HEADER BIOSYNTHETIC PROTEIN 24-MAR-20 6W9Z TITLE DE NOVO DESIGNED RECEPTOR TRANSMEMBRANE DOMAINS ENHANCE CAR-T TITLE 2 CYTOTOXICITY AND ATTENUATE CYTOKINE RELEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED RECEPTOR TRANSMEMBRANE DOMAIN PROMP C2.1; COMPND 3 CHAIN: A, B, C, D, E, F; 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_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PMM-TRPLE FUSION KEYWDS TRANSMEMBRANE DOMAIN, DE NOVO DESIGN, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.J.CALL,M.E.CALL,N.J.CHANDLER,J.V.NGUYEN,R.TRENKER REVDAT 3 18-OCT-23 6W9Z 1 REMARK REVDAT 2 16-JUN-21 6W9Z 1 COMPND REMARK SITE ATOM REVDAT 1 31-MAR-21 6W9Z 0 JRNL AUTH A.ELAZAR,N.J.CHANDLER,A.S.DAVEY,J.Y.WEINSTEIN,J.V.NGUYEN, JRNL AUTH 2 R.TRENKER,M.JENKINS,M.J.CALL,M.E.CALL,S.J.FLEISHMAN JRNL TITL DE NOVO DESIGNED RECEPTOR TRANSMEMBRANE DOMAINS ENHANCE JRNL TITL 2 CAR-T CYTOTOXICITY AND ATTENUATE CYTOKINE RELEASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 6409 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 642 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.7380 - 4.6150 0.99 1261 141 0.2414 0.2559 REMARK 3 2 4.6150 - 3.6639 1.00 1197 133 0.2169 0.2955 REMARK 3 3 3.6639 - 3.2010 1.00 1183 132 0.2046 0.2552 REMARK 3 4 3.2010 - 2.9084 1.00 1156 126 0.2075 0.2865 REMARK 3 5 2.9084 - 2.7000 0.83 970 110 0.1998 0.3046 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6W9Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247879. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95366 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JAN 26, 2018 BUILT=20180319 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6655 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 39.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.07022 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.85540 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.860 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.2 REMARK 200 STARTING MODEL: 5EH6 REMARK 200 REMARK 200 REMARK: RHOMBOID PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 MG/ML PEPTIDE IN LCP 8 V/V 2-METHYL REMARK 280 -2,4-PENTANEDIOL 0.1 M ADA PH 6.7 0.4 M POTASSIUM NITRATE 0.1 M REMARK 280 TRIPOTASSIUM CITRATE, LIPIDIC CUBIC PHASE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.10250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.81850 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.10250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.81850 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 GLU A 69 REMARK 465 GLU B 69 REMARK 465 GLU C 69 REMARK 465 GLU E 69 REMARK 465 GLU F 69 REMARK 465 PRO F 70 REMARK 465 GLU F 71 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OLB B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide LEU B 97 and SCH B REMARK 800 98 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide LEU C 97 and SCH C REMARK 800 98 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide LEU D 97 and SCH D REMARK 800 98 