HEADER ANTIVIRAL PROTEIN 18-DEC-22 8HSB TITLE CRYO-EM STRUCTURE OF CDNG-E2 COMPLEX FROM SERRATIA MARCESCENS TITLE 2 (ULTRAUFOIL) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CDNG; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TYPE VI SECRETION PROTEIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SERRATIA MARCESCENS; SOURCE 3 ORGANISM_TAXID: 615; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SERRATIA MARCESCENS; SOURCE 8 ORGANISM_TAXID: 615; SOURCE 9 GENE: AR325_02475, AR325_06795; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CGAS, CDNG, E2, CBASS, ANTIVIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.XIAO,L.WANG REVDAT 3 25-JUN-25 8HSB 1 REMARK REVDAT 2 19-JUN-24 8HSB 1 JRNL REVDAT 1 01-MAY-24 8HSB 0 JRNL AUTH Y.YAN,J.XIAO,F.HUANG,W.XIAN,B.YU,R.CHENG,H.WU,X.LU,X.WANG, JRNL AUTH 2 W.HUANG,J.LI,G.K.OYEJOBI,C.V.ROBINSON,H.WU,D.WU,X.LIU, JRNL AUTH 3 L.WANG,B.ZHU JRNL TITL PHAGE DEFENCE SYSTEM CBASS IS REGULATED BY A PROKARYOTIC E2 JRNL TITL 2 ENZYME THAT IMITATES THE UBIQUITIN PATHWAY. JRNL REF NAT MICROBIOL V. 9 1566 2024 JRNL REFN ESSN 2058-5276 JRNL PMID 38649411 JRNL DOI 10.1038/S41564-024-01684-Z REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.000 REMARK 3 NUMBER OF PARTICLES : 512003 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 8HSB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300034239. 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 : CDNG-E2 BINARY COMPLEX 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 : 8.00 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) : 1100.00 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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 7000.00 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 TYR A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 MET A 191 REMARK 465 ASP A 192 REMARK 465 SER A 193 REMARK 465 ALA A 194 REMARK 465 SER A 195 REMARK 465 ARG A 196 REMARK 465 VAL A 197 REMARK 465 GLY A 198 REMARK 465 THR A 199 REMARK 465 GLU A 200 REMARK 465 ALA A 201 REMARK 465 LEU A 202 REMARK 465 LEU A 203 REMARK 465 PRO A 204 REMARK 465 LEU A 205 REMARK 465 PRO A 206 REMARK 465 ASP A 207 REMARK 465 SER A 208 REMARK 465 THR A 209 REMARK 465 ASP A 210 REMARK 465 GLY A 389 REMARK 465 LEU A 390 REMARK 465 ALA A 391 REMARK 465 GLY A 392 REMARK 465 THR A 393 REMARK 465 ALA A 394 REMARK 465 ALA A 395 REMARK 465 GLN A 396 REMARK 465 GLU A 407 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 ASN B 3 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 O PHE A 49 NH2 ARG A 109 2.16 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 ALA A 94 35.21 -99.46 REMARK 500 GLN A 153 -0.51 166.64 REMARK 500 ALA A 163 -11.03 72.79 REMARK 500 PRO B 74 -165.88 -76.73 REMARK 500 THR B 82 -141.85 42.24 REMARK 500 ARG B 83 -173.50 54.