HEADER RNA 20-SEP-24 9DP9 TITLE STRUCTURE OF A TICK-BORNE FLAVIVIRUS XRRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (440-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: POWASSAN VIRUS; SOURCE 3 ORGANISM_TAXID: 11083; SOURCE 4 VARIANT: SPOONER ISOLATE; SOURCE 5 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS VIRUS, RNA, XRRNA, EXONUCLEASE EXPDTA ELECTRON MICROSCOPY AUTHOR C.J.LANGEBERG,J.S.KIEFT,M.E.SHERLOCK,M.J.SZUCS,Q.VICENS REVDAT 1 28-MAY-25 9DP9 0 JRNL AUTH C.J.LANGEBERG,M.J.SZUCS,M.E.SHERLOCK,Q.VICENS,J.S.KIEFT JRNL TITL TICK-BORNE FLAVIVIRUS EXORIBONUCLEASE-RESISTANT RNAS CONTAIN JRNL TITL 2 A DOUBLE LOOP STRUCTURE. JRNL REF NAT COMMUN V. 16 4515 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40374626 JRNL DOI 10.1038/S41467-025-59657-7 REMARK 2 REMARK 2 RESOLUTION. 4.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, CRYOSPARC, PHENIX, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 7K16 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 150.220 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) : 4.100 REMARK 3 NUMBER OF PARTICLES : 55485 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9DP9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1000288574. 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 : STRUCTURE OF A TICK-BORNE REMARK 245 FLAVIVIRUS XRRNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 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 : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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 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 C2 A A 412 C5 U A 415 1.01 REMARK 500 O2' G A 417 N1 A A 453 1.22 REMARK 500 OP2 A A 404 C5' U A 449 1.62 REMARK 500 N1 A A 412 C5 U A 415 1.66 REMARK 500 O2 U A 15 N2 G A 426 1.88 REMARK 500 C2 A A 412 C4 U A 415 2.00 REMARK 500 OP2 A A 404 O5' U A 449 2.01 REMARK 500 N1 A A 412 C6 U A 415 2.05 REMARK 500 C2 A A 412 C6 U A 415 2.12 REMARK 500 O4' G A 17 N7 A A 404 2.15 REMARK 500 O2' G A 417 C2 A A 453 2.17 REMARK 500 O4' G A 17 C8 A A 404 2.17 REMARK 500 O6 G A 165 O4 U A 172 2.18 REMARK 500 N3 A A 412 C5 U A 415 2.19 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 506 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 39 OP1 REMARK 620 2 U A 56 OP1 98.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 509 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 40 OP1 REMARK 620 2 U A 41 OP2 76.1 REMARK 620 3 U A 88 OP2 102.4 176.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 45 OP2 REMARK 620 2 A A 376 OP1 130.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 512 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 85 OP1 REMARK 620 2 A A 85 OP2 55.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 519 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 89 O3' REMARK 620 2 U A 90 OP2 63.