HEADER IMMUNE SYSTEM 08-JAN-25 9MRR TITLE CRYO-EM STRUCTURE OF KWAA WITH C4 SYMMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: KIWA PROTEIN KWAA; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: KWAA, ECO55CA74_24535; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KWAA TETRAMER, C4, ANTI-PHAGE DEFENSE, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR Z.ZHANG,D.J.PATEL REVDAT 1 06-AUG-25 9MRR 0 JRNL AUTH Z.ZHANG,D.J.PATEL JRNL TITL CRYO-EM STRUCTURE OF KWAA WITH C4 SYMMETRY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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 : 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) : 4.280 REMARK 3 NUMBER OF PARTICLES : 278569 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 9MRR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000291641. 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 KWAA WITH REMARK 245 C4 SYMMETRY 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 : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : DIFFRACTION REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5300.00 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: A, B, C, D 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 PRO A 31 REMARK 465 PHE A 32 REMARK 465 CYS A 33 REMARK 465 PHE A 34 REMARK 465 THR A 35 REMARK 465 SER A 36 REMARK 465 ASP A 37 REMARK 465 CYS A 38 REMARK 465 SER A 39 REMARK 465 PHE A 40 REMARK 465 ILE A 41 REMARK 465 PHE B 34 REMARK 465 THR B 35 REMARK 465 SER B 36 REMARK 465 ASP B 37 REMARK 465 CYS B 38 REMARK 465 SER B 39 REMARK 465 PHE B 40 REMARK 465 ILE B 41 REMARK 465 PRO C 31 REMARK 465 PHE C 32 REMARK 465 CYS C 33 REMARK 465 PHE C 34 REMARK 465 THR C 35 REMARK 465 SER C 36 REMARK 465 ASP C 37 REMARK 465 CYS C 38 REMARK 465 SER C 39 REMARK 465 PHE C 40 REMARK 465 ILE C 41 REMARK 465 PRO D 31 REMARK 465 PHE D 32 REMARK 465 CYS D 33 REMARK 465 PHE D 34 REMARK 465 THR D 35 REMARK 465 SER D 36 REMARK 465 ASP D 37 REMARK 465 CYS D 38 REMARK 465 SER D 39 REMARK 465 PHE D 40 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 VAL A 82 CG1 - CB - CG2 ANGL. DEV. = -10.1 DEGREES REMARK 500 ASP B 176 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 SER A 86 174.01 63.63 REMARK 500 TYR A 92 -70.22 -81.76 REMARK 500 TYR A 101 -60.51 -100.99 REMARK 500 GLU A 111 -54.84 -123.61 REMARK 500 ASN A 139 88.94 56.87 