HEADER PROTEIN BINDING 16-AUG-24 9D7K TITLE INFECTIOUS B19V CAPSID COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-1-ANTICHYMOTRYPSIN; COMPND 3 CHAIN: S; COMPND 4 SYNONYM: ACT,CELL GROWTH-INHIBITING GENE 24/25 PROTEIN,SERPIN A3 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS B19, VIRION, CAPSID, PROTEIN BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR H.LEE,S.HAFENSTEIN REVDAT 3 14-MAY-25 9D7K 1 REMARK REVDAT 2 13-NOV-24 9D7K 1 JRNL REVDAT 1 16-OCT-24 9D7K 0 JRNL AUTH H.LEE,R.ASSARAF,S.SUBRAMANIAN,D.GOETSCHIUS,J.BIERI, JRNL AUTH 2 N.M.DINUNNO,R.LEISI,C.M.BATOR,S.L.HAFENSTEIN,C.ROS JRNL TITL INFECTIOUS PARVOVIRUS B19 CIRCULATES IN THE BLOOD COATED JRNL TITL 2 WITH ACTIVE HOST PROTEASE INHIBITORS. JRNL REF NAT COMMUN V. 15 9543 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39500886 JRNL DOI 10.1038/S41467-024-53794-1 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 : 380278 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 9D7K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1000287456. 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 : HUMAN PARVOVIRUS B19 WITH REMARK 245 SERPIN A3; HUMAN PARVOVIRUS B19; REMARK 245 SERPIN A3 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 : 7.00 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 : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 10000.00 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 400 REMARK 400 COMPOUND REMARK 400 THE PROTEIN IS BOUND TO A HUMAN PARVOVIRUS B19 CAPSID THAT IS NOT REMARK 400 MODELED. 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 S 1 REMARK 465 GLU S 2 REMARK 465 ARG S 3 REMARK 465 MET S 4 REMARK 465 LEU S 5 REMARK 465 PRO S 6 REMARK 465 LEU S 7 REMARK 465 LEU S 8 REMARK 465 ALA S 9 REMARK 465 LEU S 10 REMARK 465 GLY S 11 REMARK 465 LEU S 12 REMARK 465 LEU S 13 REMARK 465 ALA S 14 REMARK 465 ALA S 15 REMARK 465 GLY S 16 REMARK 465 PHE S 17 REMARK 465 CYS S 18 REMARK 465 PRO S 19 REMARK 465 ALA S 20 REMARK 465 VAL S 21 REMARK 465 LEU S 22 REMARK 465 CYS S 23 REMARK 465 HIS S 24 REMARK 465 PRO S 25 REMARK 465 ASN S 26 REMARK 465 SER S 27 REMARK 465 PRO S 28 REMARK 465 LEU S 29 REMARK 465 ASP S 30 REMARK 465 GLU S 31 REMARK 465 GLU S 32 REMARK 465 ASN S 33 REMARK 465 LEU S 34 REMARK 465 THR S 35 REMARK 465 GLN S 36 REMARK 465 GLU S 37 REMARK 465 ASN S 38 REMARK 465 GLN S 39 REMARK 465 ASP S 40 REMARK 465 ARG S 41 REMARK 465 GLY S 42 REMARK 465 THR S 43 REMARK 465 