HEADER TRANSLATION 08-JUL-22 8DMF TITLE CRYO-EM STRUCTURE OF THE RIBOSOME-BOUND BACTEROIDES THETAIOTAOMICRON TITLE 2 EF-G2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TETRACYCLINE RESISTANCE PROTEIN TETQ; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EF-G2 PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON VPI-5482; SOURCE 3 ORGANISM_TAXID: 226186; SOURCE 4 STRAIN: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / SOURCE 5 VPI-5482 / E50; SOURCE 6 GENE: BT_2167; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS TRANSLATION ELONGATION FACTOR, BACTEROIDES THETAIOTAOMICRON EF-G2, KEYWDS 2 TRANSLATION EXPDTA ELECTRON MICROSCOPY AUTHOR C.WANG,W.HAN,E.A.GROISMAN,J.LIU REVDAT 2 12-JUN-24 8DMF 1 REMARK REVDAT 1 04-JAN-23 8DMF 0 JRNL AUTH W.HAN,B.Z.PENG,C.WANG,G.E.TOWNSEND 2ND,N.A.BARRY,F.PESKE, JRNL AUTH 2 A.L.GOODMAN,J.LIU,M.V.RODNINA,E.A.GROISMAN JRNL TITL GUT COLONIZATION BY BACTEROIDES REQUIRES TRANSLATION BY AN JRNL TITL 2 EF-G PARALOG LACKING GTPASE ACTIVITY. JRNL REF EMBO J. 12372 2022 JRNL REFN ESSN 1460-2075 JRNL PMID 36472247 JRNL DOI 10.15252/EMBJ.2022112372 REMARK 2 REMARK 2 RESOLUTION. 4.00 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 : 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) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.000 REMARK 3 NUMBER OF PARTICLES : 134023 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8DMF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000266896. 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 : RIBOSOME-BOUND BACTEROIDES REMARK 245 THETAIOTAOMICRON EF-G2 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 : 7.50 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : DIRECT ELECTRON DE-64 (8K X REMARK 245 8K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 3000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL 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: A 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: 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 LYS A 22 -60.56 -90.98 REMARK 500 ASN A 72 98.04 -67.23 REMARK 500 ILE A 165 -61.21 -99.98 REMARK 500 GLN A 230 -61.45 -94.94 REMARK 500 THR A 234 -106.12 47.94 REMARK 500 VAL A 276 143.64 -173.34 REMARK 500 ARG A 338 55.11 38.74 REMARK 500 ALA A 351 31.26 -99.44 REMARK 500 THR A 477 -164.98 -178.53 REMARK 500 VAL A 514 74.29 41.51 REMARK 500 LEU A 575 -168.43 -117.85 REMARK 500 ARG A 648 42.74 39.33 REMARK 500 LYS A 658 -110.31 35.65 REMARK 500 ALA A 694 -87.73 -120.42 REMARK 500 REMARK 500 