HEADER DNA-RNA HYBRID 22-APR-22 7XLT TITLE CRYO-EM STRUCTURE OF R-LOOP MONOCLONAL ANTIBODY S9.6 IN RECOGNIZING TITLE 2 RNA:DNA HYBRIDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: S9.6 FAB HC; COMPND 3 CHAIN: H; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: S9.6 FAB LC; COMPND 6 CHAIN: L; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 3; COMPND 9 MOLECULE: DNA; COMPND 10 CHAIN: A; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 4; COMPND 13 MOLECULE: RNA; COMPND 14 CHAIN: B; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 6 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 7 ORGANISM_TAXID: 10090; SOURCE 8 GENE: IGKC, IGK-C; SOURCE 9 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 10090; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: ARABIDOPSIS; SOURCE 13 ORGANISM_TAXID: 3701; SOURCE 14 EXPRESSION_SYSTEM: ARABIDOPSIS; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 3701; SOURCE 16 MOL_ID: 4; SOURCE 17 ORGANISM_SCIENTIFIC: ARABIDOPSIS; SOURCE 18 ORGANISM_TAXID: 3701; SOURCE 19 EXPRESSION_SYSTEM: ARABIDOPSIS; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 3701 KEYWDS RNA:DNA HYBRID, S9.6 FAB, DNA-RNA HYBRID EXPDTA ELECTRON MICROSCOPY AUTHOR Q.LI,C.LIN,Z.LUO,H.LI,X.LI,Q.SUN REVDAT 4 23-OCT-24 7XLT 1 REMARK REVDAT 3 03-AUG-22 7XLT 1 JRNL REVDAT 2 06-JUL-22 7XLT 1 AUTHOR JRNL REVDAT 1 25-MAY-22 7XLT 0 JRNL AUTH Q.LI,C.LIN,Z.LUO,H.LI,X.LI,Q.SUN JRNL TITL CRYO-EM STRUCTURE OF R-LOOP MONOCLONAL ANTIBODY S9.6 IN JRNL TITL 2 RECOGNIZING RNA:DNA HYBRIDS. JRNL REF J GENET GENOMICS V. 49 677 2022 JRNL REFN ISSN 1673-8527 JRNL PMID 35550870 JRNL DOI 10.1016/J.JGG.2022.04.011 REMARK 2 REMARK 2 RESOLUTION. 4.40 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) : 4.400 REMARK 3 NUMBER OF PARTICLES : 64305 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 7XLT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-APR-22. REMARK 100 THE DEPOSITION ID IS D_1300029102. 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 : CRYO-EM STRUCTURE OF R-LOOP REMARK 245 MONOCLONAL ANTIBODY S9.6 IN REMARK 245 RECOGNIZING RNA:DNA HYBRIDS 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 : 7.20 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 K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 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) : 5000.00 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, A, B 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 ILE H 216 REMARK 465 GLU H 217 REMARK 465 PRO H 218 REMARK 465 ARG H 219 REMARK 465 VAL H 220 REMARK 465 ASN L 217 REMARK 465 GLU L 218 REMARK 465 CYS L 219 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 H 6 -169.88 -129.98 REMARK 500 ILE H 48 -63.22 -101.48 REMARK 500 LYS H 67 -61.17 -94.50 REMARK 500 TYR H 101 117.51 -164.44 REMARK 500 ALA H 120 -136.55 57.83 REMARK 500 PRO H 155 83.11 -69.24 REMARK 500 SER H 178 19.35 58.00 REMARK 500 SER H 192 30.25 -97.18 REMARK 500 GLN L 6 76.70 -104.49 REMARK 500 GLN L 27 -166.60 -124.10 REMARK 500 VAL L 56 -53.33 -136.96 REMARK 500 GLN L 161 52.91 -97.