SPB1 REGULATES THE GTPASE ACTIVITY OF JRNL TITL 2 NOG2 DURING 60S RIBOSOMAL SUBUNIT ASSEMBLY. JRNL REF NAT COMMUN V. 14 1207 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 36864048 JRNL DOI 10.1038/S41467-023-36867-5 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : GCTF, RELION REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 6YLH REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.900 REMARK 3 NUMBER OF PARTICLES : 50091 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7UUI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-22. REMARK 100 THE DEPOSITION ID IS D_1000264951. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : MAP OF THE NUCLEOLAR POST REMARK 245 -ROTATION PRE-60S INTERMEDIATE REMARK 245 PURIFIED WITH TAGS ON TIF6 AND REMARK 245 NOG2 FROM A SPB1 D52A STRAIN. REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.80 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 5434 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 900.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 140.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 81000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: m 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET m 1 REMARK 465 GLY m 15 REMARK 465 ASP m 16 REMARK 465 THR m 17 REMARK 465 LYS m 18 REMARK 465 ASP m 19 REMARK 465 GLY m 20 REMARK 465 ASN m 21 REMARK 465 LEU m 22 REMARK 465 ARG m 23 REMARK 465 GLU m 119 REMARK 465 GLU m 120 REMARK 465 LYS m 121 REMARK 465 ASP m 122 REMARK 465 ALA m 123 REMARK 465 ASP m 124 REMARK 465 GLU m 125 REMARK 465 SER m 126 REMARK 465 LYS m 471 REMARK 465 GLU m 472 REMARK 465 GLY m 473 REMARK 465 GLU m 474 REMARK 465 GLU m 475 REMARK 465 LYS m 476 REMARK 465 PRO m 477 REMARK 465 LYS m 478 REMARK 465 LYS m 479 REMARK 465 LYS m 480 REMARK 465 GLU m 481 REMARK 465 VAL m 482 REMARK 465 GLU m 483 REMARK 465 LYS m 484 REMARK 465 THR m 485 REMARK 465 ALA m 486 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K m 502 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN m 325 OD1 REMARK 620 2 ALA m 344 O 73.7 REMARK 620 3 ILE m 346 O 75.5 68.5 REMARK 620 4 GDP m 503 O1B 98.4 133.1 155.8 REMARK 620 5 GDP m 503 O1A 102.5 73.3 140.7 63.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG m 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER m 329 OG REMARK 620 2 THR m 350 OG1 91.8 REMARK 620 3 GDP m 503 O3B 98.9 169.3 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7UOO RELATED DB: PDB REMARK 900 RELATED ID: EMD-26651 RELATED DB: EMDB REMARK 900 RELATED ID: 7UQZ RELATED DB: PDB REMARK 900 RELATED ID: EMD-26703 RELATED DB: EMDB REMARK 900 RELATED ID: 7UQB RELATED DB: PDB REMARK 900 RELATED ID: EMD-26686 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-26689 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-26799 RELATED DB: EMDB REMARK 900 NUCLEOPLASMIC PRE-60S INTERMEDIATE OF THE NOG2 CONTAINING POST- REMARK 900 ROTATION STATE FROM A SPB1 D52A STRAIN DBREF 7UUI m 1 486 UNP P53742 NOG2_YEAST 1 486 SEQRES 1 m 486 MET GLY THR GLY LYS LYS GLU LYS SER ARG ARG ILE ARG SEQRES 2 m 486 GLU GLY ASP THR LYS ASP GLY ASN LEU ARG VAL LYS GLY SEQRES 3 m 486 GLU ASN PHE TYR ARG ASP SER LYS ARG VAL LYS PHE LEU SEQRES 4 m 486 ASN MET TYR THR SER GLY LYS GLU ILE ARG ASN LYS LYS SEQRES 5 m 486 GLY ASN LEU ILE ARG ALA ALA SER PHE GLN ASP SER THR SEQRES 6 m 486 ILE PRO ASP ALA ARG VAL GLN PRO ASP ARG ARG TRP PHE SEQRES 7 m 486 GLY ASN THR ARG VAL ILE SER GLN ASP ALA LEU GLN HIS SEQRES 8 m 486 PHE ARG SER ALA LEU GLY GLU THR GLN LYS ASP THR TYR SEQRES 9 m 486 GLN VAL LEU LEU ARG ARG ASN LYS LEU PRO MET SER LEU SEQRES 10 m 486 LEU GLU GLU LYS ASP ALA ASP GLU SER PRO LYS ALA ARG SEQRES 11 m 486 ILE LEU ASP THR GLU SER TYR ALA