REMARK 500 PRO A 140 1.38 -55.28 REMARK 500 PHE A 145 48.90 -89.06 REMARK 500 ASN A 164 47.59 34.97 REMARK 500 ASP A 185 -166.82 -160.71 REMARK 500 ARG A 192 -169.27 -125.65 REMARK 500 VAL B 82 -75.90 -107.64 REMARK 500 LYS B 83 65.20 35.73 REMARK 500 SER B 86 178.88 58.82 REMARK 500 VAL B 103 71.33 -119.15 REMARK 500 MET B 106 72.45 49.37 REMARK 500 PRO B 140 40.70 -86.73 REMARK 500 LYS B 174 -169.84 -125.34 REMARK 500 ASP B 176 45.45 32.68 REMARK 500 LYS C 75 38.32 -98.16 REMARK 500 ASN C 77 -167.92 -162.37 REMARK 500 SER C 81 62.47 61.41 REMARK 500 SER D 86 178.05 61.75 REMARK 500 TYR D 150 148.54 -176.43 REMARK 500 ASN D 164 55.56 38.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-48562 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF KWAA WITH C4 SYMMETRY DBREF 9MRR A 1 195 UNP P0DW45 KWAA_ECORM 1 195 DBREF 9MRR B 1 195 UNP P0DW45 KWAA_ECORM 1 195 DBREF 9MRR C 1 195 UNP P0DW45 KWAA_ECORM 1 195 DBREF 9MRR D 1 195 UNP P0DW45 KWAA_ECORM 1 195 SEQRES 1 A 195 MET GLN ARG ASN THR TYR ASN LYS VAL GLY LEU TYR ILE SEQRES 2 A 195 LEU SER LEU ALA MET LEU PHE VAL PHE ILE ILE ILE LEU SEQRES 3 A 195 THR ALA LYS ILE PRO PHE CYS PHE THR SER ASP CYS SER SEQRES 4 A 195 PHE ILE GLY LEU LYS LYS LEU VAL LEU THR ASN ILE VAL SEQRES 5 A 195 PRO ILE VAL CYS PHE VAL PHE PHE LEU PHE SER ILE TYR SEQRES 6 A 195 PHE TYR ASN ARG LEU LYS ASN ILE THR LYS TYR ASN GLY SEQRES 7 A 195 GLN ASP SER VAL LYS ILE THR SER CYS GLN SER GLU SER SEQRES 8 A 195 TYR GLU SER LEU THR PHE LEU ALA THR TYR ILE VAL PRO SEQRES 9 A 195 PHE MET GLY PHE SER PHE GLU ASP MET GLN LYS ASN ILE SEQRES 10 A 195 ALA TYR LEU LEU LEU VAL VAL VAL ILE GLY ILE ILE PHE SEQRES 11 A 195 ILE LYS THR ASP LYS TYR TYR ALA ASN PRO THR LEU ALA SEQRES 12 A 195 LEU PHE GLY PHE LYS LEU TYR ARG VAL ASN ILE LEU HIS SEQRES 13 A 195 PRO GLY SER GLY GLU THR LYS ASN LEU ILE ALA ILE SER SEQRES 14 A 195 ASN ASP VAL LEU LYS VAL ASP ASP ASN VAL TYR TYR SER SEQRES 15 A 195 PHE PHE ASP GLU PHE VAL PHE ILE ALA ARG LYS LYS ILE SEQRES 1 B 195 MET GLN ARG ASN THR TYR ASN LYS VAL GLY LEU TYR ILE SEQRES 2 B 195 LEU SER LEU ALA MET LEU PHE VAL PHE ILE ILE ILE LEU SEQRES 3 B 195 THR ALA LYS ILE PRO PHE CYS PHE THR SER ASP CYS SER SEQRES 4 B 195 PHE ILE GLY LEU LYS LYS LEU VAL LEU THR ASN ILE VAL SEQRES 5 B 195 PRO ILE VAL CYS PHE VAL PHE PHE LEU PHE SER ILE TYR SEQRES 6 B 195 PHE TYR ASN ARG LEU