HEADER DE NOVO PROTEIN 04-AUG-26 33AS TITLE T33-FUS-1A CAGE - DESIGNED TETRAHEDRAL PROTEIN CAGE BASED ON HELICAL TITLE 2 FUSION AND MACHINE LEARNING COMPND MOL_ID: 1; COMPND 2 MOLECULE: T33-FUS-1A-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 33AS 0 JRNL AUTH P.SAN SEGUNDO-ACOSTA,J.LECOQ,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. 3.61 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) : 3.610 REMARK 3 NUMBER OF PARTICLES : 32793 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 33AS 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_1292157689. 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-1A CAGE - 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 0.000354 -0.577200 0.816603 147.06143 REMARK 350 BIOMT2 2 -0.577200 -0.666958 -0.471176 525.25428 REMARK 350 BIOMT3 2 0.816603 -0.471176 -0.333396 191.11288 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000059 457.67252 REMARK 350 BIOMT2 3 0.866025 -0.500000 -0.000033 122.64235 REMARK 350 BIOMT3 3 0.000058 0.000035 1.000000 -0.01793 REMARK 350 BIOMT1 4 0.499741 0.866175 -0.000270 -70.73044 REMARK 350 BIOMT2 4 0.288880 -0.166376 0.942798 -12.63208 REMARK 350 BIOMT3 4 0.816583 -0.471233 -0.333366 191.12177 REMARK 350 BIOMT1 5 -0.500000 0.288322 0.816622 76.41977 REMARK 350 BIOMT2 5 -0.289030 0.833333 -0.471189 179.29680 REMARK 350 BIOMT3 5 -0.816371 -0.471622 -0.333333 507.06930 REMARK 350 BIOMT1 6 -0.500000 0.866025 0.000058 122.62487 REMARK 350 BIOMT2 6 -0.866025 -0.500000 0.000035 457.67721 REMARK 350 BIOMT3 6 0.000059 -0.000033 1.000000 -0.00513 REMARK 350 BIOMT1 7 0.500259 -0.288471 -0.816410 310.39816 REMARK 350 BIOMT2 7 -0.865876 -0.166957 -0.471576 484.45294 REMARK 350 BIOMT3 7 -0.000269 0.942820 -0.333302 75.58686 REMARK 350 BIOMT1 8 -0.500000 -0.289030 -0.816371 503.98875 REMARK 350 BIOMT2 8 0.288322 0.833333 -0.471622 67.69780 REMARK 350 BIOMT3 8 0.816622 -0.471189 -0.333333 191.09932 REMARK 350 BIOMT1 9 0.500259 -0.865876 -0.000269 264.21703 REMARK 350 BIOMT2 9 -0.288471 -0.166957 0.942820 99.15888 REMARK 350 BIOMT3 9 -0.816410 -0.471576 -0.333302 507.06205 REMARK 350 BIOMT1 10 0.499741 0.288880 0.816583 -117.07064 REMARK 350 BIOMT2 10 0.866175 -0.166376 -0.471233 149.22611 REMARK 350 BIOMT3 10 -0.000270 0.942798 -0.333366 75.60377 REMARK 350 BIOMT1 11 -0.000354 0.577499 -0.816391 239.71987 REMARK 350 BIOMT2 11 0.577499 -0.666377 -0.471632 301.86504 REMARK 350 BIOMT3 11 -0.816391 -0.471632 -0.333269 507.06285 REMARK 350 BIOMT1 12 -1.000000 -0.000299 -0.000211 386.97871 REMARK 350 BIOMT2 12 -0.000299 0.333335 0.942809 -53.35931 REMARK 350 BIOMT3 12 -0.000211 0.942809 -0.333335 75.58429 