HEADER IMMUNE SYSTEM 16-DEC-24 9L1U TITLE PENTRAXIN DOMAIN OF PTX3 DIMER, CONFORMATION 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENTRAXIN-RELATED PROTEIN PTX3; COMPND 3 CHAIN: A, H; COMPND 4 SYNONYM: PENTAXIN-RELATED PROTEIN PTX3,TUMOR NECROSIS FACTOR ALPHA- COMPND 5 INDUCED PROTEIN 5,TNF ALPHA-INDUCED PROTEIN 5,TUMOR NECROSIS FACTOR- COMPND 6 INDUCIBLE GENE 14 PROTEIN,TSG-14; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PTX3, TNFAIP5, TSG14; SOURCE 6 EXPRESSION_SYSTEM: MAMMALIA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 40674 KEYWDS DIMER, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR H.H.GUO,H.W.ZHANG REVDAT 1 17-DEC-25 9L1U 0 JRNL AUTH H.H.GUO,H.W.ZHANG JRNL TITL PENTRAXIN DOMAIN OF PTX3 DIMER,CONFORMATION 2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 8.30 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) : 8.300 REMARK 3 NUMBER OF PARTICLES : 11464 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9L1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1300054341. 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 : CELL REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : PENTRAXIN DOMAIN OF PTX3 DIMER, REMARK 245 CONFORMATION 2 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 MORGAGNI REMARK 245 DETECTOR TYPE : OTHER REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : DARK FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : OTHER 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, H 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 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 ALA H 215 H GLY H 265 1.54 REMARK 500 O ALA A 215 H GLY A 265 1.58 REMARK 500 H PHE A 247 O LEU A 256 1.58 REMARK 500 O LEU H 224 H GLY H 311 1.58 REMARK 500 H VAL A 213 O THR A 268 1.58 REMARK 500 OG1 THR H 216 O SER H 330 2.04 REMARK 500 O THR A 281 OG1 THR A 292 2.04 REMARK 500 OG SER H 244 OE1 GLU H 259 2.08 REMARK 500 ND2 ASN A 315 O GLY A 322 2.15 REMARK 500 O GLY A 287 NH1 ARG A 349 2.15 REMARK 500 OE1 GLU H 205 OG SER H 276 2.18 REMARK 500 O GLY H 287 NE ARG H 349 2.18 REMARK 500 NH1 ARG H 188 OD2 ASP H 217 2.18 REMARK 500 O CYS A 271 N TRP A 284 2.19 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 PHE A 185 77.35 -112.64 REMARK 500 PHE A 193 -178.56 -172.13 REMARK 500 ALA A 260 30.48 -144.42 REMARK 500 GLN A 312 145.13 -175.78 REMARK 500 PHE H 193 -175.33 -170.95 REMARK 500 ASN H 232 78.48 -151.14 REMARK 500 TYR H 234 30.65 -97.34 REMARK 500 GLN H 237 148.06 -172.73 REMARK 500 TYR H 242 -127.59 59.93 REMARK 500 THR H 292 148.77 -171.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62755 RELATED DB: EMDB REMARK 900 PENTRAXIN DOMAIN OF PTX3 DIMER, CONFORMATION 2 DBREF 9L1U A 175 381 UNP P26022 PTX3_HUMAN 175 381 DBREF 9L1U H 175 381 UNP P26022 PTX3_HUMAN 175 381 SEQRES 1 A 207 LEU PRO ALA GLY CYS GLU THR ALA ILE LEU PHE PRO MET SEQRES 2 A 207 ARG SER LYS LYS ILE PHE GLY SER VAL HIS PRO VAL ARG SEQRES 3 A 207 PRO MET ARG LEU GLU SER PHE SER ALA CYS ILE TRP VAL SEQRES 4 A 207 LYS ALA THR ASP VAL LEU ASN LYS THR ILE LEU PHE SER SEQRES 5 A 207 TYR GLY THR LYS ARG ASN PRO TYR GLU ILE GLN LEU TYR SEQRES 6 A 207 LEU SER TYR GLN SER ILE VAL PHE VAL VAL GLY GLY GLU SEQRES 7 A 207 GLU ASN LYS LEU VAL ALA GLU ALA MET VAL SER LEU GLY SEQRES 8 A 207 ARG TRP THR HIS LEU CYS GLY THR TRP ASN SER GLU GLU SEQRES 9 A 207 GLY LEU THR SER LEU TRP VAL ASN GLY GLU LEU ALA ALA SEQRES 10 A 207 THR THR VAL GLU MET ALA THR GLY HIS ILE VAL PRO GLU SEQRES 11 A 207 GLY GLY ILE LEU GLN ILE GLY GLN GLU LYS ASN GLY