LYS ASN ILE THR LYS TYR ASN GLY SEQRES 7 B 195 GLN ASP SER VAL LYS ILE THR SER CYS GLN SER GLU SER SEQRES 8 B 195 TYR GLU SER LEU THR PHE LEU ALA THR TYR ILE VAL PRO SEQRES 9 B 195 PHE MET GLY PHE SER PHE GLU ASP MET GLN LYS ASN ILE SEQRES 10 B 195 ALA TYR LEU LEU LEU VAL VAL VAL ILE GLY ILE ILE PHE SEQRES 11 B 195 ILE LYS THR ASP LYS TYR TYR ALA ASN PRO THR LEU ALA SEQRES 12 B 195 LEU PHE GLY PHE LYS LEU TYR ARG VAL ASN ILE LEU HIS SEQRES 13 B 195 PRO GLY SER GLY GLU THR LYS ASN LEU ILE ALA ILE SER SEQRES 14 B 195 ASN ASP VAL LEU LYS VAL ASP ASP ASN VAL TYR TYR SER SEQRES 15 B 195 PHE PHE ASP GLU PHE VAL PHE ILE ALA ARG LYS LYS ILE SEQRES 1 C 195 MET GLN ARG ASN THR TYR ASN LYS VAL GLY LEU TYR ILE SEQRES 2 C 195 LEU SER LEU ALA MET LEU PHE VAL PHE ILE ILE ILE LEU SEQRES 3 C 195 THR ALA LYS ILE PRO PHE CYS PHE THR SER ASP CYS SER SEQRES 4 C 195 PHE ILE GLY LEU LYS LYS LEU VAL LEU THR ASN ILE VAL SEQRES 5 C 195 PRO ILE VAL CYS PHE VAL PHE PHE LEU PHE SER ILE TYR SEQRES 6 C 195 PHE TYR ASN ARG LEU LYS ASN ILE THR LYS TYR ASN GLY SEQRES 7 C 195 GLN ASP SER VAL LYS ILE THR SER CYS GLN SER GLU SER SEQRES 8 C 195 TYR GLU SER LEU THR PHE LEU ALA THR TYR ILE VAL PRO SEQRES 9 C 195 PHE MET GLY PHE SER PHE GLU ASP MET GLN LYS ASN ILE SEQRES 10 C 195 ALA TYR LEU LEU LEU VAL VAL VAL ILE GLY ILE ILE PHE SEQRES 11 C 195 ILE LYS THR ASP LYS TYR TYR ALA ASN PRO THR LEU ALA SEQRES 12 C 195 LEU PHE GLY PHE LYS LEU TYR ARG VAL ASN ILE LEU HIS SEQRES 13 C 195 PRO GLY SER GLY GLU THR LYS ASN LEU ILE ALA ILE SER SEQRES 14 C 195 ASN ASP VAL LEU LYS VAL ASP ASP ASN VAL TYR TYR SER SEQRES 15 C 195 PHE PHE ASP GLU PHE VAL PHE ILE ALA ARG LYS LYS ILE SEQRES 1 D 195 MET GLN ARG ASN THR TYR ASN LYS VAL GLY LEU TYR ILE SEQRES 2 D 195 LEU SER LEU ALA MET LEU PHE VAL PHE ILE ILE ILE LEU SEQRES 3 D 195 THR ALA LYS ILE PRO PHE CYS PHE THR SER ASP CYS SER SEQRES 4 D 195 PHE ILE GLY LEU LYS LYS LEU VAL LEU THR ASN ILE VAL SEQRES 5 D 195 PRO ILE VAL CYS PHE VAL PHE PHE LEU PHE SER ILE TYR SEQRES 6 D 195 PHE TYR ASN ARG LEU LYS ASN ILE THR LYS TYR ASN GLY SEQRES 7 D 195 GLN ASP SER VAL LYS ILE THR SER CYS GLN SER GLU SER SEQRES 8 D 195 TYR GLU SER LEU THR PHE LEU ALA THR TYR ILE VAL PRO SEQRES 9 D 195 PHE MET GLY PHE SER PHE GLU ASP MET GLN LYS ASN ILE SEQRES 10 D 195 ALA TYR LEU LEU LEU VAL VAL VAL ILE GLY ILE ILE PHE SEQRES 11 D 195 ILE LYS THR ASP