HEADER IMMUNE SYSTEM 05-JAN-23 8FQ7 TITLE NANOBODY WITH WIW INSERTED IN CDR3 LOOP TO INHIBIT GROWTH OF TITLE 2 ALZHEIMER'S TAU FIBRILS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY WITH WIW INSERT IN CDR3 LOOP TO TARGET TAU COMPND 3 FIBRILS; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMELUS DROMEDARIUS; SOURCE 3 ORGANISM_TAXID: 9838; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: WK6; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PMES4 KEYWDS ANTI-TAU ANTIBODY, NANOBODY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.ABSKHARON,M.R.SAWAYA,D.C.CASCIO,D.S.EISENBERG REVDAT 2 18-OCT-23 8FQ7 1 JRNL REVDAT 1 04-OCT-23 8FQ7 0 JRNL AUTH R.ABSKHARON,H.PAN,M.R.SAWAYA,P.M.SEIDLER,E.J.OLIVARES, JRNL AUTH 2 Y.CHEN,K.A.MURRAY,J.ZHANG,C.LANTZ,M.BENTZEL,D.R.BOYER, JRNL AUTH 3 D.CASCIO,B.A.NGUYEN,K.HOU,X.CHENG,E.PARDON,C.K.WILLIAMS, JRNL AUTH 4 A.L.NANA,H.V.VINTERS,S.SPINA,L.T.GRINBERG,W.W.SEELEY, JRNL AUTH 5 J.STEYAERT,C.G.GLABE,R.R.OGORZALEK LOO,J.A.LOO,D.S.EISENBERG JRNL TITL STRUCTURE-BASED DESIGN OF NANOBODIES THAT INHIBIT SEEDING OF JRNL TITL 2 ALZHEIMER'S PATIENT-EXTRACTED TAU FIBRILS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 58120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 37801475 JRNL DOI 10.1073/PNAS.2300258120 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 22605 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2268 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 55.3600 - 3.5300 0.94 1278 140 0.1897 0.1846 REMARK 3 2 3.5300 - 2.8000 0.99 1279 143 0.1875 0.2136 REMARK 3 3 2.8000 - 2.4500 0.96 1252 136 0.1892 0.2211 REMARK 3 4 2.4500 - 2.2200 0.99 1298 144 0.1804 0.1973 REMARK 3 5 2.2200 - 2.0600 0.99 1281 142 0.1696 0.2128 REMARK 3 6 2.0600 - 1.9400 0.99 1266 142 0.1814 0.2111 REMARK 3 7 1.9400 - 1.8400 0.98 1260 143 0.1758 0.2260 REMARK 3 8 1.8400 - 1.7600 0.99 1280 140 0.1849 0.1884 REMARK 3 9 1.7600 - 1.7000 0.99 1269 147 0.1892 0.2133 REMARK 3 10 1.7000 - 1.6400 0.99 1272 153 0.2136 0.2283 REMARK 3 11 1.6400 - 1.5900 1.00 1269 130 0.1946 0.2247 REMARK 3 12 1.5900 - 1.5400 0.99 1262 148 0.2004 0.2428 REMARK 3 13 1.5400 - 1.5000 0.99 1288 133 0.1951 0.2523 REMARK 3 14 1.5000 - 1.4600 0.99 1257 151 0.2214 0.2514 REMARK 3 15 1.4600 - 1.4300 0.99 1287 125 0.2378 0.2687 REMARK 3 16 1.4300 - 1.4000 0.98 1239 151 0.2647 0.2953 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.90 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 : 0.005 979 REMARK 3 ANGLE : 0.776 1326 REMARK 3 CHIRALITY : 0.078 135 REMARK 3 PLANARITY : 0.005 175 REMARK 3 DIHEDRAL : 11.267 348 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -19.1313 -2.2316 10.8733 REMARK 3 T TENSOR REMARK 3 T11: 0.0913 T22: 0.1075 REMARK 3 T33: 0.1169 T12: -0.0007 REMARK 3 T13: -0.0075 T23: -0.0256 REMARK 3 L TENSOR REMARK 3 L11: 1.8872 L22: 2.4714 REMARK 3 L33: 1.3647 L12: -0.3122 REMARK 3 L13: -0.3105 L23: 0.1053 REMARK 3 S TENSOR REMARK 3 S11: 0.0001 S12: -0.0375 S13: 0.0271 REMARK 3 S21: 0.0511 S22: -0.0007 S23: 0.0155 REMARK 3 S31: 0.0023 S32: -0.0372 S33: -0.0217 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 8FQ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000271186. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20190315 REMARK 200 DATA SCALING SOFTWARE : XSCALE 20190315 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22608 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 55.