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34992 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF SMCDNG-SME2 COMPLEX DBREF 8HSB A 1 407 PDB 8HSB 8HSB 1 407 DBREF1 8HSB B 1 162 UNP A0A0P0QAP1_SERMA DBREF2 8HSB B A0A0P0QAP1 1 162 SEQADV 8HSB LEU B 50 UNP A0A0P0QAP VAL 50 CONFLICT SEQADV 8HSB LYS B 56 UNP A0A0P0QAP ARG 56 CONFLICT SEQADV 8HSB ALA B 78 UNP A0A0P0QAP THR 78 CONFLICT SEQADV 8HSB HIS B 142 UNP A0A0P0QAP TYR 142 CONFLICT SEQADV 8HSB PRO B 155 UNP A0A0P0QAP THR 155 CONFLICT SEQRES 1 A 407 MET TYR GLY SER THR THR ALA ARG ASN LEU PRO SER GLY SEQRES 2 A 407 LYS LYS GLN ARG ILE ALA ASP LEU LEU SER GLN ILE ILE SEQRES 3 A 407 GLU THR LEU ASP LEU THR LYS THR GLN TYR ALA ASN ILE SEQRES 4 A 407 GLU SER ALA TYR ASN GLY VAL GLY THR PHE LEU SER GLU SEQRES 5 A 407 GLY ASP ASP PRO LEU LEU GLN ASP ALA VAL ILE TYR PRO SEQRES 6 A 407 GLN GLY SER VAL ARG LEU ASN THR THR VAL LYS PRO LYS SEQRES 7 A 407 ASN GLU GLU GLN TYR ASP ILE ASP LEU ILE CYS TYR LEU SEQRES 8 A 407 PRO HIS ALA THR GLN ALA ASP TYR THR GLY VAL ILE SER SEQRES 9 A 407 ALA ILE ARG GLN ARG LEU GLU SER HIS LYS THR TYR LYS SEQRES 10 A 407 THR LEU LEU SER GLU LEU PRO ARG GLY PHE ARG ILE ASN SEQRES 11 A 407 TYR ALA GLY ASP TYR HIS LEU ASP ILE THR PRO GLY ARG SEQRES 12 A 407 ASP HIS THR GLY THR ALA HIS PRO GLY GLN PRO LEU TRP SEQRES 13 A 407 VAL VAL ASP ALA GLN THR ALA TRP LYS GLU SER ASN PRO SEQRES 14 A 407 SER GLY TYR ALA GLU TRP PHE GLU SER SER ALA SER VAL SEQRES 15 A 407 GLN PRO LEU ARG THR ILE LEU VAL MET ASP SER ALA SER SEQRES 16 A 407 ARG VAL GLY THR GLU ALA LEU LEU PRO LEU PRO ASP SER SEQRES 17 A 407 THR ASP LYS LYS LEU LEU ASN HIS ILE VAL GLN ILE LEU SEQRES 18 A 407 LYS ARG HIS ARG ASP GLU TRP ALA ALA GLU GLN ASP GLU SEQRES 19 A 407 VAL ARG GLN ARG CYS ARG PRO ILE SER VAL ILE ILE THR SEQRES 20 A 407 THR LEU ALA CYS HIS ALA TYR ASN HIS ILE ILE ALA ASP SEQRES 21 A 407 ARG ARG ALA TYR ASP ASN ASP LEU ASP ILE LEU LEU ASP SEQRES 22 A 407 VAL LEU GLU LEU MET PRO ASP PHE ILE VAL SER THR GLN SEQRES 23 A 407 GLY ALA ILE HIS VAL ASN ASN PRO HIS MET PRO GLU GLU SEQRES 24 A 407 ASN PHE ALA GLU LYS TRP ASN ARG SER GLU GLN ASP GLU SEQRES 25 A 407 GLY PRO GLN ARG SER GLU ALA PHE TYR GLN TRP HIS ALA SEQRES 26 A 407 ALA ALA GLN ALA THR PHE ASN THR ILE ALA ALA SER VAL SEQRES 27 A 407 GLY GLU ASP ASN LEU PHE LEU SER LEU GLU ASP SER PHE SEQRES 28 A 407 GLY LYS THR PRO VAL ASP VAL VAL ARG GLN ARG LEU MET SEQRES 29 A 407 GLU HIS MET GLN SER ALA ARG GLU GLN GLY SER LEU HIS SEQRES 30 A 407 LEU ASP LYS LYS THR GLY GLY LEU