REMARK: NULL 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 MG A 801 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 23 OG1 REMARK 620 2 GTP A 802 O1A 118.7 REMARK 620 3 GTP A 802 O3G 59.9 141.4 REMARK 620 4 GTP A 802 O3A 157.2 57.9 107.3 REMARK 620 5 GTP A 802 O2A 93.6 51.7 89.8 66.3 REMARK 620 6 GTP A 802 O2B 118.4 118.1 61.5 60.3 103.6 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-27535 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-27543 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-27546 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-27547 RELATED DB: EMDB DBREF 8DMF A 1 718 UNP Q8A5S1 Q8A5S1_BACTN 1 718 SEQRES 1 A 718 MET LYS VAL TYR GLN THR ASN GLU ILE LYS ASN ILE ALA SEQRES 2 A 718 LEU LEU GLY SER SER GLY SER GLY LYS THR THR LEU VAL SEQRES 3 A 718 GLU ALA MET LEU PHE GLU SER GLY VAL ILE LYS ARG ARG SEQRES 4 A 718 GLY SER VAL ALA ALA LYS ASN THR VAL SER ASP TYR PHE SEQRES 5 A 718 PRO VAL GLU GLN GLU TYR GLY TYR SER VAL PHE SER THR SEQRES 6 A 718 VAL LEU HIS VAL GLU TRP ASN ASN LYS LYS LEU ASN ILE SEQRES 7 A 718 ILE ASP CYS PRO GLY SER ASP ASP PHE VAL GLY SER THR SEQRES 8 A 718 VAL THR ALA LEU ASN VAL THR ASP THR ALA ILE ILE LEU SEQRES 9 A 718 LEU ASN GLY GLN TYR GLY VAL GLU VAL GLY THR GLN ASN SEQRES 10 A 718 HIS PHE ARG TYR THR GLU LYS LEU ASN LYS PRO VAL ILE SEQRES 11 A 718 PHE LEU VAL ASN GLN LEU ASP ASN GLU LYS CYS ASP TYR SEQRES 12 A 718 ASP ASN ILE LEU GLU GLN LEU LYS GLU ALA TYR GLY SER SEQRES 13 A 718 LYS VAL VAL PRO ILE GLN TYR PRO ILE ALA THR GLY PRO SEQRES 14 A 718 GLY PHE ASN ALA LEU ILE ASP VAL LEU LEU MET LYS LYS SEQRES 15 A 718 TYR SER TRP LYS PRO GLU GLY GLY ALA PRO VAL ILE GLU SEQRES 16 A 718 ASP ILE PRO ALA GLU GLU MET ASP LYS ALA MET GLU MET SEQRES 17 A 718 HIS LYS ALA LEU VAL GLU ALA ALA ALA GLU ASN ASP GLU SEQRES 18 A 718 GLY LEU MET GLU LYS PHE PHE GLU GLN ASP SER LEU THR SEQRES 19 A 718 GLU ASP GLU MET ARG GLU GLY ILE ARG LYS GLY LEU ILE SEQRES 20 A 718 ALA ARG GLY MET PHE PRO VAL PHE CYS VAL CYS GLY GLY SEQRES 21 A 718 LYS ASP MET GLY VAL ARG ARG LEU MET GLU PHE LEU GLY SEQRES 22 A 718 ASN VAL VAL PRO PHE VAL SER GLU MET PRO LYS VAL GLU SEQRES 23 A 718 ASN THR ASP GLY LYS GLU VAL ALA PRO ASP VAL ASN GLY SEQRES 24 A 718 PRO GLU SER LEU TYR PHE PHE LYS THR SER VAL GLU PRO SEQRES 25 A 718 HIS ILE GLY GLU VAL SER TYR PHE LYS VAL MET SER GLY SEQRES 26 A 718 LYS VAL ARG GLU GLY ASP ASP LEU LEU ASN ALA ASP ARG SEQRES 27 A 718 GLY SER LYS GLU ARG ILE ALA GLN ILE TYR VAL VAL ALA SEQRES 28 A 718 GLY GLY ASN ARG VAL