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15M AMMONIUM SULFATE, 0.1 M MES PH REMARK 280 5.5, 25% PEG 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 39.14500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.14500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.11000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.14500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.14500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.11000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 39.14500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 39.14500 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 19.11000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 39.14500 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 39.14500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 19.11000 REMARK 290 REMARK 290 REMARK: NULL 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 ALA A 0 REMARK 465 HIS A 124 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 GLN A 1 CG CD OE1 NE2 REMARK 470 HIS A 120 CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 123 CG ND1 CD2 CE1 NE2 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 TYR A 107 -161.56 53.24 REMARK 500 HIS A 122 78.80 -117.21 REMARK 500 REMARK 500 REMARK: NULL DBREF 8FQ7 A -1 124 PDB 8FQ7 8FQ7 -1 124 SEQRES 1 A 126 MET ALA GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU SEQRES 2 A 126 VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 A 126 SER GLY ARG THR PHE SER SER TYR ASN MET GLY TRP PHE SEQRES 4 A 126 ARG GLN ALA PRO GLY LYS GLY ARG GLU PHE VAL ALA SER SEQRES 5 A 126 ILE THR SER SER GLY ASP LYS SER ASP TYR THR ASP SER SEQRES 6 A 126 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS SEQRES 7 A 126 ASN THR MET TYR LEU GLN MET ASN ASN LEU LYS PRO GLU SEQRES 8 A 126 ASP THR ALA THR TYR TYR CYS ALA ARG GLY GLY GLY SER SEQRES 9 A 126 VAL TRP ILE TRP TYR GLU GLY GLY GLY THR GLN VAL THR SEQRES 10 A 126 VAL SER SER HIS HIS HIS HIS HIS HIS HET GOL A 201 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *109(H2 O) HELIX 1 AA1 THR A 28 TYR A 32 5 5 HELIX 2 AA2 ASP A 62 LYS A 65 5 4 HELIX 3 AA3 ASN A 74 LYS A 76 5 3 HELIX 4 AA4 LYS A 87 THR A 91 5 5 SHEET 1 AA1 4 LEU A 4 SER A 7 0 SHEET 2 AA1 4 LEU A 18 ALA A 24 -1 O ALA A 23 N GLN A 5 SHEET 3 AA1 4 THR A 78 MET A 83 -1 O MET A 83 N LEU A 18 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N ASP A 73 O THR A 78 SHEET 1 AA2 6 LEU A 11 VAL A 12 0 SHEET 2 AA2 6 THR A 112 VAL A 116 1 O THR A 115 N VAL A 12 SHEET 3 AA2 6 ALA A 92 GLY A 99 -1 N TYR A 94 O THR A 112 SHEET 4 AA2 6 MET A 34 GLN A 39 -1 N PHE A 37 O TYR A 95 SHEET 5 AA2 6 ARG A 45 ILE A 51 -1 O ALA A 49 N TRP A 36 SHEET 6 AA2 6 SER A 58 TYR A 60 -1 O ASP A 59 N SER A 50 SHEET 1 AA3 4 LEU A 11 VAL A 12 0 SHEET 2 AA3 4 THR A 112 VAL A 116 1 O THR A 115 N VAL A 12 SHEET 3 AA3 4 ALA A 92 GLY A 99 -1 N TYR A 94 O THR A 112 SHEET 4 AA3 4 TRP A 104 ILE A 105 -1 O ILE A 105 N ARG A 98 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.04 CRYST1 78.290 78.290 38.220 90.00 90.00 90.00 I 4 8 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 0.012773 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012773 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026164 0.00000