HEADER TOXIN/RNA 10-FEB-24 8VZ6 TITLE PBABIF DIMER BOUND TO NCRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABI FAMILY PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ABIF NCRNA; COMPND 7 CHAIN: R, S; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCULTURED PREVOTELLACEAE BACTERIUM; SOURCE 3 ORGANISM_TAXID: 370804; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: UNCULTURED PREVOTELLACEAE BACTERIUM; SOURCE 8 ORGANISM_TAXID: 370804; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOXIN-ANTITOXIN, RNP, RNA-BINDING PROTEIN, HEPN, TOXIN, TOXIN-RNA KEYWDS 2 COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR M.E.WILKINSON,S.ZILBERZWIGE-TAL,H.ALTAE-TRAN,F.ZHANG REVDAT 1 12-FEB-25 8VZ6 0 JRNL AUTH S.ZILBERZWIGE-TAL,H.ALTAE-TRAN,S.KANNAN,M.E.WILKINSON, JRNL AUTH 2 S.C.VO,S.SHMAKOV,C.J.YAO,D.STREBINGER,K.K.EDMONDS,K.S.MEARS, JRNL AUTH 3 K.S.MAKAROVA,R.K.MACRAE,E.V.KOONIN,F.ZHANG JRNL TITL EMERGENCE OF A CRISPR RNA-GUIDING MECHANISM FROM A TYPE III JRNL TITL 2 TOXIN-ANTITOXIN SYSTEM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : TOPAZ, EPU, CTFFIND, ISOLDE, COOT, REMARK 3 RELION, RELION, RELION, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE 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) : 3.560 REMARK 3 NUMBER OF PARTICLES : 12790 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 8VZ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281512. 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 : ABIF RNP REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.90 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 4272 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) : 1400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3200.00 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) : 4220.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, R, B, S 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 ASN A 3 REMARK 465 A R 1 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ASN B 3 REMARK 465 A S 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 241 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 C R 20 N1 - C2 - O2 ANGL. DEV. = 4.6 DEGREES REMARK 500 C R 20 C2 - N1 - C1' ANGL. DEV. = 7.4 DEGREES REMARK 500 C R 25 C6 - N1 - C2 ANGL. DEV. = -3.7 DEGREES REMARK 500 C R 25 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 C R 25 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 LEU B 241 CA - CB - CG ANGL. DEV. = 15.3 DEGREES REMARK 500 C S 20 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 C S 20 C2 - N1 - C1' ANGL. DEV. = 7.5 DEGREES REMARK 500 C S 25 C6 - N1 - C2 ANGL. DEV. = -3.8 