HEADER DE NOVO PROTEIN 04-AUG-26 33AT TITLE T33-FUS-2 CAGE - DESIGNED TETRAHEDRAL PROTEIN CAGE BASED ON HELICAL TITLE 2 FUSION AND MACHINE LEARNING COMPND MOL_ID: 1; COMPND 2 MOLECULE: T33-FUS-2-SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PROTEIN CAGE, TETRAHEDRAL, PROTEIN DESIGN, NANOHEDRA, NANOPARTICLE, KEYWDS 2 DE NOVO PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR P.SAN SEGUNDO-ACOSTA,J.LE COQ,J.BOSKOVIC,R.A.AGLIETTI,P.BOWERS, AUTHOR 2 T.O.YEATES,R.CASTELLS-GRAELLS REVDAT 1 30-SEP-26 33AT 0 JRNL AUTH P.SAN SEGUNDO-ACOSTA,J.LE COQ,J.BOSKOVIC,R.A.AGLIETTI, JRNL AUTH 2 P.BOWERS,T.O.YEATES,R.CASTELLS-GRAELLS JRNL TITL DESIGN AND STRUCTURE OF PROTEIN CAGES BASED ON HELICAL JRNL TITL 2 FUSION AND MACHINE LEARNING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 5.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERAX, PHENIX, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT 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) : 5.110 REMARK 3 NUMBER OF PARTICLES : 46720 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 33AT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-AUG-26. REMARK 100 THE DEPOSITION ID IS D_1292157698. 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 : T33-FUS-2 - DESIGNED REMARK 245 TETRAHEDRAL PROTEIN CAGE BASED REMARK 245 ON HELICAL FUSION AND MACHINE REMARK 245 LEARNING REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.30 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOTTING 3 SECONDS, BLOT FORCE REMARK 245 0 REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : DE NOVO DESIGN PROTEIN 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 : TFS GLACIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 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) : 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA 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 350 BIOMT1 2 -0.000027 0.577415 -0.816451 184.37272 REMARK 350 BIOMT2 2 0.577415 -0.666583 -0.471444 232.21912 REMARK 350 BIOMT3 2 -0.816451 -0.471444 -0.333389 390.04709 REMARK 350 BIOMT1 3 0.500011 -0.866019 -0.000081 203.27399 REMARK 350 BIOMT2 3 -0.288601 -0.166717 0.942823 76.25927 REMARK 350 BIOMT3 3 -0.816516 -0.471399 -0.333294 390.03588 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000072 94.32477 REMARK 350 BIOMT2 4 -0.866025 -0.500000 -0.000101 352.07958 REMARK 350 BIOMT3 4 -0.000051 -0.000112 1.000000 0.02438 REMARK 350 BIOMT1 5 0.499989 0.288633 0.816518 -90.04486 REMARK 350 BIOMT2 5 0.866032 -0.166684 -0.471387 114.87937 REMARK 350 BIOMT3 5 0.000042 0.942819 -0.333305 58.09806 REMARK 350 BIOMT1 6 0.500011 -0.288601 -0.816516 238.83981 REMARK 350 BIOMT2 6 -0.866019 -0.166717 -0.471399 372.61518 REMARK 350 BIOMT3 6 -0.000081 0.942823 -0.333294 58.11416 REMARK 350 BIOMT1 7 -0.500000 -0.288639 -0.816509 387.64611 REMARK 350 BIOMT2 7 0.288595 0.833400 -0.471335 51.98179 REMARK 350 BIOMT3 7 0.816525 -0.471308 -0.333400 147.04170 REMARK 350 BIOMT1 8 0.499989 0.866032 0.000042 -54.47021 REMARK 350 BIOMT2 8 0.288633 -0.166684 0.942819 -9.63752 REMARK 350 BIOMT3 8 0.816518 -0.471387 -0.333305 147.04029 REMARK 350 BIOMT1 9 -0.500000 0.288595 0.816525 58.75817 REMARK 350 BIOMT2 9 -0.288639 0.833400 -0.471308 137.87021 REMARK 350 BIOMT3 9 -0.816509 -0.471335 -0.333400 390.04123 REMARK 350 BIOMT1 10 -0.500000 -0.866025 -0.000051 352.07224 REMARK 350 BIOMT2 10 0.866025 -0.500000 -0.000112 94.35214 REMARK 350 BIOMT3 10 0.000072 -0.000101 1.000000 0.00434 REMARK 350 BIOMT1 11 0.000027 -0.577402 0.816460 113.22407 REMARK 350 BIOMT2 11 -0.577402 -0.666616 -0.471413 404.05611 REMARK 350 BIOMT3 11 0.816460 -0.471413 -0.333411 147.06855 REMARK 350 BIOMT1 12 -1.000000 -0.000013 -0.000009 297.60323 REMARK 350 BIOMT2 12 -0.000013 0.333199 0.942856 -41.07521 REMARK 350 BIOMT3 12 -0.000009 0.942856 -0.333199 58.08437 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 LYS A 296 REMARK 465 THR A 297 REMARK 465 LYS A 298 REMARK 465 SER A 299 REMARK 465 GLY A 300 REMARK 465 TYR A 301 REMARK 465 ARG A 324 REMARK 465 PHE A 325 REMARK 465 SER A 326 REMARK 465 GLY A 476 REMARK 465 HIS A 477 REMARK 465 HIS A 478 REMARK 465 HIS A 479 REMARK 465 HIS A 480 REMARK 465 HIS A 481 REMARK 465 HIS A 482 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 A 2 CG CD NE CZ NH1 NH2 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 MET A 11 -30.42 -131.04 REMARK 500 THR A 83 -94.94 57.13 REMARK 500 ASP A 84 28.18 -141.11 REMARK 500 ASP A 101 -167.94 -77.97 REMARK 500 GLN A 137 -167.47 -162.46 REMARK 500 ARG A 441 109.79 -56.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 436 0.29 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-59315 RELATED DB: EMDB REMARK 900 T33-FUS-2 CAGE - DESIGNED TETRAHEDRAL PROTEIN CAGE BASED ON HELICAL REMARK 900 FUSION AND MACHINE LEARNING DBREF 33AT A 1 482 PDB 33AT 33AT 1 482 SEQRES 1 A 482 MET ARG GLU TYR GLU PRO GLY GLN PRO GLY MET TYR GLU SEQRES 2 A 482 LEU GLU PHE PRO ALA PRO GLN LEU SER SER SER ASP GLY SEQRES 3 A 482 ARG GLY PRO VAL LEU VAL HIS ALA LEU GLU GLY PHE SER SEQRES 4 A 482 ASP ALA GLY HIS ALA ILE ARG LEU ALA ALA ALA HIS LEU SEQRES 5 A 482 LYS ALA ALA LEU ASP THR GLU LEU VAL ALA SER PHE ALA SEQRES 6 A 482 ILE ASP GLU LEU LEU ASP TYR ARG SER ARG ARG PRO LEU SEQRES 7 A 482 MET THR PHE LYS THR ASP HIS PHE THR HIS SER ASP ASP SEQRES 8 A 482 PRO GLU LEU SER LEU TYR ALA LEU ARG ASP SER ILE GLY SEQRES 9 A 482 THR PRO PHE LEU LEU LEU ALA GLY LEU GLU PRO ASP LEU SEQRES 10 A 482 LYS TRP GLU ARG PHE ILE THR ALA VAL ARG LEU LEU ALA SEQRES 11 A 482 GLU ARG LEU GLY VAL ARG GLN THR ILE GLY LEU GLY THR SEQRES 12 A 482 VAL PRO MET ALA VAL PRO HIS THR ARG PRO ILE THR MET SEQRES 13 A 482 THR ALA HIS SER ASN ASN ARG GLU LEU ILE SER ASP PHE SEQRES 14 A 482 THR PRO SER ILE SER GLU ILE GLN VAL PRO GLY SER ALA SEQRES 15 A 482 SER ASN LEU LEU GLU TYR ARG MET ALA GLN HIS GLY HIS SEQRES 16 A 482 GLU VAL VAL GLY PHE THR VAL HIS VAL PRO HIS TYR LEU SEQRES 17 A 482 THR GLN THR ASP TYR PRO ALA ALA ALA GLN ALA LEU LEU SEQRES 18 A 482 GLU GLN VAL ALA LYS THR GLY SER LEU GLN LEU PRO LEU SEQRES 19 A 482 