HEADER STRUCTURAL PROTEIN 23-JUN-22 8A8N TITLE STRUCTURE OF SELF-ASSEMBLING ENGINEERED PROTEIN NANOCAGE (EPN) FUSED TITLE 2 WITH HEPATITIS A PX PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPN-PX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: MODEL JUST CONTAINS EPN-01 COMPONENT SINCE ASSOCIATED COMPND 6 TAG AND PX COULD NOT BE CONFIDENTALLY RESOLVED.,MODEL JUST CONTAINS COMPND 7 EPN-01 COMPONENT SINCE ASSOCIATED TAG AND PX COULD NOT BE COMPND 8 CONFIDENTALLY RESOLVED. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 BH10; SOURCE 3 ORGANISM_TAXID: 11678; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: HEK293T KEYWDS HEPATITIS A, PX, VP1-PX, NANOCAGE, ICOSAHEDRAL, PROTEIN NANOPARTICLE, KEYWDS 2 VIRUS ASSEMBLY, ENVELOPED VIRUSES, STRUCTURAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.M.E.DUYVESTEYN,D.I.STUART REVDAT 3 31-AUG-22 8A8N 1 JRNL REVDAT 2 24-AUG-22 8A8N 1 JRNL REVDAT 1 10-AUG-22 8A8N 0 JRNL AUTH T.SHIRASAKI,H.FENG,H.M.E.DUYVESTEYN,W.G.FUSCO,K.L.MCKNIGHT, JRNL AUTH 2 L.XIE,M.BOYCE,S.KUMAR,R.BAROUCH-BENTOV,O.GONZALEZ-LOPEZ, JRNL AUTH 3 R.MCNAMARA,L.WANG,A.HERTEL-WULFF,X.CHEN,S.EINAV,J.A.DUNCAN, JRNL AUTH 4 M.KAPUSTINA,E.E.FRY,D.I.STUART,S.M.LEMON JRNL TITL NONLYTIC CELLULAR RELEASE OF HEPATITIS A VIRUS REQUIRES DUAL JRNL TITL 2 CAPSID RECRUITMENT OF THE ESCRT-ASSOCIATED BRO1 DOMAIN JRNL TITL 3 PROTEINS HD-PTP AND ALIX. JRNL REF PLOS PATHOG. V. 18 10543 2022 JRNL REFN ESSN 1553-7374 JRNL PMID 35969644 JRNL DOI 10.1371/JOURNAL.PPAT.1010543 REMARK 2 REMARK 2 RESOLUTION. 6.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, CTFFIND, COOT, UCSF REMARK 3 CHIMERA, RELION, RELION, RELION, RELION, REMARK 3 PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 5KP9 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : RIGID BODY FIT MONOMER IN CHIMERA, GENERATED REMARK 3 BIOLOGICAL UNIT THEN CHECKED IN COOT AND RESIDUES TO BE ALTERED REMARK 3 DONE SO IN COOT FOLLOWED BY ONE CYCLE OF RIGID BODY REFINEMENT REMARK 3 OF ENTIRE ICOSAHEDRAL ASSEMBLY IN PHENIX, DEFINING EACH REMARK 3 MONOMERIC UNIT AS A SEPARATE BODY AND CONSIDERING NCS REMARK 3 CONSTRAINTS TO CHECK FOR CLASHES. 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) : 6.700 REMARK 3 NUMBER OF PARTICLES : 1830 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 8A8N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1292123892. 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 : EPN-PX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT TIME 4-5 S. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : ASSOCIATED MODEL JUST CONTAINS REMARK 245 EPN-01 COMPONENT SINCE ASSOCIATED TAG AND PX COULD NOT BE REMARK 245 CONFIDENTALLY RESOLVED. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 1803 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS GLACIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 700.00 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) : 4600.