HIS S 44 REMARK 465 VAL S 45 REMARK 465 ASP S 46 REMARK 465 LEU S 47 REMARK 465 ALA S 374 REMARK 465 ALA S 375 REMARK 465 THR S 376 REMARK 465 ALA S 377 REMARK 465 VAL S 378 REMARK 465 LYS S 379 REMARK 465 ILE S 380 REMARK 465 THR S 381 REMARK 465 LEU S 382 REMARK 465 LEU S 383 REMARK 465 SER S 384 REMARK 465 ALA S 385 REMARK 465 LEU S 386 REMARK 465 VAL S 387 REMARK 465 GLU S 388 REMARK 465 THR S 389 REMARK 465 ALA S 423 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG S 124 CG CD NE CZ NH1 NH2 REMARK 470 GLN S 146 CG CD OE1 NE2 REMARK 470 GLU S 155 CG CD OE1 OE2 REMARK 470 GLU S 164 CG CD OE1 OE2 REMARK 470 LYS S 197 CG CD CE NZ REMARK 470 LYS S 235 CG CD CE NZ REMARK 470 LYS S 236 CG CD CE NZ REMARK 470 LYS S 237 CG CD CE NZ 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 S 68 89.79 -155.45 REMARK 500 ASN S 93 -133.59 54.78 REMARK 500 LEU S 103 14.39 58.04 REMARK 500 MET S 401 117.15 -161.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-46607 RELATED DB: EMDB REMARK 900 INFECTIOUS B19V CAPSID DBREF 9D7K S 1 423 UNP P01011 AACT_HUMAN 1 423 SEQRES 1 S 423 MET GLU ARG MET LEU PRO LEU LEU ALA LEU GLY LEU LEU SEQRES 2 S 423 ALA ALA GLY PHE CYS PRO ALA VAL LEU CYS HIS PRO ASN SEQRES 3 S 423 SER PRO LEU ASP GLU GLU ASN LEU THR GLN GLU ASN GLN SEQRES 4 S 423 ASP ARG GLY THR HIS VAL ASP LEU GLY LEU ALA SER ALA SEQRES 5 S 423 ASN VAL ASP PHE ALA PHE SER LEU TYR LYS GLN LEU VAL SEQRES 6 S 423 LEU LYS ALA PRO ASP LYS ASN VAL ILE PHE SER PRO LEU SEQRES 7 S 423 SER ILE SER THR ALA LEU ALA PHE LEU SER LEU GLY ALA SEQRES 8 S 423 HIS ASN THR THR LEU THR GLU ILE LEU LYS GLY LEU LYS SEQRES 9 S 423 PHE ASN LEU THR GLU THR SER GLU ALA GLU ILE HIS GLN SEQRES 10 S 423 SER PHE GLN HIS LEU LEU ARG THR LEU ASN GLN SER SER SEQRES 11 S 423 ASP GLU LEU GLN LEU SER MET GLY ASN ALA MET PHE VAL SEQRES 12 S 423 LYS GLU GLN LEU SER LEU LEU ASP ARG PHE THR GLU ASP SEQRES 13 S 423 ALA LYS ARG LEU TYR GLY SER GLU ALA PHE ALA THR ASP SEQRES 14 S 423 PHE GLN ASP SER ALA ALA ALA LYS LYS LEU ILE ASN ASP SEQRES 15 S 423 TYR VAL LYS ASN GLY THR ARG GLY LYS ILE THR ASP LEU SEQRES 16 S 423 ILE LYS ASP LEU ASP SER GLN THR MET MET VAL LEU VAL SEQRES 17 S 423 ASN TYR ILE PHE PHE LYS ALA LYS TRP GLU MET PRO PHE SEQRES 18 S 423 ASP PRO GLN ASP THR HIS GLN SER ARG PHE TYR LEU SER SEQRES 19 S 423 LYS LYS LYS TRP VAL MET VAL PRO MET MET SER LEU HIS SEQRES 20 S 423 HIS LEU THR ILE PRO TYR PHE ARG ASP GLU GLU LEU SER SEQRES 21 S 423 