ALA VAL LEU ALA GLU ALA ALA ALA GLU VAL GLN ALA LYS SEQRES 20 A 482 ILE ASP GLU GLN VAL GLN ALA SER ALA GLU VAL ALA GLN SEQRES 21 A 482 VAL VAL ALA ALA LEU GLU ARG GLN TYR ALA ALA ALA GLN SEQRES 22 A 482 ALA LYS SER ALA VAL ALA ARG ARG LEU GLY LYS VAL THR SEQRES 23 A 482 ALA SER ARG VAL ALA ASP VAL MET THR LYS THR LYS SER SEQRES 24 A 482 GLY TYR ALA ALA SER ARG GLN ASN TYR MET ALA GLU LEU SEQRES 25 A 482 ILE ALA GLN ARG LEU THR GLY THR GLN GLU ILE ARG PHE SEQRES 26 A 482 SER ASN ALA ALA MET GLN ARG GLY THR GLU LEU GLU PRO SEQRES 27 A 482 HIS ALA ARG ALA ARG TYR ILE ILE GLU THR GLY GLU ILE SEQRES 28 A 482 VAL THR GLU VAL GLY LEU ILE ASP HIS PRO THR ILE ALA SEQRES 29 A 482 GLY PHE GLY ALA SER PRO ASP GLY LEU VAL GLY ASP THR SEQRES 30 A 482 GLY LEU ILE GLU ILE LYS CYS PRO ASN THR TRP THR HIS SEQRES 31 A 482 ILE GLU THR ILE LYS THR GLY LYS PRO LYS PRO GLU TYR SEQRES 32 A 482 ILE LYS GLN MET GLN THR GLN MET ALA CYS THR GLY ARG SEQRES 33 A 482 GLN TRP CYS ASP PHE VAL SER TYR ASP ASP ARG LEU PRO SEQRES 34 A 482 ASP ASP MET GLN TYR PHE ARG THR ARG ILE GLU ARG ASP SEQRES 35 A 482 ASP ALA LEU ILE ALA GLU ILE GLU THR GLU VAL SER ALA SEQRES 36 A 482 PHE LEU ALA GLU LEU GLU ALA GLU ILE GLU TYR LEU LYS SEQRES 37 A 482 ARG LYS ALA ALA LYS LEU ALA GLY HIS HIS HIS HIS HIS SEQRES 38 A 482 HIS HELIX 1 AA1 ASP A 40 GLY A 42 5 3 HELIX 2 AA2 HIS A 43 ALA A 55 1 13 HELIX 3 AA3 ASP A 71 ARG A 75 5 5 HELIX 4 AA4 LYS A 118 GLY A 134 1 17 HELIX 5 AA5 ASN A 162 SER A 167 5 6 HELIX 6 AA6 SER A 181 HIS A 193 1 13 HELIX 7 AA7 TYR A 213 SER A 229 1 17 HELIX 8 AA8 LEU A 234 GLN A 253 1 20 HELIX 9 AA9 VAL A 258 ALA A 263 1 6 HELIX 10 AB1 ALA A 264 ARG A 281 1 18 HELIX 11 AB2 ARG A 289 THR A 295 1 7 HELIX 12 AB3 ALA A 303 GLY A 319 1 17 HELIX 13 AB4 ALA A 328 GLY A 349 1 22 HELIX 14 AB5 ASN A 386 GLY A 397 1 12 HELIX 15 AB6 LYS A 400 GLY A 415 1 16 HELIX 16 AB7 PRO A 429 GLN A 433 1 5 HELIX 17 AB8 ASP A 442 ALA A 475 1 34 SHEET 1 AA1 5 TYR A 12 LEU A 14 0 SHEET 2 AA1 5 GLU A 59 PHE A 64 -1 O SER A 63 N GLU A 13 SHEET 3 AA1 5 LEU A 94 ARG A 100 -1 O ALA A 98 N GLU A 59 SHEET 4 AA1 5 PRO A 106 LEU A 113 -1 O LEU A 109 N TYR A 97 SHEET 5 AA1 5 VAL A 30 GLU A 36 1 N VAL A 32 O LEU A 108 SHEET 1 AA2 2 MET A 79 LYS A 82 0 SHEET 2 AA2 2 HIS A 85 SER A 89 -1 O HIS A 88 N THR A 80 SHEET 1 AA3 2 THR A 143 PRO A 145 0 SHEET 2 AA3 2 VAL A 202 VAL A 204 1 O VAL A 204 N VAL A 144 SHEET 1 AA4 2 HIS A 159 SER A 160 0 SHEET 2 AA4 2 VAL A 198 GLY A 199 -1 O GLY A 199 N HIS A 159 SHEET 1 AA5 3 VAL A 285 THR A 286 0 SHEET 2 AA5 3 PHE A 366 ALA A 368 1 O GLY A 367 N VAL A 285 SHEET 3 AA5 3 ILE A 358 ASP A 359 -1 N ILE A 358 O ALA A 368 SHEET 1 AA6 5 VAL A 352 THR A 353 0 SHEET 2 AA6 5 GLY A 372 VAL A 374 -1 O LEU A 373 N THR A 353 SHEET 3 AA6 5 GLY A 378 LYS A 383 -1 O ILE A 380 N GLY A 372 SHEET 4 AA6 5 TRP A 418 TYR A 424 1 O ASP A 420 N LEU A 379 SHEET 5 AA6 5 TYR A 434 GLU A 440 -1 O ILE A 439 N CYS A 419 CISPEP 1 PHE A 16 PRO A 17 0 -0.26 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 209 0 0 17 19 0 0 6 3589 1 0 38 END