HEADER RNA BINDING PROTEIN 21-FEB-24 8W35 TITLE ACA2 FROM PECTOBACTERIUM PHAGE ZF40 BOUND TO RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-CRISPR ASSOCIATED (ACA) PROTEIN, ACA2; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: IR2 AND IR-RBS RNA; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PECTOBACTERIUM PHAGE ZF40; SOURCE 3 ORGANISM_TAXID: 1127516; SOURCE 4 GENE: ZF40_0030; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: PECTOBACTERIUM PHAGE ZF40; SOURCE 10 ORGANISM_TAXID: 1127516 KEYWDS HTH PROTEIN, CRISPR, RNA-BINDING PROTEIN, RNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR M.E.WILKINSON,N.BIRKHOLZ,D.KIMANIUS,P.C.FINERAN REVDAT 2 14-AUG-24 8W35 1 REMARK REVDAT 1 24-JUL-24 8W35 0 JRNL AUTH N.BIRKHOLZ,K.KAMATA,M.FEUSSNER,M.E.WILKINSON, JRNL AUTH 2 C.CUBA SAMANIEGO,A.MIGUR,D.KIMANIUS,M.CEELEN,S.C.WENT, JRNL AUTH 3 B.USHER,T.R.BLOWER,C.M.BROWN,C.L.BEISEL,Z.WEINBERG, JRNL AUTH 4 R.D.FAGERLUND,S.A.JACKSON,P.C.FINERAN JRNL TITL PHAGE ANTI-CRISPR CONTROL BY AN RNA- AND DNA-BINDING JRNL TITL 2 HELIX-TURN-HELIX PROTEIN. JRNL REF NATURE V. 631 670 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 38987591 JRNL DOI 10.1038/S41586-024-07644-1 REMARK 2 REMARK 2 RESOLUTION. 2.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : TOPAZ, EPU, CTFFIND, ISOLDE, COOT, REMARK 3 PHENIX, RELION, RELION, RELION 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) : 2.610 REMARK 3 NUMBER OF PARTICLES : 301832 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: BLUSH REGULARISATION USED DURING REFINEMENT REMARK 4 REMARK 4 8W35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281782. 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 : ANTI-CRISPR ASSOCIATED (ACA) REMARK 245 PROTEIN, ACA2 BOUND TO ITS 5' REMARK 245 UTR RNA (IR2 AND IR-RBS) REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 5.10 REMARK 245 SAMPLE SUPPORT DETAILS : 25 MA PLASMA REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 11232 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) : 1500.00 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) : 7220.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 SER A -3 REMARK 465 HIS A -2 REMARK 465 GLY A -1 REMARK 465 SER B -3 REMARK 465 HIS B -2 REMARK 465 GLY B -1 REMARK 465 A C 30 REMARK 465 A C 31 REMARK 465 C C 32 REMARK 465 U C 38 REMARK 465 U C 39 REMARK 465 C C 40 REMARK 465 C C 41 REMARK 465 A C 42 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 91 40.05 -108.