HEADER DE NOVO PROTEIN 09-OCT-23 8UI2 TITLE T33-ML28 - DESIGNED TETRAHEDRAL PROTEIN CAGE USING MACHINE LEARNING TITLE 2 ALGORITHMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: T33-ML28-REDESIGNED-TANDEM-BMC-T-FOLD; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: T33-ML28-REDESIGNED-CUTA-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 8UI2 1 JRNL REVDAT 1 06-MAR-24 8UI2 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. 2.73 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) : 2.730 REMARK 3 NUMBER OF PARTICLES : 857483 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 8UI2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000278171. 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-ML28 DESIGNED TETRAHEDRAL REMARK 245 PROTEIN CAGE USING MACHINE REMARK 245 LEARNING REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL 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) : 2500.00 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: 24-MER 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 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 -0.500005 -0.866033 0.000000 255.05884 REMARK 350 BIOMT2 2 0.866033 -0.500004 0.000000 68.34210 REMARK 350 BIOMT3 2 0.000000 0.000000 0.999999 0.00010 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 3 -0.500005 0.866033 0.000000 68.34214 REMARK 350 BIOMT2 3 -0.866033 -0.500004 0.000000 255.05881 REMARK 350 BIOMT3 3 0.000000 0.000000 0.999999 0.00010 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 4 0.000000 0.577355 -0.816500 133.57979 REMARK 350 BIOMT2 4 0.577355 -0.666672 -0.471406 168.24596 REMARK 350 BIOMT3 4 -0.816500 -0.471406 -0.333333 282.56959 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 5 0.500005 -0.288678 -0.816500 173.03765 REMARK 350 BIOMT2 5 -0.866033 -0.166668 -0.471406 269.94277 REMARK 350 BIOMT3 5 0.000000 0.942813 -0.333333 42.09811 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 6 -0.500005 -0.288678 -0.816500 280.83863 REMARK 350 BIOMT2 6 0.288678 0.833340 -0.471406 37.66406 REMARK 350 BIOMT3 6 0.816500 -0.471406 -0.333333 106.53221 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 7 0.000000 -0.577355 0.816500 82.02021 REMARK 350 BIOMT2 7 -0.577355 -0.666672 -0.471406 292.72377 REMARK 350 BIOMT3 7 0.816500 -0.471406 -0.333333 106.53221 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 8 -0.500005 0.288678 0.816500 42.56235 REMARK 350 BIOMT2 8 -0.288678 0.833340 -0.471406 99.90296 REMARK 350 BIOMT3 8 -0.816500 -0.471406 -0.333333 282.56959 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 9 0.500005 0.288678 0.816500 -65.23863 REMARK 350 BIOMT2 9 0.866033 -0.166668 -0.471406 83.22606 REMARK 350 BIOMT3 9 0.000000 0.942813 -0.333333 42.09811 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 10 -1.000009 0.000000 0.000000 215.60098 REMARK 350 BIOMT2 10 0.000000 0.333336 0.942813 -29.76883 REMARK 350 BIOMT3 10 0.000000 0.942813 -0.333333 42.09811 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 11 0.500005 0.866033 0.000000 -39.45884 REMARK 350 BIOMT2 11 0.288678 -0.166668 0.942813 -6.98783 REMARK 350 BIOMT3 11 0.816500 -0.471406 -0.333333 106.53221 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 12 0.500005 -0.866033 0.000000 147.25786 REMARK 350 BIOMT2 12 -0.288678 -0.166668 0.942813 55.25108 REMARK 350 BIOMT3 12 -0.816500 -0.471406 -0.333333 282.56959 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 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 GLY A 8 REMARK 465 GLY A 9 REMARK 465 SER A 10 REMARK 465 HIS A 11 REMARK 465 HIS A 12 REMARK 465 TRP A 13 REMARK 465 GLY A 14 REMARK 465 GLY A 15 REMARK 465 ASP A 16 REMARK 465 PRO A 17 REMARK 465 MET B 1 REMARK 465 SER B 105 REMARK 465 ALA B 106 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 PRO A 56 46.44 -98.11 REMARK 500 GLU A 107 -4.94 72.80 REMARK 500 VAL A 142 -61.18 -90.10 REMARK 500 GLU B 46 118.31 -161.