CYS THR VAL VAL GLU LEU LYS TYR THR GLY ASN ALA SER SEQRES 22 S 423 ALA LEU PHE ILE LEU PRO ASP GLN ASP LYS MET GLU GLU SEQRES 23 S 423 VAL GLU ALA MET LEU LEU PRO GLU THR LEU LYS ARG TRP SEQRES 24 S 423 ARG ASP SER LEU GLU PHE ARG GLU ILE GLY GLU LEU TYR SEQRES 25 S 423 LEU PRO LYS PHE SER ILE SER ARG ASP TYR ASN LEU ASN SEQRES 26 S 423 ASP ILE LEU LEU GLN LEU GLY ILE GLU GLU ALA PHE THR SEQRES 27 S 423 SER LYS ALA ASP LEU SER GLY ILE THR GLY ALA ARG ASN SEQRES 28 S 423 LEU ALA VAL SER GLN VAL VAL HIS LYS ALA VAL LEU ASP SEQRES 29 S 423 VAL PHE GLU GLU GLY THR GLU ALA SER ALA ALA THR ALA SEQRES 30 S 423 VAL LYS ILE THR LEU LEU SER ALA LEU VAL GLU THR ARG SEQRES 31 S 423 THR ILE VAL ARG PHE ASN ARG PRO PHE LEU MET ILE ILE SEQRES 32 S 423 VAL PRO THR ASP THR GLN ASN ILE PHE PHE MET SER LYS SEQRES 33 S 423 VAL THR ASN PRO LYS GLN ALA HELIX 1 AA1 GLY S 48 ALA S 68 1 21 HELIX 2 AA2 SER S 76 LEU S 89 1 14 HELIX 3 AA3 HIS S 92 GLY S 102 1 11 HELIX 4 AA4 LEU S 103 PHE S 105 5 3 HELIX 5 AA5 SER S 111 GLN S 128 1 18 HELIX 6 AA6 LEU S 150 LEU S 160 1 11 HELIX 7 AA7 ASP S 172 THR S 188 1 17 HELIX 8 AA8 ASP S 222 THR S 226 5 5 HELIX 9 AA9 LYS S 283 MET S 290 1 8 HELIX 10 AB1 LEU S 292 SER S 302 1 11 HELIX 11 AB2 LEU S 324 GLY S 332 1 9 HELIX 12 AB3 GLU S 334 THR S 338 5 5 SHEET 1 AA1 7 VAL S 73 PHE S 75 0 SHEET 2 AA1 7 PHE S 413 VAL S 417 -1 O LYS S 416 N VAL S 73 SHEET 3 AA1 7 PHE S 399 PRO S 405 -1 N ILE S 403 O PHE S 413 SHEET 4 AA1 7 ALA S 272 PRO S 279 -1 N LEU S 275 O ILE S 402 SHEET 5 AA1 7 CYS S 261 LYS S 267 -1 N THR S 262 O LEU S 278 SHEET 6 AA1 7 ILE S 251 ASP S 256 -1 N ASP S 256 O CYS S 261 SHEET 7 AA1 7 GLU S 304 ARG S 306 -1 O GLU S 304 N TYR S 253 SHEET 1 AA2 4 GLN S 134 MET S 137 0 SHEET 2 AA2 4 VAL S 206 LYS S 214 -1 O LYS S 214 N GLN S 134 SHEET 3 AA2 4 ALA S 140 LYS S 144 -1 N ALA S 140 O VAL S 208 SHEET 4 AA2 4 ALA S 167 THR S 168 1 O THR S 168 N VAL S 143 SHEET 1 AA3 4 GLN S 134 MET S 137 0 SHEET 2 AA3 4 VAL S 206 LYS S 214 -1 O LYS S 214 N GLN S 134 SHEET 3 AA3 4 GLN S 356 VAL S 362 1 O GLN S 356 N LEU S 207 SHEET 4 AA3 4 SER S 319 ASN S 323 -1 N TYR S 322 O HIS S 359 SHEET 1 AA4 4 HIS S 227 TYR S 232 0 SHEET 2 AA4 4 TRP S 238 HIS S 247 -1 O MET S 243 N HIS S 227 SHEET 3 AA4 4 ILE S 308 PRO S 314 -1 O LEU S 313 N MET S 244 SHEET 4 AA4 4 THR S 391 ARG S 394 1 O VAL S 393 N GLU S 310 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 2844 GLN S 422 MASTER 209 0 0 12 19 0 0 6 2843 1 0 33 END