HEADER DE NOVO PROTEIN 03-OCT-23 8UF0 TITLE T33-ML23 - DESIGNED TETRAHEDRAL PROTEIN CAGE USING MACHINE LEARNING TITLE 2 ALGORITHMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: T33-ML23-REDESIGNED-CUTA-FOLD; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: T33-ML23-REDESIGNED-TANDEM-BMC-T-FOLD; COMPND 7 CHAIN: B; COMPND 8 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_STRAIN: LOBSTR; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PSAM; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: LOBSTR; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PSAM KEYWDS NANOHEDRA, PROTEIN CAGE, TETRAHEDRAL, DE NOVO PROTEIN INTERFACE, KEYWDS 2 MACHINE LEARNING, TWO COMPONENTS, PROTEINMPNN, NANOPARTICLE, DE NOVO KEYWDS 3 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR R.CASTELLS-GRAELLS,K.MEADOR,M.R.SAWAYA,T.O.YEATES REVDAT 2 03-APR-24 8UF0 1 JRNL REVDAT 1 15-NOV-23 8UF0 0 JRNL AUTH K.MEADOR,R.CASTELLS-GRAELLS,R.AGUIRRE,M.R.SAWAYA,M.A.ARBING, JRNL AUTH 2 T.SHERMAN,C.SENARATHNE,T.O.YEATES JRNL TITL A SUITE OF DESIGNED PROTEIN CAGES USING MACHINE LEARNING AND JRNL TITL 2 PROTEIN FRAGMENT-BASED PROTOCOLS. JRNL REF STRUCTURE 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 38513658 JRNL DOI 10.1016/J.STR.2024.02.017 REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, 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 : 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) : 2.020 REMARK 3 NUMBER OF PARTICLES : 390028 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 8UF0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000277965. 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-ML23 DESIGNED TETRAHEDRAL REMARK 245 PROTEIN CAGE USING MACHINE REMARK 245 LEARNING REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.60 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 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 : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 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: 48-MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 -0.000005 -0.577352 0.816495 83.75574 REMARK 350 BIOMT2 2 -0.577352 -0.666663 -0.471408 298.91383 REMARK 350 BIOMT3 2 0.816495 -0.471408 -0.333332 108.78594 REMARK 350 BIOMT1 3 0.000005 0.577349 -0.816498 136.40503 REMARK 350 BIOMT2 3 0.577349 -0.666670 -0.471402 171.80438 REMARK 350 BIOMT3 3 -0.816498 -0.471402 -0.333335 288.54558 REMARK 350 BIOMT1 4 -1.000000 0.000003 0.000002 220.15955 REMARK 350 BIOMT2 4 0.000003 0.333333 0.942809 -30.39808 REMARK 350 BIOMT3 4 0.000002 0.942809 -0.333333 42.98860 REMARK 350 BIOMT1 5 -0.500000 -0.866025 -0.000002 260.45239 REMARK 350 BIOMT2 5 0.866025 -0.500000 0.000000 69.78786 REMARK 350 BIOMT3 5 -0.000001 -0.000001 1.000000 0.00025 REMARK 350 BIOMT1 6 0.500003 0.866024 0.000004 -40.29262 REMARK 350 BIOMT2 6 0.288672 -0.166670 0.942809 -7.13442 REMARK 350 BIOMT3 6 0.816496 -0.471406 -0.333332 108.78576 REMARK 350 BIOMT1 7 -0.500000 0.288679 0.816495 43.46247 REMARK 350 BIOMT2 7 -0.288670 0.833334 -0.471407 102.01600 REMARK 350 BIOMT3 7 -0.816498 -0.471401 -0.333334 288.54548 REMARK 350 BIOMT1 8 0.499997 -0.288678 -0.816497 176.69807 REMARK 350 BIOMT2 8 -0.866027 -0.166663 -0.471403 275.65068 REMARK 350 BIOMT3 8 0.000003 0.942809 -0.333334 42.98864 REMARK 350 BIOMT1 9 -0.500000 0.866025 -0.000001 69.78814 REMARK 350 BIOMT2 9 -0.866025 -0.500000 -0.000001 260.45232 REMARK 350 BIOMT3 9 -0.000002 0.000000 1.000000 0.00013 REMARK 350 BIOMT1 10 -0.500000 -0.288670 -0.816498 286.77712 REMARK 350 BIOMT2 10 0.288679 0.833334 -0.471401 38.46068 REMARK 350 BIOMT3 10 0.816495 -0.471407 -0.333334 108.78606 REMARK 350 BIOMT1 11 0.499997 -0.866027 0.000003 150.37226 REMARK 350 BIOMT2 11 -0.288678 -0.166663 