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 514 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 340 OP1 REMARK 620 2 A A 340 OP2 59.1 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-47099 RELATED DB: EMDB REMARK 900 STRUCTURE OF A TICK-BORNE FLAVIVIRUS XRRNA DBREF 9DP9 A 3 457 PDB 9DP9 9DP9 3 457 SEQRES 1 A 440 U A G G G G G U G A U G U SEQRES 2 A 440 G G C A G C G C A C U U G SEQRES 3 A 440 A U A U G G A U G C A G U SEQRES 4 A 440 U C A C A G A C U A A A U SEQRES 5 A 440 G U C G G U C G G G G A A SEQRES 6 A 440 G A U G U A U U C U U C U SEQRES 7 A 440 C A U A A G A U A U A G U SEQRES 8 A 440 C G G A C C U C U C C U U SEQRES 9 A 440 A A U G G G A G C U A G C SEQRES 10 A 440 G G A U G A A G U G A U G SEQRES 11 A 440 C A A C A C U G G A G C C SEQRES 12 A 440 G C U G G G A A C U A A U SEQRES 13 A 440 U U G U A U G C G A A A G SEQRES 14 A 440 U A U A U U G A U U A G U SEQRES 15 A 440 U U U G G A G A A A G U U SEQRES 16 A 440 A U C A G G C A U G C A C SEQRES 17 A 440 C U G G U A G C U A G U C SEQRES 18 A 440 U U U A A A C C A A U A G SEQRES 19 A 440 A U U G C A U C G G U U U SEQRES 20 A 440 A A A A G G C A A G A C C SEQRES 21 A 440 G U C A A A U U G C G G G SEQRES 22 A 440 A A A G G G G U C A A C A SEQRES 23 A 440 G C C G U U C A G U A C C SEQRES 24 A 440 A A G U C U C A G G G G A SEQRES 25 A 440 A A C U U U G A G A U G G SEQRES 26 A 440 C C U U G C A A A G G G U SEQRES 27 A 440 A U G G U A A U A A G C U SEQRES 28 A 440 G A C G G A C A U G G U C SEQRES 29 A 440 C U A A C C A C G C A G C SEQRES 30 A 440 C A A G U C C U A A G U C SEQRES 31 A 440 A A G U G A C G G G A A A SEQRES 32 A 440 A G G U C G U C C C C G A SEQRES 33 A 440 C G C A U C A U C C C U C SEQRES 34 A 440 U A U G C G A G A C C HET MG A 501 1 HET MG A 502 1 HET MG A 503 1 HET MG A 504 1 HET MG A 505 1 HET MG A 506 1 HET MG A 507 1 HET MG A 508 1 HET MG A 509 1 HET MG A 510 1 HET MG A 511 1 HET MG A 512 1 HET MG A 513 1 HET MG A 514 1 HET MG A 515 1 HET MG A 516 1 HET MG A 517 1 HET MG A 518 1 HET MG A 519 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 19(MG 2+) LINK OP2 U A 36 MG MG A 508 1555 1555 2.82 LINK OP1 A A 39 MG MG A 506 1555 1555 2.15 LINK OP1 G A 40 MG MG A 509 1555 1555 2.58 LINK OP2 U A 41 MG MG A 509 1555 1555 2.12 LINK OP1 U A 42 MG MG A 510 1555 1555 2.29 LINK OP2 C A 45 MG MG A 502 1555 1555 2.58 LINK OP1 U A 56 MG MG A 506 1555 1555 2.59 LINK OP1 A A 85 MG MG A 512 1555 1555 2.98 LINK OP2 A A 85 MG MG A 512 1555 1555 2.39 LINK OP2 U A 88 MG MG A 509 1555 1555 2.16 LINK OP1 U A 88 MG MG A 511 1555 1555 2.55 LINK OP1 A A 89 MG MG A 518 1555 1555 2.45 LINK O3' A A 89 MG MG A 519 1555 1555 2.25 LINK OP2 U A 90 MG MG A 519 1555 1555 2.47 LINK O2' A A 211 MG MG A 516 1555 1555 2.65 LINK OP1 A A 308 MG MG A 505 1555 1555 2.95 LINK OP1 A A 340 MG MG A 514 1555 1555 2.47 LINK OP2 A A 340 MG MG A 514 1555 1555 2.71 LINK OP1 A A 376 MG MG A 502 1555 1555 2.43 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 CONECT 719 9425 CONECT 781 9423 CONECT 803 9426 CONECT 827 9426 CONECT 846 9427 CONECT 909 9419 CONECT 1144 9423 CONECT 1760 9429 CONECT 1761 9429 CONECT 1827 9428 CONECT 1828 9426 CONECT 1847 9435 CONECT 1854 9436 CONECT 1870 9436 CONECT 4341 9433 CONECT 6404 9422 CONECT 7090 9431 CONECT 7091 9431 CONECT 7867 9419 CONECT 9419 909 7867 CONECT 9422 6404 CONECT 9423 781 1144 CONECT 9425 719 CONECT 9426 803 827 1828 CONECT 9427 846 CONECT 9428 1827 CONECT 9429 1760 1761 CONECT 9431 7090 7091 CONECT 9433 4341 CONECT 9435 1847 CONECT 9436 1854 1870 MASTER 172 0 19 0 0 0 0 6 9435 1 31 34 END