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide LEU E 97 and SCH E REMARK 800 98 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide LEU F 97 and SCH F REMARK 800 98 DBREF 6W9Z A 69 98 PDB 6W9Z 6W9Z 69 98 DBREF 6W9Z B 69 98 PDB 6W9Z 6W9Z 69 98 DBREF 6W9Z C 69 98 PDB 6W9Z 6W9Z 69 98 DBREF 6W9Z D 69 98 PDB 6W9Z 6W9Z 69 98 DBREF 6W9Z E 69 98 PDB 6W9Z 6W9Z 69 98 DBREF 6W9Z F 69 98 PDB 6W9Z 6W9Z 69 98 SEQRES 1 A 30 GLU PRO GLU LEU THR VAL ALA LEU ILE LEU GLY ILE PHE SEQRES 2 A 30 LEU GLY THR PHE ILE ALA PHE TRP VAL VAL TYR LEU LEU SEQRES 3 A 30 ARG ARG LEU SCH SEQRES 1 B 30 GLU PRO GLU LEU THR VAL ALA LEU ILE LEU GLY ILE PHE SEQRES 2 B 30 LEU GLY THR PHE ILE ALA PHE TRP VAL VAL TYR LEU LEU SEQRES 3 B 30 ARG ARG LEU SCH SEQRES 1 C 30 GLU PRO GLU LEU THR VAL ALA LEU ILE LEU GLY ILE PHE SEQRES 2 C 30 LEU GLY THR PHE ILE ALA PHE TRP VAL VAL TYR LEU LEU SEQRES 3 C 30 ARG ARG LEU SCH SEQRES 1 D 30 GLU PRO GLU LEU THR VAL ALA LEU ILE LEU GLY ILE PHE SEQRES 2 D 30 LEU GLY THR PHE ILE ALA PHE TRP VAL VAL TYR LEU LEU SEQRES 3 D 30 ARG ARG LEU SCH SEQRES 1 E 30 GLU PRO GLU LEU THR VAL ALA LEU ILE LEU GLY ILE PHE SEQRES 2 E 30 LEU GLY THR PHE ILE ALA PHE TRP VAL VAL TYR LEU LEU SEQRES 3 E 30 ARG ARG LEU SCH SEQRES 1 F 30 GLU PRO GLU LEU THR VAL ALA LEU ILE LEU GLY ILE PHE SEQRES 2 F 30 LEU GLY THR PHE ILE ALA PHE TRP VAL VAL TYR LEU LEU SEQRES 3 F 30 ARG ARG LEU SCH HET SCH A 98 9 HET SCH B 98 9 HET SCH C 98 9 HET SCH D 98 9 HET SCH E 98 9 HET SCH F 98 9 HET OLB B 101 25 HET OLB D 101 25 HETNAM SCH S-METHYL-THIO-CYSTEINE HETNAM OLB (2S)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE FORMUL 1 SCH 6(C4 H9 N O2 S2) FORMUL 7 OLB 2(C21 H40 O4) FORMUL 9 HOH *2(H2 O) HELIX 1 AA1 PRO A 70 SCH A 98 1 29 HELIX 2 AA2 GLU B 71 SCH B 98 1 28 HELIX 3 AA3 GLU C 71 LEU C 97 1 27 HELIX 4 AA4 PRO D 70 SCH D 98 1 29 HELIX 5 AA5 GLU E 71 SCH E 98 1 28 HELIX 6 AA6 THR F 73 SCH F 98 1 26 LINK C LEU A 97 N SCH A 98 1555 1555 1.33 LINK C LEU B 97 N SCH B 98 1555 1555 1.33 LINK C LEU C 97 N SCH C 98 1555 1555 1.33 LINK C LEU D 97 N SCH D 98 1555 1555 1.33 LINK C LEU E 97 N SCH E 98 1555 1555 1.33 LINK C LEU F 97 N SCH F 98 1555 1555 1.33 SITE 1 AC1 10 LEU A 72 LEU A 76 PHE B 88 TRP B 89 SITE 2 AC1 10 TYR B 92 LEU C 72 THR C 73 TRP D 89 SITE 3 AC1 10 TYR D 92 LEU F 97 SITE 1 AC2 9 LEU B 93 LEU B 94 ARG B 95 ARG B 96 SITE 2 AC2 9 HOH B 201 PHE C 88 TYR C 92 ARG C 95 SITE 3 AC2 9 ARG D 95 SITE 1 AC3 7 LEU C 93 LEU C 94 ARG C 96 ARG E 95 SITE 2 AC3 7 PHE F 88 VAL F 91 TYR F 92 SITE 1 AC4 9 PHE A 88 VAL A 91 TYR A 92 ARG A 95 SITE 2 AC4 9 LEU D 93 LEU D 94 ARG D 95 ARG D 96 SITE 3 AC4 9 LEU F 94 SITE 1 AC5 7 LEU A 72 ARG C 95 PHE D 88 ARG D 95 SITE 2 AC5 7 LEU E 93 LEU E 94 ARG E 96 SITE 1 AC6 8 VAL B 91 ARG B 95 OLB B 101 LEU C 72 SITE 2 AC6 8 LEU F 93 LEU F 94 ARG F 95 ARG F 96 CRYST1 44.100 56.205 91.637 90.00 90.00 90.00 P 2 21 21 24 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 0.022676 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017792 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010913 0.00000