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 2 REMARK 465 GLY A 168 REMARK 465 HIS A 169 REMARK 465 ARG A 170 REMARK 465 SER A 171 REMARK 465 PRO A 172 REMARK 465 PHE A 173 REMARK 465 GLU A 174 REMARK 465 GLY A 483 REMARK 465 HIS A 484 REMARK 465 HIS A 485 REMARK 465 HIS A 486 REMARK 465 HIS A 487 REMARK 465 HIS A 488 REMARK 465 HIS A 489 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 ASP A 3 CG OD1 OD2 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 ASP A 84 -7.83 75.85 REMARK 500 GLU A 260 -4.91 68.97 REMARK 500 LYS A 285 -6.50 68.87 REMARK 500 PRO A 311 48.56 -81.73 REMARK 500 ASN A 385 16.86 -141.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-59308 RELATED DB: EMDB REMARK 900 T33-FUS-1A CAGE - DESIGNED TETRAHEDRAL PROTEIN CAGE BASED ON REMARK 900 HELICAL FUSION AND MACHINE LEARNING DBREF 33AS A 2 489 PDB 33AS 33AS 2 489 SEQRES 1 A 488 MET ASP PRO GLN ASP LEU TYR THR TRP GLU PRO LYS GLY SEQRES 2 A 488 LEU ALA VAL VAL ASP MET ALA LEU ALA GLN GLU SER ALA SEQRES 3 A 488 GLY LEU VAL MET LEU TYR HIS PHE ASP GLY TYR ILE ASP SEQRES 4 A 488 ALA GLY GLU THR GLY ASP GLN ILE VAL ASP GLN VAL LEU SEQRES 5 A 488 ASP SER LEU PRO HIS GLN VAL VAL ALA ARG PHE ASP HIS SEQRES 6 A 488 ASP ARG LEU VAL ASP TYR ARG ALA ARG ARG PRO LEU LEU SEQRES 7 A 488 THR PHE LYS ARG ASP THR TRP SER ASP TYR GLU GLU PRO SEQRES 8 A 488 THR ILE GLU VAL ARG LEU VAL GLN ASP ALA THR GLY ALA SEQRES 9 A 488 PRO PHE LEU PHE LEU SER GLY PRO GLU PRO ASP VAL GLU SEQRES 10 A 488 TRP GLU ARG PHE ALA ALA ALA VAL GLY GLN ILE VAL GLU SEQRES 11 A 488 ARG LEU GLY VAL ARG LEU SER VAL SER PHE HIS GLY ILE SEQRES 12 A 488 PRO MET GLY VAL PRO HIS THR ARG PRO VAL GLY ILE THR SEQRES 13 A 488 PRO HIS GLY SER ARG THR ASP LEU VAL PRO GLY HIS ARG SEQRES 14 A 488 SER PRO PHE GLU GLU ALA GLN VAL PRO GLY SER ALA GLU SEQRES 15 A 488 ALA LEU VAL GLU TYR ARG LEU ALA GLN ALA GLY HIS ASP SEQRES 16 A 488 VAL LEU GLY VAL ALA ALA HIS VAL PRO HIS TYR VAL ALA SEQRES 17 A 488 ARG SER ALA TYR PRO ASP ALA ALA LEU THR VAL LEU GLU SEQRES 18 A 488 ALA ILE THR ALA ALA THR GLY LEU VAL LEU PRO GLY ILE SEQRES 19 A 488 ALA HIS SER LEU ARG THR ASP ALA HIS ARG THR GLN THR SEQRES 20 A 488 GLU ILE ASP ARG GLN ILE GLN GLU GLY ASP GLU GLU LEU SEQRES 21 A 488 ILE ALA LEU VAL ARG GLY LEU GLU ARG ARG ALA ASP GLY SEQRES 22 A 488 GLU ARG ILE ASP ALA GLN LEU LYS ALA LEU LYS VAL ILE SEQRES 23 A 488 PRO VAL ILE ALA ILE ASP ASN ALA GLU ASP ILE ILE PRO SEQRES 24 A 488 LEU GLY LYS VAL LEU ALA GLU ASN GLY LEU PRO ALA ALA SEQRES 25 A 488 GLU ILE THR PHE ARG SER ASP ALA ALA VAL GLU ALA ILE SEQRES 26 A 488 ARG LEU LEU ARG GLN ALA GLN PRO GLU MET LEU ILE GLY SEQRES 27 A 488 ALA GLY THR ILE LEU ASN