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33286 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF R-LOOP MONOCLONAL ANTIBODY S9.6 IN RECOGNIZING REMARK 900 RNA:DNA HYBRIDS DBREF 7XLT H 1 220 PDB 7XLT 7XLT 1 220 DBREF 7XLT L 1 219 PDB 7XLT 7XLT 1 219 DBREF 7XLT A 1 40 PDB 7XLT 7XLT 1 40 DBREF 7XLT B 1 40 PDB 7XLT 7XLT 1 40 SEQRES 1 H 220 GLU VAL GLN LEU GLN GLN SER GLY PRO GLU LEU VAL LYS SEQRES 2 H 220 PRO GLY ALA SER VAL LYS MET SER CYS LYS ALA SER GLY SEQRES 3 H 220 TYR THR PHE THR SER TYR VAL MET HIS TRP VAL LYS GLN SEQRES 4 H 220 LYS PRO GLY GLN GLY LEU GLU TRP ILE GLY PHE ILE ASN SEQRES 5 H 220 LEU TYR ASN ASP GLY THR LYS TYR ASN GLU LYS PHE LYS SEQRES 6 H 220 GLY LYS ALA THR LEU THR SER ASP LYS SER SER SER THR SEQRES 7 H 220 ALA TYR MET GLU LEU SER SER LEU THR SER LYS ASP SER SEQRES 8 H 220 ALA VAL TYR TYR CYS ALA ARG ASP TYR TYR GLY SER ARG SEQRES 9 H 220 TRP PHE ASP TYR TRP GLY GLN GLY THR THR LEU THR VAL SEQRES 10 H 220 SER SER ALA LYS THR THR ALA PRO SER VAL TYR PRO LEU SEQRES 11 H 220 ALA PRO VAL CYS GLY ASP THR THR GLY SER SER VAL THR SEQRES 12 H 220 LEU GLY CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO VAL SEQRES 13 H 220 THR LEU THR TRP ASN SER GLY SER LEU SER SER GLY VAL SEQRES 14 H 220 HIS THR PHE PRO ALA VAL LEU GLN SER ASP LEU TYR THR SEQRES 15 H 220 LEU SER SER SER VAL THR VAL THR SER SER THR TRP PRO SEQRES 16 H 220 SER GLN SER ILE THR CYS ASN VAL ALA HIS PRO ALA SER SEQRES 17 H 220 SER THR LYS VAL ASP LYS LYS ILE GLU PRO ARG VAL SEQRES 1 L 219 ASP VAL LEU MET THR GLN THR PRO LEU SER LEU PRO VAL SEQRES 2 L 219 SER LEU GLY ASP GLN ALA SER ILE SER CYS ARG SER SER SEQRES 3 L 219 GLN SER ILE VAL HIS SER ASN GLY ASN THR TYR LEU GLU SEQRES 4 L 219 TRP TYR LEU GLN LYS PRO GLY GLN SER PRO LYS LEU LEU SEQRES 5 L 219 ILE TYR LYS VAL SER ASN ARG PHE SER GLY VAL PRO ASP SEQRES 6 L 219 ARG PHE SER GLY SER GLY SER GLY THR ASP PHE THR LEU SEQRES 7 L 219 LYS ILE SER ARG VAL GLU ALA GLU ASP LEU GLY VAL TYR SEQRES 8 L 219 TYR CYS PHE GLN GLY SER HIS VAL PRO TYR THR PHE GLY SEQRES 9 L 219 GLY GLY THR LYS LEU GLU ILE LYS ARG ALA ASP ALA ALA SEQRES 10 L 219 PRO THR VAL SER ILE PHE PRO PRO SER SER GLU GLN LEU SEQRES 11 L 219 THR SER GLY GLY ALA SER VAL VAL CYS PHE LEU ASN ASN SEQRES 12 L 219 PHE TYR PRO LYS ASP ILE ASN VAL LYS TRP LYS ILE ASP SEQRES 13 L 219 GLY SER GLU ARG GLN ASN GLY VAL LEU ASN SER TRP THR SEQRES 14 L 219 ASP GLN ASP SER LYS ASP SER THR TYR SER MET SER SER SEQRES 15 L 219 THR LEU THR LEU THR LYS ASP GLU TYR GLU ARG HIS ASN SEQRES 16 L 219 SER TYR THR CYS GLU ALA THR HIS LYS THR SER THR SER SEQRES 17 L 219 PRO ILE VAL LYS SER PHE ASN ARG