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : 92000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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: A 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 -18 REMARK 465 GLY A -17 REMARK 465 ALA A -16 REMARK 465 ARG A -15 REMARK 465 ALA A -14 REMARK 465 SER A -13 REMARK 465 GLY A -12 REMARK 465 SER A -11 REMARK 465 LYS A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 SER A -7 REMARK 465 GLY A -6 REMARK 465 SER A -5 REMARK 465 ASP A -4 REMARK 465 SER A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 THR A 202 REMARK 465 GLU A 203 REMARK 465 GLN A 204 REMARK 465 LYS A 205 REMARK 465 LEU A 206 REMARK 465 ILE A 207 REMARK 465 SER A 208 REMARK 465 GLU A 209 REMARK 465 GLU A 210 REMARK 465 ASP A 211 REMARK 465 LEU A 212 REMARK 465 MET A 213 REMARK 465 MET A 214 REMARK 465 SER A 215 REMARK 465 ARG A 216 REMARK 465 ILE A 217 REMARK 465 ALA A 218 REMARK 465 ALA A 219 REMARK 465 GLY A 220 REMARK 465 ASP A 221 REMARK 465 LEU A 222 REMARK 465 GLU A 223 REMARK 465 SER A 224 REMARK 465 SER A 225 REMARK 465 VAL A 226 REMARK 465 ASP A 227 REMARK 465 ASP A 228 REMARK 465 PRO A 229 REMARK 465 ARG A 230 REMARK 465 SER A 231 REMARK 465 GLU A 232 REMARK 465 GLU A 233 REMARK 465 ASP A 234 REMARK 465 LYS A 235 REMARK 465 ARG A 236 REMARK 465 PHE A 237 REMARK 465 GLU A 238 REMARK 465 SER A 239 REMARK 465 HIS A 240 REMARK 465 ILE A 241 REMARK 465 GLU A 242 REMARK 465 CYS A 243 REMARK 465 ARG A 244 REMARK 465 LYS A 245 REMARK 465 PRO A 246 REMARK 465 TYR A 247 REMARK 465 LYS A 248 REMARK 465 GLU A 249 REMARK 465 LEU A 250 REMARK 465 ARG A 251 REMARK 465 LEU A 252 REMARK 465 GLU A 253 REMARK 465 VAL A 254 REMARK 465 GLY A 255 REMARK 465 LYS A 256 REMARK 465 GLN A 257 REMARK 465 ARG A 258 REMARK 465 LEU A 259 REMARK 465 LYS A 260 REMARK 465 TYR A 261 REMARK 465 ALA A 262 REMARK 465 GLN A 263 REMARK 465 GLU A 264 REMARK 465 GLU A 265 REMARK 465 LEU A 266 REMARK 465 SER A 267 REMARK 465 ASN A 268 REMARK 465 GLU A 269 REMARK 465 VAL A 270 REMARK 465 LEU A 271 REMARK 465 PRO A 272 REMARK 465 PRO A 273 REMARK 465 PRO A 274 REMARK 465 ARG A 275 REMARK 465 LYS A 276 REMARK 465 MET A 277 REMARK 465 LYS A 278 REMARK 465 GLY A 279 REMARK 465 LEU A 280 REMARK 465 PHE A 281 REMARK 465 SER A 282 REMARK 465 GLN A 283 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 LYS A 0 CB 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 LYS A 9 -7.30 70.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-15234 RELATED DB: EMDB REMARK 900 STRUCTURE OF SELF-ASSEMBLING ENGINEERED PROTEIN NANOCAGE (EPN) REMARK 900 FUSED WITH HEPATITIS A PX PROTEIN DBREF 8A8N A 0 203 UNP Q9WXS1 Q9WXS1_THEMA 2 205 DBREF 8A8N A 213 283 UNP V9Z3B5 V9Z3B5_9PICO 38 108 SEQADV 8A8N MET A -18 UNP Q9WXS1 INITIATING METHIONINE SEQADV 8A8N GLY A -17 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N ALA A -16 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N ARG A -15 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N ALA A -14 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N SER A -13 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N GLY A -12 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N SER A -11 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N LYS A -10 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N SER A -9 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N GLY A -8 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N SER A -7 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N GLY A -6 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N SER A -5 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N ASP A -4 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N SER A -3 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N GLY