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-42286 RELATED DB: EMDB REMARK 900 T33-ML28 - DESIGNED TETRAHEDRAL PROTEIN CAGE USING MACHINE LEARNING REMARK 900 ALGORITHMS DBREF 8UI2 A 1 205 PDB 8UI2 8UI2 1 205 DBREF 8UI2 B 1 106 PDB 8UI2 8UI2 1 106 SEQRES 1 A 205 MET HIS HIS HIS HIS HIS HIS GLY GLY SER HIS HIS TRP SEQRES 2 A 205 GLY GLY ASP PRO ALA ARG PRO ALA LEU GLY VAL LEU GLU SEQRES 3 A 205 LEU LYS SER TYR ALA LEU GLY VAL ALA VAL ALA ASP ALA SEQRES 4 A 205 ALA LEU ARG ALA ALA PRO VAL GLU LEU LEU LYS CYS GLU SEQRES 5 A 205 PRO VAL GLU PRO GLY LYS ALA LEU ILE MET ILE ARG GLY SEQRES 6 A 205 GLU PRO GLU ALA VAL ALA ARG ALA MET ALA ALA ALA LEU SEQRES 7 A 205 GLU THR ALA LYS ALA GLY SER GLY ASN LEU ILE ASP HIS SEQRES 8 A 205 ALA PHE ILE GLY ARG ILE HIS PRO ALA LEU LEU PRO PHE SEQRES 9 A 205 LEU LEU GLU GLU THR ALA ALA PRO PRO ILE GLU ASP PRO SEQRES 10 A 205 ASP GLU ALA VAL LEU VAL VAL GLU THR LYS THR VAL ALA SEQRES 11 A 205 ALA ALA ILE GLU ALA ALA ASP ALA ALA LEU ASP VAL ALA SEQRES 12 A 205 PRO VAL ARG LEU LEU ARG MET ARG LEU SER GLU HIS ILE SEQRES 13 A 205 GLY GLY LYS ALA TYR PHE VAL LEU ALA GLY ASP GLU GLU SEQRES 14 A 205 ALA VAL ARG LYS ALA ALA ARG ALA VAL ARG ALA VAL ALA SEQRES 15 A 205 GLY GLU LYS LEU ILE ASP LEU ARG ILE ILE PRO ARG PRO SEQRES 16 A 205 HIS GLU ALA LEU ARG GLY ARG LEU PHE PHE SEQRES 1 B 106 MET PRO ILE ALA LEU THR VAL VAL PRO PRO GLU GLU ALA SEQRES 2 B 106 GLU PRO LEU ALA ARG GLU LEU VAL GLU ALA GLY LEU ALA SEQRES 3 B 106 ALA GLU VAL LEU LEU VAL PRO VAL ARG ARG ILE TYR ARG SEQRES 4 B 106 GLU LYS GLY LYS VAL ARG GLU GLU GLU VAL THR LEU LEU SEQRES 5 B 106 LEU ILE LEU VAL SER ARG GLU GLY VAL PRO ALA LEU ARG SEQRES 6 B 106 ALA TRP ILE GLU ALA ARG HIS PRO ASP ASP ILE PRO LEU SEQRES 7 B 106 PHE ILE VAL LEU ALA VAL ASP GLU GLU ALA SER ASN LYS SEQRES 8 B 106 ARG TYR LEU GLY TYR ILE ALA ALA GLU THR HIS LEU TYR SEQRES 9 B 106 SER ALA HELIX 1 AA1 SER A 29 ALA A 44 1 16 HELIX 2 AA2 GLU A 66 LYS A 82 1 17 HELIX 3 AA3 LEU A 101 LEU A 106 1 6 HELIX 4 AA4 THR A 128 ALA A 143 1 16 HELIX 5 AA5 ASP A 167 GLY A 183 1 17 HELIX 6 AA6 HIS A 196 PHE A 204 1 9 HELIX 7 AA7 PRO B 9 GLU B 11 5 3 HELIX 8 AA8 GLU B 12 ALA B 23 1 12 HELIX 9 AA9 GLY B 60 ALA B 70 1 11 HELIX 10 AB1 ASN B 90 THR B 101 1 12 SHEET 1 AA1 4 GLU A 47 VAL A 54 0 SHEET 2 AA1 4 LYS A 58 GLY A 65 -1 O MET A 62 N LEU A 49 SHEET 3 AA1 4 ALA A 21 LEU A 27 -1 N LEU A 25 O ILE A 61 SHEET 4 AA1 4 LEU A 88 ILE A 94 -1 O ILE A 89 N GLU A 26 SHEET 1 AA2 4 ARG A 146 LEU A 152 0 SHEET 2 AA2 4 ALA A 160 GLY A 166 -1 O TYR A 161 N ARG A 151 SHEET 3 AA2 4 ALA A 120 THR A 126 -1 N ALA A 120 O GLY A 166 SHEET 4 AA2 4 LEU A 186 ILE A 192 -1 O ILE A 187 N GLU A 125 SHEET 1 AA3 4 GLU B 28 GLU B 40 0 SHEET 2 AA3 4 LYS B 43 LEU B 55 -1 O LEU B 51 N VAL B 32 SHEET 3 AA3 4 ILE B 3 VAL B 8 -1 N THR B 6 O LEU B 52 SHEET 4 AA3 4 ILE B 80 LEU B 82 -1 O LEU B 82 N ILE B 3 CISPEP 1 GLU A 55 PRO A 56 0 -1.95 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