ASN GLU CYS SEQRES 1 A 40 DT DC DT DG DT DT DC DT DT DC DG DT DG SEQRES 2 A 40 DT DT DC DC DT DC DG DT DC DT DG DT DT SEQRES 3 A 40 DC DT DT DC DG DT DG DT DT DC DC DT DC SEQRES 4 A 40 DG SEQRES 1 B 40 C G A G G A A C A C G A A SEQRES 2 B 40 G A A C A G A C G A G G A SEQRES 3 B 40 A C A C G A A G A A C A G SEQRES 4 B 40 A HELIX 1 AA1 THR H 87 SER H 91 5 5 HELIX 2 AA2 LEU H 176 LEU H 180 5 5 HELIX 3 AA3 SER H 192 TRP H 194 5 3 HELIX 4 AA4 SER L 126 THR L 131 1 6 HELIX 5 AA5 LYS L 188 GLU L 192 1 5 SHEET 1 AA1 4 LEU H 4 GLN H 6 0 SHEET 2 AA1 4 VAL H 18 ALA H 24 -1 O LYS H 23 N GLN H 5 SHEET 3 AA1 4 THR H 78 LEU H 83 -1 O LEU H 83 N VAL H 18 SHEET 4 AA1 4 ALA H 68 ASP H 73 -1 N THR H 71 O TYR H 80 SHEET 1 AA2 5 GLU H 10 VAL H 12 0 SHEET 2 AA2 5 THR H 113 VAL H 117 1 O THR H 116 N GLU H 10 SHEET 3 AA2 5 ALA H 92 ASP H 99 -1 N ALA H 92 O LEU H 115 SHEET 4 AA2 5 VAL H 33 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 AA2 5 GLU H 46 ASN H 52 -1 O GLU H 46 N LYS H 38 SHEET 1 AA3 4 GLU H 10 VAL H 12 0 SHEET 2 AA3 4 THR H 113 VAL H 117 1 O THR H 116 N GLU H 10 SHEET 3 AA3 4 ALA H 92 ASP H 99 -1 N ALA H 92 O LEU H 115 SHEET 4 AA3 4 PHE H 106 TRP H 109 -1 O TYR H 108 N ARG H 98 SHEET 1 AA4 4 SER H 126 PRO H 129 0 SHEET 2 AA4 4 SER H 141 LYS H 149 -1 O LYS H 149 N SER H 126 SHEET 3 AA4 4 THR H 182 THR H 190 -1 O LEU H 183 N VAL H 148 SHEET 4 AA4 4 VAL H 169 HIS H 170 -1 N HIS H 170 O SER H 186 SHEET 1 AA5 3 THR H 157 TRP H 160 0 SHEET 2 AA5 3 CYS H 201 ALA H 204 -1 O ASN H 202 N THR H 159 SHEET 3 AA5 3 THR H 210 ASP H 213 -1 O ASP H 213 N CYS H 201 SHEET 1 AA6 4 MET L 4 GLN L 6 0 SHEET 2 AA6 4 ALA L 19 SER L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AA6 4 ASP L 75 ILE L 80 -1 O PHE L 76 N CYS L 23 SHEET 4 AA6 4 SER L 68 SER L 70 -1 N SER L 70 O THR L 77 SHEET 1 AA7 4 LYS L 50 ILE L 53 0 SHEET 2 AA7 4 TRP L 40 GLN L 43 -1 N TRP L 40 O ILE L 53 SHEET 3 AA7 4 VAL L 90 PHE L 94 -1 O TYR L 92 N TYR L 41 SHEET 4 AA7 4 PHE L 103 LYS L 108 -1 O THR L 107 N TYR L 91 SHEET 1 AA8 4 THR L 119 PHE L 123 0 SHEET 2 AA8 4 GLY L 134 ASN L 142 -1 O VAL L 138 N PHE L 123 SHEET 3 AA8 4 SER L 179 THR L 187 -1 O LEU L 186 N ALA L 135 SHEET 4 AA8 4 VAL L 164 SER L 167 -1 N SER L 167 O SER L 181 SHEET 1 AA9 3 ASN L 150 ILE L 155 0 SHEET 2 AA9 3 TYR L 197 THR L 202 -1 O GLU L 200 N LYS L 152 SHEET 3 AA9 3 ILE L 210 PHE L 214 -1 O PHE L 214 N TYR L 197 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 2 CYS H 146 CYS H 201 1555 1555 2.04 SSBOND 3 CYS L 23 CYS L 93 1555 1555 2.04 SSBOND 4 CYS L 139 CYS L 199 1555 1555 2.04 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 TER 1636 LYS H 215 TER 3313 ARG L 216 TER 4115 DG A 40 TER 4989 A B 40 CONECT 159 747 CONECT 747 159 CONECT 1119 1532 CONECT 1532 1119 CONECT 1799 2352 CONECT 2352 1799 CONECT 2682 3179 CONECT 3179 2682 MASTER 143 0 0 5 35 0 0 6 4985 4 8 42 END