ASP ALA PHE GLY PRO SEQRES 12 m 486 LYS ALA GLN ARG LYS ARG PRO ARG LEU ALA ALA SER ASN SEQRES 13 m 486 LEU GLU ASP LEU VAL LYS ALA THR ASN GLU ASP ILE THR SEQRES 14 m 486 LYS TYR GLU GLU LYS GLN VAL LEU ASP ALA THR LEU GLY SEQRES 15 m 486 LEU MET GLY ASN GLN GLU ASP LYS GLU ASN GLY TRP THR SEQRES 16 m 486 SER ALA ALA LYS GLU ALA ILE PHE SER LYS GLY GLN SER SEQRES 17 m 486 LYS ARG ILE TRP ASN GLU LEU TYR LYS VAL ILE ASP SER SEQRES 18 m 486 SER ASP VAL VAL ILE HIS VAL LEU ASP ALA ARG ASP PRO SEQRES 19 m 486 LEU GLY THR ARG CYS LYS SER VAL GLU GLU TYR MET LYS SEQRES 20 m 486 LYS GLU THR PRO HIS LYS HIS LEU ILE TYR VAL LEU ASN SEQRES 21 m 486 LYS CYS ASP LEU VAL PRO THR TRP VAL ALA ALA ALA TRP SEQRES 22 m 486 VAL LYS HIS LEU SER LYS GLU ARG PRO THR LEU ALA PHE SEQRES 23 m 486 HIS ALA SER ILE THR ASN SER PHE GLY LYS GLY SER LEU SEQRES 24 m 486 ILE GLN LEU LEU ARG GLN PHE SER GLN LEU HIS THR ASP SEQRES 25 m 486 ARG LYS GLN ILE SER VAL GLY PHE ILE GLY TYR PRO ASN SEQRES 26 m 486 THR GLY LYS SER SER ILE ILE ASN THR LEU ARG LYS LYS SEQRES 27 m 486 LYS VAL CYS GLN VAL ALA PRO ILE PRO GLY GLU THR LYS SEQRES 28 m 486 VAL TRP GLN TYR ILE THR LEU MET LYS ARG ILE PHE LEU SEQRES 29 m 486 ILE ASP CYS PRO GLY ILE VAL PRO PRO SER SER LYS ASP SEQRES 30 m 486 SER GLU GLU ASP ILE LEU PHE ARG GLY VAL VAL ARG VAL SEQRES 31 m 486 GLU HIS VAL THR HIS PRO GLU GLN TYR ILE PRO GLY VAL SEQRES 32 m 486 LEU LYS ARG CYS GLN VAL LYS HIS LEU GLU ARG THR TYR SEQRES 33 m 486 GLU ILE SER GLY TRP LYS ASP ALA THR GLU PHE ILE GLU SEQRES 34 m 486 ILE LEU ALA ARG LYS GLN GLY ARG LEU LEU LYS GLY GLY SEQRES 35 m 486 GLU PRO ASP GLU SER GLY VAL SER LYS GLN ILE LEU ASN SEQRES 36 m 486 ASP PHE ASN ARG GLY LYS ILE PRO TRP PHE VAL LEU PRO SEQRES 37 m 486 PRO GLU LYS GLU GLY GLU GLU LYS PRO LYS LYS LYS GLU SEQRES 38 m 486 VAL GLU LYS THR ALA HET MG m 501 1 HET K m 502 1 HET GDP m 503 28 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 K K 1+ FORMUL 4 GDP C10 H15 N5 O11 P2 HELIX 1 AA1 GLY m 2 LYS m 5 5 4 HELIX 2 AA2 LYS m 6 GLU m 14 1 9 HELIX 3 AA3 ASP m 32 ASN m 40 1 9 HELIX 4 AA4 MET m 41 SER m 44 5 4 HELIX 5 AA5 ASP m 74 GLY m 79 5 6 HELIX 6 AA6 SER m 85 ASP m 102 1 18 HELIX 7 AA7 ARG m 109 LEU m 113 5 5 HELIX 8 AA8 PRO m 114 LEU m 118 5 5 HELIX 9 AA9 ARG m 130 GLU m 135 1 6 HELIX 10 AB1 SER m 136 PHE m 141 1 6 HELIX 11 AB2 ASN m 156 THR m 180 1 25 HELIX 12 AB3 GLY m 185 ASN m 192 1 8 HELIX 13 AB4 GLU m 200 LYS m 205 5 6 HELIX 14 AB5 SER m 208 SER m 222 1 15 HELIX 15 AB6 ASP m 233 ARG m 238 1 6 HELIX 16 AB7 CYS m 239 THR m 250 1 12 HELIX 17 AB8 PRO m 266 SER m 278 1 13 HELIX 18 AB9 GLY m 295 HIS m 310 1 16 HELIX 19 AC1 GLY m 327 LYS m 337 1 11 HELIX 20 AC2 SER m 378 ARG m 385 1 8 HELIX 21 AC3 ARG m 389 VAL m 393 5 5 HELIX 22 AC4 PRO m 396 GLN m 398 5 3 HELIX 23 AC5 TYR m 399 LYS m 405 1 7 HELIX 24 AC6 GLN m 408 GLU m 417 1 10 HELIX 25 AC7 ASP m 423 GLY m 436 1 14 HELIX 26 AC8 ASP m 445 ARG m 459 1 15 SHEET 1 AA1 6 THR m 283 ALA m 285 0 SHEET 2 AA1 6 HIS m 254 ASN m 260 1 N LEU m 259 O LEU m 284 SHEET 3 AA1 6 VAL m 224 ASP m 230 1 N VAL m 225 O HIS m 254 SHEET 4 AA1 6 ILE m 316 GLY m 322 1 O GLY m 319 N ILE m 226 SHEET 5 AA1 6 ILE m 362 ASP m 366 1 O PHE m 363 N VAL m 318 SHEET 6 AA1 6 GLN m 354 THR m 357 -1 N ILE m 356 O LEU m 364 LINK OD1 ASN m 325 K K m 502 1555 1555 2.81 LINK OG SER m 329 MG MG m 501 1555 1555 2.15 LINK O ALA m 344 K K m 502 1555 1555 2.80 LINK O ILE m 346 K K m 502 1555 1555 3.33 LINK OG1 THR m 350 MG MG m 501 1555 1555 2.67 LINK MG MG m 501 O3B GDP m 503 1555 1555 2.08 LINK K K m 502 O1B GDP m 503 1555 1555 2.78 LINK K K m 502 O1A GDP m 503 1555 1555 3.23 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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