CYS SEQRES 12 A 207 CYS VAL GLY GLY GLY PHE ASP GLU THR LEU ALA PHE SER SEQRES 13 A 207 GLY ARG LEU THR GLY PHE ASN ILE TRP ASP SER VAL LEU SEQRES 14 A 207 SER ASN GLU GLU ILE ARG GLU THR GLY GLY ALA GLU SER SEQRES 15 A 207 CYS HIS ILE ARG GLY ASN ILE VAL GLY TRP GLY VAL THR SEQRES 16 A 207 GLU ILE GLN PRO HIS GLY GLY ALA GLN TYR VAL SER SEQRES 1 H 207 LEU PRO ALA GLY CYS GLU THR ALA ILE LEU PHE PRO MET SEQRES 2 H 207 ARG SER LYS LYS ILE PHE GLY SER VAL HIS PRO VAL ARG SEQRES 3 H 207 PRO MET ARG LEU GLU SER PHE SER ALA CYS ILE TRP VAL SEQRES 4 H 207 LYS ALA THR ASP VAL LEU ASN LYS THR ILE LEU PHE SER SEQRES 5 H 207 TYR GLY THR LYS ARG ASN PRO TYR GLU ILE GLN LEU TYR SEQRES 6 H 207 LEU SER TYR GLN SER ILE VAL PHE VAL VAL GLY GLY GLU SEQRES 7 H 207 GLU ASN LYS LEU VAL ALA GLU ALA MET VAL SER LEU GLY SEQRES 8 H 207 ARG TRP THR HIS LEU CYS GLY THR TRP ASN SER GLU GLU SEQRES 9 H 207 GLY LEU THR SER LEU TRP VAL ASN GLY GLU LEU ALA ALA SEQRES 10 H 207 THR THR VAL GLU MET ALA THR GLY HIS ILE VAL PRO GLU SEQRES 11 H 207 GLY GLY ILE LEU GLN ILE GLY GLN GLU LYS ASN GLY CYS SEQRES 12 H 207 CYS VAL GLY GLY GLY PHE ASP GLU THR LEU ALA PHE SER SEQRES 13 H 207 GLY ARG LEU THR GLY PHE ASN ILE TRP ASP SER VAL LEU SEQRES 14 H 207 SER ASN GLU GLU ILE ARG GLU THR GLY GLY ALA GLU SER SEQRES 15 H 207 CYS HIS ILE ARG GLY ASN ILE VAL GLY TRP GLY VAL THR SEQRES 16 H 207 GLU ILE GLN PRO HIS GLY GLY ALA GLN TYR VAL SER HELIX 1 AA1 LEU A 175 CYS A 179 5 5 HELIX 2 AA2 SER A 344 GLY A 352 1 9 HELIX 3 AA3 SER H 344 GLY H 352 1 9 SHEET 1 AA1 7 GLU A 288 THR A 293 0 SHEET 2 AA1 7 THR A 281 VAL A 285 -1 N LEU A 283 O ALA A 290 SHEET 3 AA1 7 TRP A 267 TRP A 274 -1 N CYS A 271 O TRP A 284 SHEET 4 AA1 7 PHE A 207 LYS A 214 -1 N VAL A 213 O THR A 268 SHEET 5 AA1 7 GLY A 331 THR A 334 -1 O ARG A 332 N LYS A 214 SHEET 6 AA1 7 ALA A 182 PHE A 185 -1 N ILE A 183 O LEU A 333 SHEET 7 AA1 7 GLN A 378 VAL A 380 -1 O VAL A 380 N ALA A 182 SHEET 1 AA2 2 PHE A 193 VAL A 196 0 SHEET 2 AA2 2 ILE A 371 HIS A 374 -1 O HIS A 374 N PHE A 193 SHEET 1 AA3 4 THR A 222 ILE A 223 0 SHEET 2 AA3 4 ILE A 236 LEU A 240 -1 O LEU A 240 N THR A 222 SHEET 3 AA3 4 ILE A 245 VAL A 249 -1 O VAL A 248 N GLN A 237 SHEET 4 AA3 4 LYS A 255 LEU A 256 -1 O LEU A 256 N PHE A 247 SHEET 1 AA4 2 PHE A 225 GLY A 228 0 SHEET 2 AA4 2 ILE A 307 ILE A 310 -1 O GLN A 309 N SER A 226 SHEET 1 AA5 2 ASN A 337 ILE A 338 0 SHEET 2 AA5 2 VAL A 364 GLY A 365 -1 O VAL A 364 N ILE A 338 SHEET 1 AA6 2 PHE H 193 HIS H 197 0 SHEET 2 AA6 2 GLU H 370 HIS H 374 -1 O HIS H 374 N PHE H 193 SHEET 1 AA7 4 PHE H 207 SER H 208 0 SHEET 2 AA7 4 THR H 268 TRP H 274 -1 O TRP H 274 N PHE H 207 SHEET 3 AA7 4 THR H 281 VAL H 285 -1 O TRP H 284 N CYS H 271 SHEET 4 AA7 4 GLU H 288 THR H 293 -1 O GLU H 288 N VAL H 285 SHEET 1 AA8 4 PHE H 207 SER H 208 0 SHEET 2 AA8 4 THR H 268 TRP H 274 -1 O TRP H 274 N PHE H 207 SHEET 3 AA8 4 ILE H 211 ALA H 215 -1 N ILE H 211 O LEU H 270 SHEET 4 AA8 4 GLY H 331 THR H 334 -1 O ARG H 332 N LYS H 214 SHEET 1 AA9 5 LYS H 255 GLU H 259 0 SHEET 2 AA9 5 SER H 244 VAL H 249 -1 N PHE H 247 O LEU H 256 SHEET 3 AA9 5 ASN H 232 LEU H 240 -1 N TYR H 239 O VAL H 246 SHEET 4 AA9 5 ILE H 223 THR H 229 -1 N THR H 229 O ASN H 232 SHEET 5 AA9 5 ILE H 307 ILE H 310 -1 O GLN H 309 N SER H 226 SSBOND 1 CYS A 210 CYS A 271 1555 1555 2.03 SSBOND 2 CYS H 179 CYS H 357 1555 1555 2.03 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 3125 SER A 381 TER 6250 SER H 381 CONECT 558 1551 CONECT 1551 558 CONECT 3181 5890 CONECT 5890 3181 MASTER 147 0 0 3 32 0 0 6 3162 2 4 32 END