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-43762 RELATED DB: EMDB REMARK 900 PECTOBACTERIUM PHAGE ZF40 ACA2 BOUND TO ITS RNA DBREF 8W35 A 1 116 UNP H9C180 H9C180_9CAUD 1 116 DBREF 8W35 B 1 116 UNP H9C180 H9C180_9CAUD 1 116 DBREF 8W35 C 1 42 PDB 8W35 8W35 1 42 SEQADV 8W35 SER A -3 UNP H9C180 EXPRESSION TAG SEQADV 8W35 HIS A -2 UNP H9C180 EXPRESSION TAG SEQADV 8W35 GLY A -1 UNP H9C180 EXPRESSION TAG SEQADV 8W35 SER A 0 UNP H9C180 EXPRESSION TAG SEQADV 8W35 SER B -3 UNP H9C180 EXPRESSION TAG SEQADV 8W35 HIS B -2 UNP H9C180 EXPRESSION TAG SEQADV 8W35 GLY B -1 UNP H9C180 EXPRESSION TAG SEQADV 8W35 SER B 0 UNP H9C180 EXPRESSION TAG SEQRES 1 A 120 SER HIS GLY SER MET THR ASN LYS GLU LEU GLN ALA ILE SEQRES 2 A 120 ARG LYS LEU LEU MET LEU ASP VAL SER GLU ALA ALA GLU SEQRES 3 A 120 HIS ILE GLY ARG VAL SER ALA ARG SER TRP GLN TYR TRP SEQRES 4 A 120 GLU SER GLY ARG SER ALA VAL PRO ASP ASP VAL GLU GLN SEQRES 5 A 120 GLU MET LEU ASP LEU ALA SER VAL ARG ILE GLU MET MET SEQRES 6 A 120 SER ALA ILE ASP LYS ARG LEU ALA ASP GLY GLU ARG PRO SEQRES 7 A 120 LYS LEU ARG PHE TYR ASN LYS LEU ASP GLU TYR LEU ALA SEQRES 8 A 120 ASP ASN PRO ASP HIS ASN VAL ILE GLY TRP ARG LEU SER SEQRES 9 A 120 GLN SER VAL ALA ALA LEU TYR TYR THR GLU GLY HIS ALA SEQRES 10 A 120 ASP LEU ILE SEQRES 1 B 120 SER HIS GLY SER MET THR ASN LYS GLU LEU GLN ALA ILE SEQRES 2 B 120 ARG LYS LEU LEU MET LEU ASP VAL SER GLU ALA ALA GLU SEQRES 3 B 120 HIS ILE GLY ARG VAL SER ALA ARG SER TRP GLN TYR TRP SEQRES 4 B 120 GLU SER GLY ARG SER ALA VAL PRO ASP ASP VAL GLU GLN SEQRES 5 B 120 GLU MET LEU ASP LEU ALA SER VAL ARG ILE GLU MET MET SEQRES 6 B 120 SER ALA ILE ASP LYS ARG LEU ALA ASP GLY GLU ARG PRO SEQRES 7 B 120 LYS LEU ARG PHE TYR ASN LYS LEU ASP GLU TYR LEU ALA SEQRES 8 B 120 ASP ASN PRO ASP HIS ASN VAL ILE GLY TRP ARG LEU SER SEQRES 9 B 120 GLN SER VAL ALA ALA LEU TYR TYR THR GLU GLY HIS ALA SEQRES 10 B 120 ASP LEU ILE SEQRES 1 C 42 A U C G G U U C G A G A U SEQRES 2 C 42 G G C U C G A A U C G C U SEQRES 3 C 42 C C U A A C G A G G A U U SEQRES 4 C 42 C C A HELIX 1 AA1 THR A 2 LEU A 13 1 12 HELIX 2 AA2 ASP A 16 ILE A 24 1 9 HELIX 3 AA3 SER A 28 SER A 37 1 10 HELIX 4 AA4 PRO A 43 ALA A 69 1 27 HELIX 5 AA5 LYS A 81 ASN A 89 1 9 HELIX 6 AA6 ASN A 93 GLU A 110 1 18 HELIX 7 AA7 THR B 2 LEU B 13 1 12 HELIX 8 AA8 ASP B 16 ILE B 24 1 9 HELIX 9 AA9 SER B 28 GLY B 38 1 11 HELIX 10 AB1 PRO B 43 ALA B 69 1 27 HELIX 11 AB2 LYS B 81 ASN B 89 1 9 HELIX 12 AB3 ASN B 93 GLU B 110 1 18 SHEET 1 AA1 2 LYS A 75 LEU A 76 0 SHEET 2 AA1 2 ASP A 114 LEU A 115 1 O ASP A 114 N LEU A 76 SHEET 1 AA2 2 LYS B 75 LEU B 76 0 SHEET 2 AA2 2 ASP B 114 LEU B 115 1 O ASP B 114 N LEU B 76 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