DEGREES REMARK 500 C S 25 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 C S 25 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-43682 RELATED DB: EMDB REMARK 900 PBABIF DIMER BOUND TO NCRNA DBREF 8VZ6 A 1 300 PDB 8VZ6 8VZ6 1 300 DBREF 8VZ6 R 1 50 PDB 8VZ6 8VZ6 1 50 DBREF 8VZ6 B 1 300 PDB 8VZ6 8VZ6 1 300 DBREF 8VZ6 S 1 50 PDB 8VZ6 8VZ6 1 50 SEQRES 1 A 300 MET SER ASN ARG ILE PRO PHE PRO LYS PRO TYR THR SER SEQRES 2 A 300 ALA HIS ASP LEU VAL SER LEU LEU GLN SER ARG GLY LEU SEQRES 3 A 300 THR ILE ALA ASP THR ALA LYS THR GLU ARG TYR LEU GLU SEQRES 4 A 300 PHE ILE GLY TYR TYR ARG LEU SER ALA TYR MET TYR PRO SEQRES 5 A 300 LEU LEU GLN MET PRO LYS GLU GLN HIS ARG TYR LYS PRO SEQRES 6 A 300 ASN THR THR PHE ASP GLN VAL MET MET LEU TYR ARG PHE SEQRES 7 A 300 ASP LYS LYS LEU ARG LEU LEU ILE PHE ASN GLU ILE GLU SEQRES 8 A 300 LYS ILE GLU VAL ALA VAL ARG SER ALA ILE VAL ASN ILE SEQRES 9 A 300 GLY SER ASP MET ILE GLY SER PRO PHE TRP MET THR ASP SEQRES 10 A 300 GLY SER ASN PHE ILE ASP PRO ARG LYS PHE ARG HIS THR SEQRES 11 A 300 MET ASP LEU ILE ASP ALA GLU LEU GLY ARG SER ARG GLU SEQRES 12 A 300 ASP PHE ILE VAL HIS PHE LYS GLN THR TYR SER ASP ALA SEQRES 13 A 300 TYR PRO PRO ALA TRP ILE LEU ALA GLU VAL LEU PRO PHE SEQRES 14 A 300 GLY VAL ILE THR ASN ILE PHE SER ASN ILE LYS THR ALA SEQRES 15 A 300 ARG ILE LYS LYS SER ILE ALA ARG LYS PHE GLY LEU GLN SEQRES 16 A 300 VAL ALA PRO PHE GLU SER TRP LEU THR ILE VAL ALA LEU SEQRES 17 A 300 THR ARG ASN SER CYS CYS HIS HIS ALA ARG VAL TRP ASN SEQRES 18 A 300 LYS GLN ASN THR ILE ARG PRO MET ILE PRO ASN ARG MET SEQRES 19 A 300 THR GLY ARG TRP ILE ILE LEU PRO THR ASP ALA LEU ARG SEQRES 20 A 300 ILE TYR PHE ASN LEU CYS ILE ILE LYS TYR PHE LEU ASP SEQRES 21 A 300 ILE ILE SER PRO GLN ASN ASP MET LYS ALA LYS ILE ASP SEQRES 22 A 300 ALA LEU LEU SER SER TYR SER SER ILE ASP ILE ASN ALA SEQRES 23 A 300 MET GLY PHE PRO ARG GLY TRP GLU SER GLU PRO LEU TRP SEQRES 24 A 300 GLN SEQRES 1 R 50 A C U A G A A C C C G C C SEQRES 2 R 50 A A G C C U C U C A A C G SEQRES 3 R 50 A U G C U C A A A U G U G SEQRES 4 R 50 C G G G U C G U U U U SEQRES 1 B 300 MET SER ASN ARG ILE PRO PHE PRO LYS PRO TYR THR SER SEQRES 2 B 300 ALA HIS ASP LEU VAL SER LEU LEU GLN SER ARG GLY LEU SEQRES 3 B 300 THR ILE ALA ASP THR ALA LYS THR GLU ARG TYR LEU GLU SEQRES 4 B 300 PHE ILE GLY TYR TYR ARG LEU SER ALA TYR MET TYR PRO SEQRES 5 B 300 LEU LEU GLN MET PRO LYS GLU GLN HIS ARG TYR LYS PRO SEQRES 6 B 300 ASN THR THR PHE ASP GLN VAL MET MET LEU TYR ARG PHE SEQRES 7 B 300 ASP LYS LYS LEU ARG LEU LEU ILE PHE ASN GLU ILE GLU SEQRES 8 B 300 LYS ILE GLU VAL ALA VAL ARG SER ALA ILE