LYS TYR TYR ALA ASN PRO THR LEU ALA SEQRES 12 D 195 LEU PHE GLY PHE LYS LEU TYR ARG VAL ASN ILE LEU HIS SEQRES 13 D 195 PRO GLY SER GLY GLU THR LYS ASN LEU ILE ALA ILE SER SEQRES 14 D 195 ASN ASP VAL LEU LYS VAL ASP ASP ASN VAL TYR TYR SER SEQRES 15 D 195 PHE PHE ASP GLU PHE VAL PHE ILE ALA ARG LYS LYS ILE HELIX 1 AA1 MET A 1 ALA A 28 1 28 HELIX 2 AA2 LEU A 43 ASN A 50 1 8 HELIX 3 AA3 ASN A 50 TYR A 76 1 27 HELIX 4 AA4 LEU A 95 PHE A 108 1 14 HELIX 5 AA5 ASP A 112 THR A 133 1 22 HELIX 6 AA6 PRO A 140 PHE A 145 1 6 HELIX 7 AA7 GLN B 2 LEU B 16 1 15 HELIX 8 AA8 LEU B 16 ALA B 28 1 13 HELIX 9 AA9 LEU B 43 THR B 49 1 7 HELIX 10 AB1 ASN B 50 TYR B 76 1 27 HELIX 11 AB2 LEU B 95 ILE B 102 1 8 HELIX 12 AB3 ASP B 112 LYS B 132 1 21 HELIX 13 AB4 LEU B 142 GLY B 146 5 5 HELIX 14 AB5 GLN C 2 LEU C 16 1 15 HELIX 15 AB6 LEU C 16 THR C 27 1 12 HELIX 16 AB7 LEU C 43 ASN C 50 1 8 HELIX 17 AB8 ASN C 50 LYS C 75 1 26 HELIX 18 AB9 VAL C 103 PHE C 108 1 6 HELIX 19 AC1 ASP C 112 THR C 133 1 22 HELIX 20 AC2 ASN C 139 LEU C 144 1 6 HELIX 21 AC3 GLN D 2 ASN D 7 1 6 HELIX 22 AC4 ASN D 7 LEU D 16 1 10 HELIX 23 AC5 LEU D 16 THR D 27 1 12 HELIX 24 AC6 GLY D 42 ASN D 50 1 9 HELIX 25 AC7 ASN D 50 THR D 74 1 25 HELIX 26 AC8 SER D 94 THR D 96 5 3 HELIX 27 AC9 PHE D 97 ILE D 102 1 6 HELIX 28 AD1 ASP D 112 THR D 133 1 22 HELIX 29 AD2 LYS D 135 ASN D 139 5 5 HELIX 30 AD3 THR D 141 GLY D 146 5 6 SHEET 1 AA1 4 LYS A 148 VAL A 152 0 SHEET 2 AA1 4 LEU A 165 SER A 169 -1 O SER A 169 N LYS A 148 SHEET 3 AA1 4 PHE A 189 ALA A 191 1 O PHE A 189 N ILE A 168 SHEET 4 AA1 4 TYR A 181 PHE A 183 -1 N SER A 182 O ILE A 190 SHEET 1 AA2 2 LEU A 155 HIS A 156 0 SHEET 2 AA2 2 GLY A 160 GLU A 161 -1 O GLY A 160 N HIS A 156 SHEET 1 AA3 3 LYS B 148 ARG B 151 0 SHEET 2 AA3 3 ILE B 166 SER B 169 -1 O SER B 169 N LYS B 148 SHEET 3 AA3 3 PHE B 189 ALA B 191 1 O ALA B 191 N ILE B 168 SHEET 1 AA4 4 LYS C 148 VAL C 152 0 SHEET 2 AA4 4 LEU C 165 SER C 169 -1 O LEU C 165 N VAL C 152 SHEET 3 AA4 4 PHE C 189 ARG C 192 1 O ALA C 191 N ILE C 168 SHEET 4 AA4 4 TYR C 180 PHE C 183 -1 N SER C 182 O ILE C 190 SHEET 1 AA5 2 LYS D 148 VAL D 152 0 SHEET 2 AA5 2 LEU D 165 SER D 169 -1 O SER D 169 N LYS D 148 SHEET 1 AA6 2 TYR D 181 PHE D 183 0 SHEET 2 AA6 2 PHE D 189 ALA D 191 -1 O ILE D 190 N SER D 182 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 206 0 0 30 17 0 0 6 6048 4 0 60 END