A -2 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N SER A -1 UNP Q9WXS1 EXPRESSION TAG SEQADV 8A8N ILE A 1 UNP Q9WXS1 MET 3 CONFLICT SEQADV 8A8N LYS A 24 UNP Q9WXS1 GLU 26 CONFLICT SEQADV 8A8N LEU A 31 UNP Q9WXS1 GLU 33 CONFLICT SEQADV 8A8N MET A 59 UNP Q9WXS1 LYS 61 CONFLICT SEQADV 8A8N VAL A 185 UNP Q9WXS1 ASP 187 CONFLICT SEQADV 8A8N ALA A 188 UNP Q9WXS1 ARG 190 CONFLICT SEQADV 8A8N GLN A 204 UNP Q9WXS1 LINKER SEQADV 8A8N LYS A 205 UNP Q9WXS1 LINKER SEQADV 8A8N LEU A 206 UNP Q9WXS1 LINKER SEQADV 8A8N ILE A 207 UNP Q9WXS1 LINKER SEQADV 8A8N SER A 208 UNP Q9WXS1 LINKER SEQADV 8A8N GLU A 209 UNP Q9WXS1 LINKER SEQADV 8A8N GLU A 210 UNP Q9WXS1 LINKER SEQADV 8A8N ASP A 211 UNP Q9WXS1 LINKER SEQADV 8A8N LEU A 212 UNP Q9WXS1 LINKER SEQRES 1 A 302 MET GLY ALA ARG ALA SER GLY SER LYS SER GLY SER GLY SEQRES 2 A 302 SER ASP SER GLY SER LYS ILE GLU GLU LEU PHE LYS LYS SEQRES 3 A 302 HIS LYS ILE VAL ALA VAL LEU ARG ALA ASN SER VAL GLU SEQRES 4 A 302 GLU ALA LYS LYS LYS ALA LEU ALA VAL PHE LEU GLY GLY SEQRES 5 A 302 VAL HIS LEU ILE GLU ILE THR PHE THR VAL PRO ASP ALA SEQRES 6 A 302 ASP THR VAL ILE LYS GLU LEU SER PHE LEU LYS GLU MET SEQRES 7 A 302 GLY ALA ILE ILE GLY ALA GLY THR VAL THR SER VAL GLU SEQRES 8 A 302 GLN CYS ARG LYS ALA VAL GLU SER GLY ALA GLU PHE ILE SEQRES 9 A 302 VAL SER PRO HIS LEU ASP GLU GLU ILE SER GLN PHE CYS SEQRES 10 A 302 LYS GLU LYS GLY VAL PHE TYR MET PRO GLY VAL MET THR SEQRES 11 A 302 PRO THR GLU LEU VAL LYS ALA MET LYS LEU GLY HIS THR SEQRES 12 A 302 ILE LEU LYS LEU PHE PRO GLY GLU VAL VAL GLY PRO GLN SEQRES 13 A 302 PHE VAL LYS ALA MET LYS GLY PRO PHE PRO ASN VAL LYS SEQRES 14 A 302 PHE VAL PRO THR GLY GLY VAL ASN LEU ASP ASN VAL CYS SEQRES 15 A 302 GLU TRP PHE LYS ALA GLY VAL LEU ALA VAL GLY VAL GLY SEQRES 16 A 302 SER ALA LEU VAL LYS GLY THR PRO VAL GLU VAL ALA GLU SEQRES 17 A 302 LYS ALA LYS ALA PHE VAL GLU LYS ILE ARG GLY CYS THR SEQRES 18 A 302 GLU GLN LYS LEU ILE SER GLU GLU ASP LEU MET MET SER SEQRES 19 A 302 ARG ILE ALA ALA GLY ASP LEU GLU SER SER VAL ASP ASP SEQRES 20 A 302 PRO ARG SER GLU GLU ASP LYS ARG PHE GLU SER HIS ILE SEQRES 21 A 302 GLU CYS ARG LYS PRO TYR LYS GLU LEU ARG LEU GLU VAL SEQRES 22 A 302 GLY LYS GLN ARG LEU LYS TYR ALA GLN GLU GLU LEU SER SEQRES 23 A 302 ASN GLU VAL LEU PRO PRO PRO ARG LYS MET LYS GLY LEU SEQRES 24 A 302 PHE SER GLN HELIX 1 AA1 LYS A 0 LYS A 9 1 10 HELIX 2 AA2 SER A 18 GLY A 32 1 15 HELIX 3 AA3 ASP A 45 SER A 54 1 10 HELIX 4 AA4 PHE A 55 GLY A 60 5 6 HELIX 5 AA5 SER A 70 SER A 80 1 11 HELIX 6 AA6 ASP A 91 GLY A 102 1 12 HELIX 7 AA7 THR A 111 LEU A 121 1 11 HELIX 8 AA8 PRO A 130 GLY A 135 1 6 HELIX 9 AA9 GLY A 135 GLY A 144 1 10 HELIX 10 AB1 ASN A 161 GLY A 169 1 9 HELIX 11 AB2 GLY A 176 LYS A 181 1 6 HELIX 12 AB3 THR A 183 GLY A 200 1 18 SHEET 1 AA1 4 ILE A 62 GLY A 66 0 SHEET 2 AA1 4 LEU A 36 THR A 40 1 N ILE A 37 O ILE A 62 SHEET 3 AA1 4 ILE A 10 LEU A 14 1 N ALA A 12 O GLU A 38 SHEET 4 AA1 4 VAL A 173 VAL A 175 1 O VAL A 175 N VAL A 11 SHEET 1 AA2 2 PHE A 84 VAL A 86 0 SHEET 2 AA2 2 PHE A 104 MET A 106 1 O MET A 106 N ILE A 85 SHEET 1 AA3 3 GLY A 108 VAL A 109 0 SHEET 2 AA3 3 ILE A 125 LEU A 128 1 O LYS A 127 N VAL A 109 SHEET 3 AA3 3 LYS A 150 PRO A 153 1 O LYS A 150 N LEU A 126 SSBOND 1 CYS A 163 CYS A 201 1555 1555 2.03 CISPEP 1 PHE A 129 PRO A 130 0 1.06 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