VAL ASN ILE SEQRES 9 B 300 GLY SER ASP MET ILE GLY SER PRO PHE TRP MET THR ASP SEQRES 10 B 300 GLY SER ASN PHE ILE ASP PRO ARG LYS PHE ARG HIS THR SEQRES 11 B 300 MET ASP LEU ILE ASP ALA GLU LEU GLY ARG SER ARG GLU SEQRES 12 B 300 ASP PHE ILE VAL HIS PHE LYS GLN THR TYR SER ASP ALA SEQRES 13 B 300 TYR PRO PRO ALA TRP ILE LEU ALA GLU VAL LEU PRO PHE SEQRES 14 B 300 GLY VAL ILE THR ASN ILE PHE SER ASN ILE LYS THR ALA SEQRES 15 B 300 ARG ILE LYS LYS SER ILE ALA ARG LYS PHE GLY LEU GLN SEQRES 16 B 300 VAL ALA PRO PHE GLU SER TRP LEU THR ILE VAL ALA LEU SEQRES 17 B 300 THR ARG ASN SER CYS CYS HIS HIS ALA ARG VAL TRP ASN SEQRES 18 B 300 LYS GLN ASN THR ILE ARG PRO MET ILE PRO ASN ARG MET SEQRES 19 B 300 THR GLY ARG TRP ILE ILE LEU PRO THR ASP ALA LEU ARG SEQRES 20 B 300 ILE TYR PHE ASN LEU CYS ILE ILE LYS TYR PHE LEU ASP SEQRES 21 B 300 ILE ILE SER PRO GLN ASN ASP MET LYS ALA LYS ILE ASP SEQRES 22 B 300 ALA LEU LEU SER SER TYR SER SER ILE ASP ILE ASN ALA SEQRES 23 B 300 MET GLY PHE PRO ARG GLY TRP GLU SER GLU PRO LEU TRP SEQRES 24 B 300 GLN SEQRES 1 S 50 A C U A G A A C C C G C C SEQRES 2 S 50 A A G C C U C U C A A C G SEQRES 3 S 50 A U G C U C A A A U G U G SEQRES 4 S 50 C G G G U C G U U U U HELIX 1 AA1 SER A 13 ARG A 24 1 12 HELIX 2 AA2 ASP A 30 ILE A 41 1 12 HELIX 3 AA3 GLY A 42 TYR A 51 1 10 HELIX 4 AA4 PRO A 52 LEU A 54 5 3 HELIX 5 AA5 PRO A 57 HIS A 61 5 5 HELIX 6 AA6 THR A 68 GLY A 110 1 43 HELIX 7 AA7 PHE A 113 PHE A 121 5 9 HELIX 8 AA8 ASP A 123 GLY A 139 1 17 HELIX 9 AA9 PHE A 145 TYR A 153 1 9 HELIX 10 AB1 PRO A 159 ALA A 164 1 6 HELIX 11 AB2 PRO A 168 SER A 177 1 10 HELIX 12 AB3 THR A 181 PHE A 192 1 12 HELIX 13 AB4 GLN A 195 HIS A 215 1 21 HELIX 14 AB5 ILE A 248 SER A 263 1 16 HELIX 15 AB6 ASP A 267 TYR A 279 1 13 HELIX 16 AB7 ASP A 283 MET A 287 5 5 HELIX 17 AB8 GLY A 292 GLN A 300 5 9 HELIX 18 AB9 HIS B 15 ARG B 24 1 10 HELIX 19 AC1 ASP B 30 ILE B 41 1 12 HELIX 20 AC2 GLY B 42 TYR B 51 1 10 HELIX 21 AC3 PRO B 52 LEU B 54 5 3 HELIX 22 AC4 PRO B 57 HIS B 61 5 5 HELIX 23 AC5 THR B 68 GLY B 110 1 43 HELIX 24 AC6 PHE B 113 PHE B 121 5 9 HELIX 25 AC7 ASP B 123 GLY B 139 1 17 HELIX 26 AC8 PHE B 145 TYR B 153 1 9 HELIX 27 AC9 PRO B 159 ALA B 164 1 6 HELIX 28 AD1 PRO B 168 SER B 177 1 10 HELIX 29 AD2 THR B 181 PHE B 192 1 12 HELIX 30 AD3 GLN B 195 HIS B 215 1 21 HELIX 31 AD4 ILE B 248 SER B 263 1 16 HELIX 32 AD5 ASP B 267 TYR B 279 1 13 HELIX 33 AD6 ASP B 283 MET B 287 5 5 HELIX 34 AD7 GLY B 292 GLN B 300 5 9 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 2443 GLN A 300 TER 3479 U R 50 TER 5922 GLN B 300 TER 6958 U S 50 MASTER 146 0 0 34 0 0 0 6 6954 4 0 56 END