HEADER RNA BINDING PROTEIN 26-MAY-25 9V65 TITLE CRYO-EM STRUCTURE OF FREE-STATE VBAGO COMPND MOL_ID: 1; COMPND 2 MOLECULE: VBAGO; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VERRUCOMICROBIOTA BACTERIUM; SOURCE 3 ORGANISM_TAXID: 2026799; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MESOPHILIC PROKARYOTIC ARGONAUTE, RNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.WU REVDAT 1 15-APR-26 9V65 0 JRNL AUTH T.CHEN,X.TAO,S.LI,Q.DUANMU,J.WANG,K.CHEN,K.MU,H.YANG,Y.LI, JRNL AUTH 2 Y.LIU,L.MA,S.WU JRNL TITL STRUCTURAL INSIGHTS INTO C-TERMINUS-MEDIATED RNA TARGET JRNL TITL 2 CLEAVAGE BY A MESOPHILIC PROKARYOTIC ARGONAUTE. JRNL REF NAT COMMUN 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 41932907 JRNL DOI 10.1038/S41467-026-71422-Y REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 84950 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 9V65 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 30-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300059488. 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 : VBAGO 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOCONTINUUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 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) : 5400.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 A 1 REMARK 465 SER A 2 REMARK 465 GLU A 3 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 ASP A 173 -0.72 76.07 REMARK 500 SER A 196 -139.53 62.82 REMARK 500 ASN A 223 -166.88 -79.78 REMARK 500 ASN A 269 34.95 -99.08 REMARK 500 THR A 297 2.28 59.79 REMARK 500 ALA A 369 49.92 -84.08 REMARK 500 SER A 370 14.44 -140.23 REMARK 500 ASN A 465 76.60 -101.64 REMARK 500 ASP A 477 43.88 -142.46 REMARK 500 LEU A 491 35.79 -97.27 REMARK 500 ASP A 587 139.76 78.44 REMARK 500 LYS A 643 48.86 -82.95 REMARK 500 ASP A 644 18.27 -144.77 REMARK 500 PRO A 742 42.62 -83.88 REMARK 500 SER A 755 -11.30 -141.17 REMARK 500 GLU A 761 -131.92 60.41 REMARK 500 ASN A 765 73.70 57.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-64797 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF FREE-STATE VBAGO DBREF 9V65 A 1 782 PDB 9V65 9V65 1 782 SEQRES 1 A 782 MET SER GLU LYS GLN LEU GLY ALA THR LEU PHE PRO ILE SEQRES 2 A 782 THR GLY LEU PRO ALA GLN ALA PHE ARG LEU ARG VAL LEU SEQRES 3 A 782 ARG VAL ARG GLU THR ILE PRO MET ASP THR GLN THR PRO SEQRES 4 A 782 VAL ARG LEU ASN ARG TRP ALA THR GLN LEU TRP LYS GLU SEQRES 5 A 782 LEU LYS GLN ALA VAL VAL PRO THR GLY ARG PHE GLU TRP SEQRES 6 A 782 PRO ALA PHE LEU THR PRO ASP VAL GLU SER LEU THR VAL SEQRES 7 A 782 GLY ARG VAL LEU THR VAL GLN ASP VAL PRO ASP ARG GLU SEQRES 8 A 782 TYR SER ILE GLU VAL ILE GLY GLU THR VAL GLU VAL ASN SEQRES 9 A 782 PRO ALA SER ALA SER SER GLU GLU LEU GLN LEU ALA GLY SEQRES 10 A 782 GLU MET ILE LYS ARG ALA ILE SER ASP ALA PHE GLY ARG SEQRES 11 A 782 ASN SER ASP LYS TYR TRP ARG LYS HIS TRP ASN LEU TYR SEQRES 12 A 782 PHE ARG LEU GLU PRO GLU ASN LEU GLN ASP ARG ARG ASP SEQRES 13 A 782 ARG VAL PHE ALA TYR ARG GLY LEU LYS PHE SER VAL VAL SEQRES 14 A 782 PHE LEU GLY ASP LYS PRO TRP