GLY GLU GLN ALA LEU ALA ALA SEQRES 28 A 488 LYS GLU ALA GLY ALA THR PHE VAL VAL SER PRO GLY PHE SEQRES 29 A 488 ASN PRO ASN THR VAL ARG ALA CYS ASP GLU ILE GLY ILE SEQRES 30 A 488 PRO ILE VAL PRO GLY VAL ASN ASN PRO SER THR VAL GLU SEQRES 31 A 488 ALA ALA LEU GLU MET GLY ILE THR THR LEU LYS PHE PHE SEQRES 32 A 488 PRO ALA GLU ALA SER GLY GLY ILE SER MET VAL LYS SER SEQRES 33 A 488 LEU VAL GLY PRO TYR GLY ASP ILE ARG LEU MET PRO THR SEQRES 34 A 488 GLY GLY ILE THR PRO SER ASN ILE ASP ASN TYR LEU ALA SEQRES 35 A 488 ILE PRO GLN VAL LEU ALA CYS GLY GLY THR TRP MET VAL SEQRES 36 A 488 ASP LYS LYS LEU VAL THR ASN GLY GLU TRP ASP GLU ILE SEQRES 37 A 488 ALA ARG LEU THR ARG GLU ILE VAL GLU GLN VAL ASN PRO SEQRES 38 A 488 GLY HIS HIS HIS HIS HIS HIS HELIX 1 AA1 ASP A 3 ASP A 6 5 4 HELIX 2 AA2 GLU A 11 SER A 26 1 16 HELIX 3 AA3 ASP A 40 GLY A 42 5 3 HELIX 4 AA4 GLU A 43 LEU A 56 1 14 HELIX 5 AA5 ASP A 65 VAL A 70 1 6 HELIX 6 AA6 GLU A 118 GLY A 134 1 17 HELIX 7 AA7 ARG A 162 VAL A 166 5 5 HELIX 8 AA8 SER A 181 ALA A 193 1 13 HELIX 9 AA9 TYR A 207 ALA A 209 5 3 HELIX 10 AB1 TYR A 213 GLY A 229 1 17 HELIX 11 AB2 LEU A 232 GLU A 256 1 25 HELIX 12 AB3 GLU A 260 LYS A 285 1 26 HELIX 13 AB4 ASN A 294 GLU A 296 5 3 HELIX 14 AB5 ASP A 297 ASN A 308 1 12 HELIX 15 AB6 ALA A 321 GLN A 333 1 13 HELIX 16 AB7 ASN A 345 GLY A 356 1 12 HELIX 17 AB8 ASN A 366 ILE A 376 1 11 HELIX 18 AB9 ASN A 386 MET A 396 1 11 HELIX 19 AC1 GLY A 411 GLY A 420 1 10 HELIX 20 AC2 ASN A 437 ALA A 443 1 7 HELIX 21 AC3 ASP A 457 ASN A 463 1 7 HELIX 22 AC4 GLU A 465 ASN A 481 1 17 SHEET 1 AA1 8 TYR A 8 TRP A 10 0 SHEET 2 AA1 8 HIS A 58 PHE A 64 -1 O ARG A 63 N THR A 9 SHEET 3 AA1 8 GLU A 95 GLN A 100 -1 O VAL A 96 N VAL A 61 SHEET 4 AA1 8 PRO A 106 PRO A 113 -1 O PHE A 109 N ARG A 97 SHEET 5 AA1 8 LEU A 29 ASP A 36 1 N LEU A 32 O LEU A 108 SHEET 6 AA1 8 VAL A 135 MET A 146 1 O VAL A 139 N MET A 31 SHEET 7 AA1 8 VAL A 197 PRO A 205 1 O VAL A 200 N SER A 140 SHEET 8 AA1 8 ILE A 156 GLY A 160 -1 N HIS A 159 O GLY A 199 SHEET 1 AA2 2 LEU A 79 LYS A 82 0 SHEET 2 AA2 2 THR A 85 TYR A 89 -1 O SER A 87 N THR A 80 SHEET 1 AA3 6 ILE A 380 VAL A 381 0 SHEET 2 AA3 6 PHE A 359 VAL A 361 1 N VAL A 360 O VAL A 381 SHEET 3 AA3 6 LEU A 337 GLY A 341 1 N ALA A 340 O VAL A 361 SHEET 4 AA3 6 ALA A 312 THR A 316 1 N ALA A 313 O LEU A 337 SHEET 5 AA3 6 VAL A 286 ILE A 290 1 N ILE A 290 O GLU A 314 SHEET 6 AA3 6 CYS A 450 GLY A 452 1 O GLY A 452 N VAL A 289 SHEET 1 AA4 2 GLY A 383 VAL A 384 0 SHEET 2 AA4 2 LYS A 402 PHE A 403 1 O LYS A 402 N VAL A 384 CISPEP 1 PHE A 404 PRO A 405 0 -7.76 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 190 0 0 22 18 0 0 6 3590 1 0 38 END