ILE ALA THR GLY LEU SEQRES 31 A 407 ALA GLY THR ALA ALA GLN ALA GLY VAL PRO LYS ASN THR SEQRES 32 A 407 PHE TYR GLY GLU SEQRES 1 B 162 MET ASN ASN VAL VAL ILE ARG HIS HIS CYS LYS PRO LEU SEQRES 2 B 162 THR ILE ALA GLN GLN TYR ARG ALA LEU LYS ALA GLY GLY SEQRES 3 B 162 PRO TYR GLU ARG LEU ARG ILE ILE HIS HIS ASP ARG THR SEQRES 4 B 162 LEU LEU TRP GLU GLY TRP LEU GLN PRO SER LEU PHE SER SEQRES 5 B 162 ARG ARG TYR LYS VAL ALA VAL ARG TYR SER LEU GLY THR SEQRES 6 B 162 PRO PRO ILE CYS VAL VAL THR GLU PRO ASP LEU PHE ALA SEQRES 7 B 162 LEU ALA GLY THR ARG ALA ILE PRO HIS LEU TYR PRO ALA SEQRES 8 B 162 ASP LYS HIS ILE PRO GLY ALA ARG LEU CYS LEU PHE LEU SEQRES 9 B 162 PRO ARG SER GLN ALA ASP ASP GLY LEU SER GLU TRP ARG SEQRES 10 B 162 ALA GLN LEU LYS ILE SER ASP THR LEU ILE PRO TRP ALA SEQRES 11 B 162 SER LEU TRP LEU PHE TYR PHE GLU GLN TRP LEU HIS THR SEQRES 12 B 162 GLY HIS TRP GLU GLY GLY GLY LYS HIS PRO ARG PRO SER SEQRES 13 B 162 GLU VAL LYS ASN GLU ARG HELIX 1 AA1 PRO A 11 ASP A 30 1 20 HELIX 2 AA2 THR A 32 GLU A 52 1 21 HELIX 3 AA3 ASP A 98 HIS A 113 1 16 HELIX 4 AA4 HIS A 113 LEU A 119 1 7 HELIX 5 AA5 ASN A 168 VAL A 182 1 15 HELIX 6 AA6 LYS A 212 GLN A 232 1 21 HELIX 7 AA7 ASP A 233 CYS A 239 1 7 HELIX 8 AA8 ILE A 242 ASP A 260 1 19 HELIX 9 AA9 ASN A 266 MET A 278 1 13 HELIX 10 AB1 PRO A 279 ILE A 282 5 4 HELIX 11 AB2 ALA A 302 ARG A 307 1 6 HELIX 12 AB3 SER A 308 GLN A 310 5 3 HELIX 13 AB4 ASP A 311 SER A 337 1 27 HELIX 14 AB5 GLY A 339 GLY A 352 1 14 HELIX 15 AB6 GLY A 352 GLY A 374 1 23 HELIX 16 AB7 THR B 14 GLY B 25 1 12 HELIX 17 AB8 PHE B 77 GLY B 81 5 5 HELIX 18 AB9 PRO B 90 HIS B 94 5 5 HELIX 19 AC1 THR B 125 GLY B 144 1 20 SHEET 1 AA1 5 VAL A 62 GLN A 66 0 SHEET 2 AA1 5 ASP A 86 LEU A 91 -1 O TYR A 90 N VAL A 62 SHEET 3 AA1 5 LEU A 137 ARG A 143 1 O ASP A 138 N LEU A 87 SHEET 4 AA1 5 PHE A 127 ILE A 129 -1 N PHE A 127 O ILE A 139 SHEET 5 AA1 5 LEU A 120 GLU A 122 -1 N SER A 121 O ARG A 128 SHEET 1 AA2 2 LEU A 155 VAL A 157 0 SHEET 2 AA2 2 LYS A 165 SER A 167 -1 O SER A 167 N LEU A 155 SHEET 1 AA3 2 VAL A 283 THR A 285 0 SHEET 2 AA3 2 ALA A 288 HIS A 290 -1 O ALA A 288 N THR A 285 SHEET 1 AA4 2 HIS A 377 LEU A 378 0 SHEET 2 AA4 2 LEU A 385 ILE A 386 -1 O ILE A 386 N HIS A 377 SHEET 1 AA5 5 ARG B 30 ILE B 34 0 SHEET 2 AA5 5 THR B 39 LEU B 46 -1 O THR B 39 N ILE B 34 SHEET 3 AA5 5 TYR B 55 SER B 62 -1 O TYR B 55 N LEU B 46 SHEET 4 AA5 5 THR B 65 VAL B 71 -1 O VAL B 70 N ALA B 58 SHEET 5 AA5 5 ALA B 98 LEU B 100 -1 O LEU B 100 N CYS B 69 CISPEP 1 GLU B 73 PRO B 74 0 -2.37 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 2974 GLY A 406 TER 4280 ARG B 162 MASTER 174 0 0 19 16 0 0 6 4278 2 0 45 END