LEU ALA ALA ASP ILE LEU SEQRES 15 A 782 THR THR TYR HIS GLY GLN HIS ALA LEU SER GLU TYR SER SEQRES 16 A 782 SER GLU GLN ARG GLN ARG GLU LEU HIS PHE HIS VAL SER SEQRES 17 A 782 GLU ARG ILE GLU ALA ASP ASP ARG ALA MET PHE LEU ARG SEQRES 18 A 782 ASP ASN GLY LYS ILE LYS ILE PRO CYS ARG PHE VAL GLY SEQRES 19 A 782 SER THR GLY LYS THR VAL THR GLN TYR THR PHE PRO ILE SEQRES 20 A 782 ASN GLY GLY GLN LYS ASN VAL ARG GLU TYR TYR GLU GLN SEQRES 21 A 782 ARG TYR GLY ILE ARG VAL PRO GLU ASN ASP GLU ALA VAL SEQRES 22 A 782 PHE VAL ARG ASP ARG GLU GLY CYS ASP SER TRP PRO VAL SEQRES 23 A 782 PRO ALA SER ARG LEU PHE PRO LEU PHE THR THR GLU TYR SEQRES 24 A 782 ASP GLU VAL ARG ASN CYS SER VAL VAL PRO GLN MET PRO SEQRES 25 A 782 PRO ASP GLU ARG VAL GLU THR ILE ARG ALA PHE LEU ASN SEQRES 26 A 782 ASP LEU ARG ASP VAL SER PHE ALA GLY SER THR LEU ALA SEQRES 27 A 782 ILE GLY HIS SER HIS PHE GLN THR ALA GLU ARG SER VAL SEQRES 28 A 782 PHE PRO ALA PRO ALA LEU GLU PHE GLY ASN GLY GLN THR SEQRES 29 A 782 LEU THR VAL ASP ALA SER LEU PRO ILE GLU GLU GLY TYR SEQRES 30 A 782 ASN ARG TYR ARG GLN GLY LYS MET THR MET LEU TYR GLU SEQRES 31 A 782 HIS GLY PRO PHE SER SER GLN SER LEU PRO ASP LEU VAL SEQRES 32 A 782 LEU LEU TYR PRO ASP ASN LEU ASP ARG ASN ALA ARG GLU SEQRES 33 A 782 LYS LEU ARG GLN ARG LEU GLY GLU GLU ILE LYS GLU LEU SEQRES 34 A 782 CYS GLY VAL ALA PRO ARG ILE ALA ARG GLN ILE SER TYR SEQRES 35 A 782 PRO LEU GLY LYS GLN PRO HIS ALA GLY ALA GLY LEU LEU SEQRES 36 A 782 ALA ALA ALA ASP GLU LEU VAL ARG ASN ASN ASP GLY THR SEQRES 37 A 782 PHE LEU PRO VAL ILE VAL LEU ALA ASP ALA LEU ARG GLU SEQRES 38 A 782 HIS ILE TYR ASP LEU LEU LYS ARG ARG LEU SER SER LEU SEQRES 39 A 782 ALA SER GLN CYS VAL ARG GLU ARG THR VAL ALA ARG VAL SEQRES 40 A 782 ALA ARG ASP GLU GLN ALA VAL GLY GLY SER ARG LEU ARG SEQRES 41 A 782 ASN LEU ALA LEU GLY ILE LEU THR ALA ALA GLY LEU GLN SEQRES 42 A 782 PRO TRP VAL LEU ALA LYS PRO LEU HIS TYR ASP PHE TYR SEQRES 43 A 782 MET GLY VAL ASP LEU LEU ALA ASN GLN VAL ILE TYR VAL SEQRES 44 A 782 PHE VAL CYS GLY LYS GLY GLY ARG ASN VAL TRP VAL GLN SEQRES 45 A 782 ARG GLY ASP GLN LEU ARG ARG ARG GLY ILE THR GLU LYS SEQRES 46 A 782 ILE ASP ARG VAL GLN LEU ALA ASP GLN PHE LYS THR GLY SEQRES 47 A 782 VAL ARG GLU ALA LYS ARG LEU GLY VAL PRO LEU ASN SER SEQRES 48 A 782 LEU VAL VAL HIS ARG ASP GLY ARG TRP TRP SER ASN GLU SEQRES 49 A 782 ASP LEU ALA ILE THR GLU ALA VAL ALA GLU LEU GLN GLY SEQRES 50 A 782 ASP GLY THR LEU SER LYS ASP CYS GLN VAL GLY VAL VAL SEQRES 51 A 782 GLU VAL ARG LYS SER HIS LEU PRO VAL ARG LEU PHE SER SEQRES 52 A 782 VAL LEU ASN ALA THR LYS GLY SER LEU GLU ASN PRO MET SEQRES 53 A 782 PRO GLY SER HIS LEU ILE LEU ASN ASN THR GLU ALA ILE SEQRES 54 A 782 LEU THR PRO THR GLY GLN PRO GLY ARG TRP ASP LYS GLN SEQRES 55 A 782 GLY ARG THR ALA GLY THR LEU LEU LEU ARG ILE THR ARG SEQRES 56 A 782 ASN PRO ASN GLY SER PRO LEU ASP ILE ARG LYS ILE ALA SEQRES 57 A 782 GLU ASP ALA TYR GLY LEU THR HIS LEU ASN TRP ASN ALA SEQRES 58 A 782 PRO ASP ILE GLU ILE SER LEU PRO VAL THR ILE ARG TRP SEQRES 59 A 782 SER ASP GLU ARG