LYS VAL GLU GLU LEU GLN ALA GLY SEQRES 29 A 718 ASP ILE GLY ALA ALA VAL LYS LEU LYS ASP VAL LYS THR SEQRES 30 A 718 GLY ASN THR LEU ASN GLY LYS ASP CYS ASP TYR LYS PHE SEQRES 31 A 718 ASN PHE ILE LYS TYR PRO ASN SER LYS TYR SER ARG ALA SEQRES 32 A 718 ILE LYS PRO VAL ASN GLU ALA ASP VAL GLU LYS MET MET SEQRES 33 A 718 THR ILE LEU ASN ARG MET ARG GLU GLU ASP PRO THR TRP SEQRES 34 A 718 VAL ILE GLU GLN SER LYS GLU LEU LYS GLN THR LEU VAL SEQRES 35 A 718 HIS GLY GLN GLY GLU PHE HIS LEU ARG THR LEU LYS TRP SEQRES 36 A 718 ARG LEU GLU ASN ASN GLU LYS LEU GLN VAL LYS PHE GLU SEQRES 37 A 718 GLU PRO LYS ILE PRO TYR ARG GLU THR ILE THR LYS ALA SEQRES 38 A 718 ALA ARG ALA ASP TYR ARG HIS LYS LYS GLN SER GLY GLY SEQRES 39 A 718 ALA GLY GLN PHE GLY GLU VAL HIS LEU ILE VAL GLU PRO SEQRES 40 A 718 TYR LYS GLU GLY MET PRO VAL PRO ASP THR TYR LYS PHE SEQRES 41 A 718 ASN GLY GLN GLU PHE LYS ILE THR VAL ARG GLY THR GLU SEQRES 42 A 718 GLU ILE PRO LEU GLU TRP GLY GLY LYS LEU VAL PHE ILE SEQRES 43 A 718 ASN SER ILE VAL GLY GLY SER ILE ASP ALA ARG PHE LEU SEQRES 44 A 718 PRO ALA ILE MET LYS GLY ILE MET SER ARG LEU GLU GLN SEQRES 45 A 718 GLY PRO LEU THR GLY SER TYR ALA ARG ASP VAL ARG VAL SEQRES 46 A 718 ILE VAL TYR ASP GLY LYS MET HIS PRO VAL ASP SER ASN SEQRES 47 A 718 GLU ILE SER PHE MET LEU ALA GLY ARG ASN ALA PHE SER SEQRES 48 A 718 GLU ALA PHE LYS ASN ALA GLY PRO LYS ILE LEU GLU PRO SEQRES 49 A 718 ILE TYR ASP VAL GLU VAL PHE VAL PRO SER ASP ARG MET SEQRES 50 A 718 GLY ASP VAL MET GLY ASP LEU GLN GLY ARG ARG ALA MET SEQRES 51 A 718 ILE MET GLY MET SER SER GLU LYS GLY PHE GLU LYS LEU SEQRES 52 A 718 VAL ALA LYS VAL PRO LEU LYS GLU MET SER SER TYR SER SEQRES 53 A 718 THR ALA LEU SER SER LEU THR GLY GLY ARG ALA SER PHE SEQRES 54 A 718 ILE MET LYS PHE ALA SER TYR GLU LEU VAL PRO THR ASP SEQRES 55 A 718 VAL GLN ASP LYS LEU ILE LYS ASP PHE GLU ALA LYS GLN SEQRES 56 A 718 THR GLU GLU HET MG A 801 1 HET GTP A 802 32 HETNAM MG MAGNESIUM ION HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 GTP C10 H16 N5 O14 P3 HELIX 1 AA1 GLN A 5 ASN A 7 5 3 HELIX 2 AA2 GLY A 21 SER A 33 1 13 HELIX 3 AA3 PHE A 52 TYR A 58 1 7 HELIX 4 AA4 PHE A 87 THR A 98 1 12 HELIX 5 AA5 GLU A 112 ASN A 126 1 15 HELIX 6 AA6 ASP A 142 TYR A 154 1 13 HELIX 7 AA7 THR A 167 PHE A 171 5 5 HELIX 8 AA8 PRO A 198 GLU A 200 5 3 HELIX 9 AA9 GLU A 201 ASP A 220 1 20 HELIX 10 AB1 GLU A 235 ALA A 248 1 14 HELIX 11 AB2 GLY A 264 VAL A 275 1 12 HELIX 12 AB3 ASP A 411 ASP A 426 1 16 HELIX 13 AB4 GLY A 446 ASN A 459 1 14 HELIX 14 AB5 ASP A 555 