HEADER DE NOVO PROTEIN 04-AUG-26 33AV TITLE T33-FUS-1B ASYMMETRIC UNIT - DESIGNED TETRAHEDRAL PROTEIN CAGE BASED TITLE 2 ON HELICAL FUSION AND MACHINE LEARNING COMPND MOL_ID: 1; COMPND 2 MOLECULE: T33-FUS-1B-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 KEYWDS PROTEIN CAGE, TETRAHEDRAL, PROTEIN DESIGN, NANOHEDRA, NANOPARTICLE, KEYWDS 2 DE NOVO PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR P.SAN SEGUNDO-ACOSTA,J.LECOQ,J.BOSKOVIC,R.A.AGLIETTI,P.BOWERS, AUTHOR 2 T.O.YEATES,R.CASTELLS-GRAELLS REVDAT 1 30-SEP-26 33AV 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. 3.90 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) : 3.900 REMARK 3 NUMBER OF PARTICLES : 220000 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: THE PARTICLES WERE EXPANDED IN T SYMMETRY REMARK 4 REMARK 4 33AV 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_1292157614. 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-1B ASYMMETRIC UNIT - REMARK 245 DESIGNED TETRAHEDRAL PROTEIN REMARK 245 CAGE BASED ON HELICAL FUSION REMARK 245 AND MACHINE LEARNING REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.30 REMARK 245 SAMPLE SUPPORT DETAILS : 45S 0.1 BAR 15 MA 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: 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 1 REMARK 465 GLY A 482 REMARK 465 HIS 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 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 2 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 250 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES 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 SER A 25 -168.29 -74.42 REMARK 500 ASP A 100 -160.43 -74.46 REMARK 500 GLU A 117 65.05 60.49 REMARK 500 HIS A 168 -169.79 -103.71 REMARK 500 GLU A 258 53.46 -91.51 REMARK 500 GLU A 259 -6.03 69.62 REMARK 500 LYS A 284 -0.11 67.69 REMARK 500 THR A 398 -111.88 51.02 REMARK 500 GLU A 464 48.23 36.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-59317 RELATED DB: EMDB REMARK 900 T33-FUS-1B ASYMMETRIC UNIT - DESIGNED TETRAHEDRAL PROTEIN CAGE REMARK 900 BASED ON HELICAL FUSION AND MACHINE LEARNING DBREF 33AV A 1 488 PDB 33AV 33AV 1 488 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 ALA ARG TYR ASP GLY SEQRES 22 A 488 ALA VAL 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 ARG 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 LEU 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 2 ASP A 5 5 4 HELIX 2 AA2 GLU A 10 GLN A 23 1 14 HELIX 3 AA3 ASP A 39 GLY A 41 5 3 HELIX 4 AA4 GLU A 42 LEU A 55 1 14 HELIX 5 AA5 ASP A 64 VAL A 69 1 6 HELIX 6 AA6 GLU A 117 GLY A 133 1 17 HELIX 7 AA7 SER A 180 ALA A 192 1 13 HELIX 8 AA8 PRO A 204 ARG A 209 1 6 HELIX 9 AA9 TYR A 212 GLY A 228 1 17 HELIX 10 AB1 LEU A 231 ASP A 257 1 27 HELIX 11 AB2 LEU A 260 LYS A 284 1 25 HELIX 12 AB3 ASN A 293 GLU A 295 5 3 HELIX 13 AB4 ASP A 296 ASN A 307 1 12 HELIX 14 AB5 ALA A 320 GLN A 332 1 13 HELIX 15 AB6 ASN A 344 GLY A 355 1 12 HELIX 16 AB7 ASN A 365 GLY A 376 1 12 HELIX 17 AB8 ASN A 385 MET A 395 1 11 HELIX 18 AB9 GLY A 410 VAL A 418 1 9 HELIX 19 AC1 ASN A 436 ILE A 443 1 8 HELIX 20 AC2 THR A 452 VAL A 455 5 4 HELIX 21 AC3 ASP A 456 ASN A 462 1 7 HELIX 22 AC4 GLU A 464 ASN A 480 1 17 SHEET 1 AA1 8 TYR A 7 TRP A 9 0 SHEET 2 AA1 8 HIS A 57 PHE A 63 -1 O ARG A 62 N THR A 8 SHEET 3 AA1 8 GLU A 94 GLN A 99 -1 O VAL A 95 N ALA A 61 SHEET 4 AA1 8 PRO A 105 PRO A 112 -1 O PHE A 108 N ARG A 96 SHEET 5 AA1 8 LEU A 28 ASP A 35 1 N HIS A 33 O LEU A 109 SHEET 6 AA1 8 VAL A 134 PRO A 144 1 O ARG A 135 N LEU A 28 SHEET 7 AA1 8 VAL A 196 VAL A 203 1 O LEU A 197 N SER A 137 SHEET 8 AA1 8 ILE A 155 GLY A 159 -1 N THR A 156 O ALA A 200 SHEET 1 AA2 6 ILE A 379 VAL A 380 0 SHEET 2 AA2 6 PHE A 358 VAL A 360 1 N VAL A 359 O VAL A 380 SHEET 3 AA2 6 LEU A 336 GLY A 340 1 N ALA A 339 O VAL A 360 SHEET 4 AA2 6 ALA A 311 THR A 315 1 N ALA A 312 O LEU A 336 SHEET 5 AA2 6 VAL A 285 ILE A 289 1 N ILE A 289 O THR A 315 SHEET 6 AA2 6 CYS A 449 GLY A 451 1 O GLY A 451 N VAL A 288 SHEET 1 AA3 3 GLY A 382 VAL A 383 0 SHEET 2 AA3 3 LEU A 400 PHE A 402 1 O LYS A 401 N VAL A 383 SHEET 3 AA3 3 LEU A 426 PRO A 428 1 O MET A 427 N PHE A 402 CISPEP 1 PHE A 403 PRO A 404 0 -5.16 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 171 0 0 22 17 0 0 6 3644 1 0 38 END