LEU ARG GLU ILE VAL THR ASN PRO SER SEQRES 60 A 782 ALA THR ASP ASP THR GLU VAL GLU PRO GLN GLU THR CYS SEQRES 61 A 782 ILE VAL FORMUL 2 HOH *(H2 O) HELIX 1 AA1 GLN A 37 LYS A 54 1 18 HELIX 2 AA2 SER A 109 ARG A 130 1 22 HELIX 3 AA3 GLU A 197 GLU A 202 1 6 HELIX 4 AA4 LEU A 203 SER A 208 1 6 HELIX 5 AA5 VAL A 254 GLY A 263 1 10 HELIX 6 AA6 TYR A 299 ASN A 304 1 6 HELIX 7 AA7 PRO A 312 LEU A 324 1 13 HELIX 8 AA8 ASN A 325 ARG A 328 5 4 HELIX 9 AA9 PRO A 372 HIS A 391 1 20 HELIX 10 AB1 ASP A 411 CYS A 430 1 20 HELIX 11 AB2 GLY A 453 ASN A 464 1 12 HELIX 12 AB3 HIS A 482 LEU A 491 1 10 HELIX 13 AB4 GLU A 501 ASP A 510 1 10 HELIX 14 AB5 LEU A 519 GLY A 531 1 13 HELIX 15 AB6 ARG A 588 LEU A 605 1 18 HELIX 16 AB7 TRP A 621 GLY A 639 1 19 HELIX 17 AB8 ASP A 723 HIS A 736 1 14 SHEET 1 AA1 4 PHE A 344 THR A 346 0 SHEET 2 AA1 4 GLN A 5 ALA A 8 -1 N LEU A 6 O THR A 346 SHEET 3 AA1 4 LEU A 661 VAL A 664 -1 O PHE A 662 N GLY A 7 SHEET 4 AA1 4 LEU A 672 GLU A 673 -1 O GLU A 673 N SER A 663 SHEET 1 AA2 9 TYR A 135 HIS A 139 0 SHEET 2 AA2 9 LEU A 142 ARG A 145 -1 O PHE A 144 N TRP A 136 SHEET 3 AA2 9 VAL A 158 LEU A 171 -1 O LEU A 164 N TYR A 143 SHEET 4 AA2 9 LYS A 174 GLY A 187 -1 O LEU A 182 N GLY A 163 SHEET 5 AA2 9 LEU A 291 PHE A 295 -1 O PHE A 295 N TYR A 185 SHEET 6 AA2 9 PHE A 219 ASP A 222 -1 N LEU A 220 O PHE A 292 SHEET 7 AA2 9 LYS A 227 THR A 239 -1 O CYS A 230 N PHE A 219 SHEET 8 AA2 9 GLU A 271 ASP A 277 -1 O ARG A 276 N ARG A 231 SHEET 9 AA2 9 TRP A 284 PRO A 287 -1 O VAL A 286 N VAL A 273 SHEET 1 AA3 7 TYR A 135 HIS A 139 0 SHEET 2 AA3 7 LEU A 142 ARG A 145 -1 O PHE A 144 N TRP A 136 SHEET 3 AA3 7 VAL A 158 LEU A 171 -1 O LEU A 164 N TYR A 143 SHEET 4 AA3 7 LYS A 174 GLY A 187 -1 O LEU A 182 N GLY A 163 SHEET 5 AA3 7 LEU A 10 THR A 14 -1 N PHE A 11 O LEU A 177 SHEET 6 AA3 7 THR A 336 ILE A 339 -1 O ALA A 338 N THR A 14 SHEET 7 AA3 7 VAL A 330 SER A 331 -1 N VAL A 330 O LEU A 337 SHEET 1 AA4 5 VAL A 58 THR A 60 0 SHEET 2 AA4 5 ALA A 67 PRO A 71 -1 O ALA A 67 N THR A 60 SHEET 3 AA4 5 ARG A 22 VAL A 28 -1 N ARG A 24 O THR A 70 SHEET 4 AA4 5 TYR A 92 GLU A 102 -1 O VAL A 101 N LEU A 23 SHEET 5 AA4 5 VAL A 81 VAL A 84 -1 N LEU A 82 O ILE A 94 SHEET 1 AA5 2 THR A 244 ILE A 247 0 SHEET 2 AA5 2 GLY A 250 ASN A 253 -1 O GLY A 250 N ILE A 247 SHEET 1 AA6 4 ARG A 438 TYR A 442 0 SHEET 2 AA6 4 ASP A 401 PRO A 407 1 N LEU A 404 O ILE A 440 SHEET 3 AA6 4 PHE A 469 LEU A 475 1 O VAL A 472 N VAL A 403 SHEET 4 AA6 4 VAL A 499 ARG A 500 1 O VAL A 499 N ILE A 473 SHEET 1 AA7 8 ASN A 568 VAL A 571 0 SHEET 2 AA7 8 GLN A 555 CYS A 562 -1 N PHE A 560 O TRP A 570 SHEET 3 AA7 8 PHE A 545 LEU A 552 -1 N TYR A 546 O VAL A 561 SHEET 4 AA7 8 SER A 611 ASP A 617 1 O SER A 611 N PHE A 545 SHEET 5 AA7 8 GLN A 646 ARG A 653 1 O VAL A 650 N VAL A 614 SHEET 6 AA7 8 LEU A 709 ARG A 715 -1 O THR A 714 N VAL A 649 SHEET 7 AA7 8 GLU A 687 THR A 691 -1 N ALA A 688 O LEU A 711 SHEET 8 AA7 8 SER A 679 ILE A 682 -1 N LEU A 681 O ILE A 689 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 MASTER 144 0 0 17 39 0 0 6 6210 1 0 61 END