ARG A 557 5 3 HELIX 15 AB6 PHE A 558 GLU A 571 1 14 HELIX 16 AB7 ASN A 598 ALA A 617 1 20 HELIX 17 AB8 ARG A 636 GLY A 646 1 11 HELIX 18 AB9 LYS A 670 MET A 672 5 3 HELIX 19 AC1 SER A 674 GLY A 684 1 11 HELIX 20 AC2 PRO A 700 THR A 716 1 17 SHEET 1 AA1 7 THR A 65 GLU A 70 0 SHEET 2 AA1 7 LYS A 75 ASP A 80 -1 O LEU A 76 N VAL A 69 SHEET 3 AA1 7 ILE A 9 LEU A 15 1 N LYS A 10 O ASN A 77 SHEET 4 AA1 7 THR A 100 ASN A 106 1 O ILE A 102 N LEU A 15 SHEET 5 AA1 7 VAL A 129 ASN A 134 1 O ASN A 134 N LEU A 105 SHEET 6 AA1 7 PRO A 253 CYS A 256 1 O PRO A 253 N PHE A 131 SHEET 7 AA1 7 VAL A 159 PRO A 160 1 N VAL A 159 O VAL A 254 SHEET 1 AA2 3 GLN A 162 PRO A 164 0 SHEET 2 AA2 3 ALA A 173 ASP A 176 -1 O ILE A 175 N TYR A 163 SHEET 3 AA2 3 LYS A 181 SER A 184 -1 O LYS A 181 N ASP A 176 SHEET 1 AA3 6 GLU A 342 ARG A 343 0 SHEET 2 AA3 6 ASP A 332 ASN A 335 -1 N LEU A 333 O GLU A 342 SHEET 3 AA3 6 THR A 380 ASN A 382 -1 O ASN A 382 N LEU A 334 SHEET 4 AA3 6 SER A 302 TYR A 304 -1 N LEU A 303 O LEU A 381 SHEET 5 AA3 6 SER A 318 SER A 324 -1 O LYS A 321 N TYR A 304 SHEET 6 AA3 6 ILE A 366 ALA A 369 -1 O GLY A 367 N PHE A 320 SHEET 1 AA4 2 LYS A 326 ARG A 328 0 SHEET 2 AA4 2 GLU A 360 GLN A 362 -1 O LEU A 361 N VAL A 327 SHEET 1 AA5 2 ILE A 347 VAL A 350 0 SHEET 2 AA5 2 ARG A 355 VAL A 358 -1 O VAL A 356 N VAL A 349 SHEET 1 AA6 4 VAL A 430 SER A 434 0 SHEET 2 AA6 4 GLN A 439 GLY A 444 -1 O LEU A 441 N GLU A 432 SHEET 3 AA6 4 TYR A 400 PRO A 406 -1 N ARG A 402 O VAL A 442 SHEET 4 AA6 4 VAL A 465 GLU A 468 -1 O LYS A 466 N LYS A 405 SHEET 1 AA7 3 TYR A 579 ALA A 580 0 SHEET 2 AA7 3 ARG A 475 ILE A 478 1 N GLU A 476 O TYR A 579 SHEET 3 AA7 3 PRO A 619 LEU A 622 -1 O LEU A 622 N ARG A 475 SHEET 1 AA8 5 ALA A 482 HIS A 488 0 SHEET 2 AA8 5 GLY A 499 PRO A 507 -1 O GLY A 499 N HIS A 488 SHEET 3 AA8 5 VAL A 583 GLY A 590 -1 O ARG A 584 N GLU A 506 SHEET 4 AA8 5 LYS A 542 VAL A 544 1 N VAL A 544 O VAL A 585 SHEET 5 AA8 5 GLU A 534 PRO A 536 -1 N ILE A 535 O LEU A 543 SHEET 1 AA9 4 MET A 650 MET A 654 0 SHEET 2 AA9 4 PHE A 660 PRO A 668 -1 O VAL A 664 N MET A 652 SHEET 3 AA9 4 ILE A 625 PRO A 633 -1 N VAL A 632 O GLU A 661 SHEET 4 AA9 4 MET A 691 PHE A 693 -1 O LYS A 692 N ASP A 627 LINK OG1 THR A 23 MG MG A 801 1555 1555 2.58 LINK MG MG A 801 O1A GTP A 802 1555 1555 2.97 LINK MG MG A 801 O3G GTP A 802 1555 1555 2.17 LINK MG MG A 801 O3A GTP A 802 1555 1555 1.98 LINK MG MG A 801 O2A GTP A 802 1555 1555 2.66 LINK MG MG A 801 O2B GTP A 802 1555 1555 2.92 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