0.942809 56.41958 REMARK 350 BIOMT3 11 -0.816497 -0.471403 -0.333334 288.54556 REMARK 350 BIOMT1 12 0.500003 0.288672 0.816496 -66.61720 REMARK 350 BIOMT2 12 0.866024 -0.166670 -0.471406 84.98755 REMARK 350 BIOMT3 12 0.000004 0.942809 -0.333332 42.98838 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 17 REMARK 465 MET B 1 REMARK 465 HIS B 2 REMARK 465 HIS B 3 REMARK 465 HIS B 4 REMARK 465 HIS B 5 REMARK 465 HIS B 6 REMARK 465 HIS B 7 REMARK 465 GLY B 8 REMARK 465 GLY B 9 REMARK 465 SER B 10 REMARK 465 HIS B 11 REMARK 465 HIS B 12 REMARK 465 TRP B 13 REMARK 465 GLY B 14 REMARK 465 GLY B 15 REMARK 465 PHE B 204 REMARK 465 PHE B 205 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 A 51 61.00 62.38 REMARK 500 CYS B 51 45.94 -141.11 REMARK 500 HIS B 155 10.71 59.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-42181 RELATED DB: EMDB REMARK 900 T33-ML23 - DESIGNED TETRAHEDRAL PROTEIN CAGE USING MACHINE LEARNING REMARK 900 ALGORITHMS DBREF 8UF0 A 17 117 PDB 8UF0 8UF0 17 117 DBREF 8UF0 B 1 205 PDB 8UF0 8UF0 1 205 SEQRES 1 A 101 MET ALA ILE ILE GLU THR THR THR PRO THR GLU GLU GLU SEQRES 2 A 101 ALA LYS ALA ILE ALA LYS LYS LEU LEU GLU ASN ARG LEU SEQRES 3 A 101 ILE ALA GLU ALA ILE ILE THR PRO ALA LEU THR LYS ILE SEQRES 4 A 101 TYR ARG GLU ASN GLY GLU ILE LYS SER GLU THR VAL THR SEQRES 5 A 101 ARG VAL THR LEU TYR THR GLU GLU GLU ASN VAL PRO LYS SEQRES 6 A 101 ALA VAL THR TYR ILE LYS ALA ILE HIS PRO ASP PRO ILE SEQRES 7 A 101 PRO PRO ILE ILE VAL ILE THR PRO THR ASP ALA ASN PRO SEQRES 8 A 101 ALA TYR LYS GLY TRP VAL ALA PHE GLU THR SEQRES 1 B 205 MET HIS HIS HIS HIS HIS HIS GLY GLY SER HIS HIS TRP SEQRES 2 B 205 GLY GLY ASP PRO GLU ARG PRO ALA LEU GLY ILE LEU GLU SEQRES 3 B 205 LEU SER SER TYR ALA ARG GLY VAL LYS VAL ALA ASP ALA SEQRES 4 B 205 ALA LEU LYS ALA ALA PRO VAL LYS LEU LEU LYS CYS GLU SEQRES 5 B 205 PRO VAL GLU PRO GLY ARG ALA LEU ILE MET LEU LEU GLY SEQRES 6 B 205 GLU PRO GLU ASP VAL ALA LYS ALA MET ILE ALA ALA LEU SEQRES 7 B 205 ASP VAL ALA GLY LEU GLY SER GLY ASN LEU ILE ASP TYR SEQRES 8 B 205 ALA LEU ILE PRO GLU ILE HIS PRO GLN LEU LEU PRO PHE SEQRES 9 B 205 LEU LYS GLU TYR LYS LYS SER GLU PRO ILE LYS ASP PRO SEQRES 10 B 205 ASN LYS ALA ILE ILE VAL ALA GLU VAL SER THR VAL ALA SEQRES 11 B 205 ALA ALA ILE GLU ALA ALA ASP VAL ALA LEU ARG LEU ALA SEQRES 12 B 205 ASN VAL GLU LEU THR SER MET ARG LEU ALA GLU HIS ILE SEQRES 13 B 205 GLY GLY ARG ALA SER PHE THR LEU ILE GLY ASP LYS GLU SEQRES 14 B 205 ASP VAL GLU LYS ALA ALA ARG ALA ILE ARG GLY VAL ALA SEQRES 15 B 205 GLY GLU ARG LEU LEU ASP LEU GLU ILE ILE GLU LYS PRO SEQRES 16 B 205 VAL GLU ALA LEU ILE GLY ASN GLU PHE PHE FORMUL 3 HOH *67(H2 O) HELIX 1 AA1 THR A 26 ASN A 40 1 15 HELIX 2 AA2 GLU A 75 GLU A 77 5 3 HELIX 3 AA3 ASN A 78 HIS A 90 1 13 HELIX 4 AA4 ASN A 106 THR A 117 1 12 HELIX 5 AA5 SER B 29 ALA B 44 1 16 HELIX 6 AA6 GLU B 66 GLY B 82 1 17 HELIX 7 AA7 LEU B 101 GLU B 107 1 7 HELIX 8 AA8 THR B 128 ALA B 143 1 16 HELIX 9 AA9 ASP B 167 GLY B 183 1 17 HELIX 10 AB1 VAL B 196 GLU B 203 1 8 SHEET 1 AA1 4 GLU A 45 GLU A 58 0 SHEET 2 AA1 4 GLU A 61 TYR A 73 -1 O GLU A 61 N GLU A 58 SHEET 3 AA1 4 ILE A 19 THR A 24 -1 N THR A 22 O VAL A 70 SHEET 4 AA1 4 ILE A 98 ILE A 100 -1 O ILE A 100 N ILE A 19 SHEET 1 AA2 4 LYS B 47 VAL B 54 0 SHEET 2 AA2 4 ARG B 58 GLY B 65 -1 O ARG B 58 N VAL B 54 SHEET 3 AA2 4 ALA B 21 LEU B 27 -1 N ALA B 21 O GLY B 65 SHEET 4 AA2 4 LEU B 88 ILE B 94 -1 O ILE B 89 N GLU B 26 SHEET 1 AA3 4 GLU B 146 ARG B 151 0 SHEET 2 AA3 4 ALA B 160 GLY B 166 -1 O SER B 161 N ARG B 151 SHEET 3 AA3 4 ALA B 120 VAL B 126 -1 N ALA B 120 O GLY B 166 SHEET 4 AA3 4 LEU B 186 ILE B 192 -1 O LEU B 187 N GLU B 125 CISPEP 1 GLU B 55 PRO B 56 0 -9.06 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