HEADER IMMUNE SYSTEM 01-FEB-23 8CDS TITLE CRYSTAL STRUCTURE OF THE XHNUP93-NB4I VHH ANTIBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5-NUP93 INHIBITORY VHH ANTIBODY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 3 ORGANISM_COMMON: ALPACA; SOURCE 4 ORGANISM_TAXID: 30538; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITORY VHH ANTIBODY, NANOBODY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.GUTTLER,M.S.COLOM,D.GORLICH REVDAT 3 12-JUN-24 8CDS 1 JRNL REVDAT 2 22-MAY-24 8CDS 1 JRNL REVDAT 1 21-FEB-24 8CDS 0 JRNL AUTH M.SOLA COLOM,Z.FU,P.GUNKEL,T.GUTTLER,S.TRAKHANOV, JRNL AUTH 2 V.SRINIVASAN,K.GREGOR,T.PLEINER,D.GORLICH JRNL TITL A CHECKPOINT FUNCTION FOR NUP98 IN NUCLEAR PORE FORMATION JRNL TITL 2 SUGGESTED BY NOVEL INHIBITORY NANOBODIES. JRNL REF EMBO J. V. 43 2198 2024 JRNL REFN ESSN 1460-2075 JRNL PMID 38649536 JRNL DOI 10.1038/S44318-024-00081-W REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14-3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 14720 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.760 REMARK 3 FREE R VALUE TEST SET COUNT : 1436 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 30.7100 - 3.3000 0.99 1406 145 0.1190 0.1241 REMARK 3 2 3.3000 - 2.6200 0.98 1348 158 0.1443 0.1863 REMARK 3 3 2.6200 - 2.2900 0.98 1342 150 0.1469 0.2002 REMARK 3 4 2.2900 - 2.0800 0.97 1326 147 0.1332 0.1988 REMARK 3 5 2.0800 - 1.9300 0.97 1338 132 0.1254 0.1861 REMARK 3 6 1.9300 - 1.8100 0.96 1322 142 0.1230 0.1923 REMARK 3 7 1.8100 - 1.7200 0.95 1303 144 0.1323 0.2114 REMARK 3 8 1.7200 - 1.6500 0.95 1312 135 0.1533 0.2185 REMARK 3 9 1.6500 - 1.5800 0.95 1274 143 0.1482 0.2279 REMARK 3 10 1.5800 - 1.5300 0.94 1313 140 0.1749 0.2541 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.176 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.05 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 : 0.006 1058 REMARK 3 ANGLE : 0.804 1442 REMARK 3 CHIRALITY : 0.057 157 REMARK 3 PLANARITY : 0.004 187 REMARK 3 DIHEDRAL : 9.199 640 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 8CDS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128325. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 31, 2020 BUILT=20200417 REMARK 200 DATA SCALING SOFTWARE : XSCALE JAN 31, 2020 REMARK 200 BUILT=20200417 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40137 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 30.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 6.219 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 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) : 2.48900 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 (%): 32.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M IMIDAZOLE PH 8, 30% (W/V) PEG REMARK 280 8,000, 0.2 M NACL, PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 21.05250 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 GLY A 1 DBREF 8CDS A 1 127 PDB 8CDS 8CDS 1 127 SEQRES 1 A 127 GLY SER GLN VAL GLN LEU VAL GLU SER GLY GLY GLY VAL SEQRES 2 A 127 VAL GLN THR GLY ASP SER LEU MET LEU SER CYS THR VAL SEQRES 3 A 127 SER GLY HIS THR ILE ASP ASN TRP ALA MET GLY TRP PHE SEQRES 4 A 127 ARG GLN THR PRO ARG LYS GLN ARG GLU PHE VAL ALA ALA SEQRES 5 A 127 ILE ASP LYS ARG GLY THR GLY ALA ILE TYR GLY ASN SER SEQRES 6 A 127 VAL LYS GLY ARG PHE THR VAL SER ARG ASP ASN ALA LYS SEQRES 7 A 127 ASN MET VAL TYR LEU ARG MET ASN SER LEU LYS PRO GLU SEQRES 8 A 127 ASP THR ALA VAL TYR PHE CYS ALA VAL ASP GLN LEU ASN SEQRES 9 A 127 ALA GLY LEU GLY ASP VAL SER TYR ASP TYR ASP TYR TRP SEQRES 10 A 127 GLY GLN GLY THR GLN VAL THR VAL SER SER HET EDO A 200 4 HET PEG A 201 7 HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 PEG C4 H10 O3 FORMUL 4 HOH *144(H2 O) HELIX 1 AA1 ASN A 64 LYS A 67 5 4 HELIX 2 AA2 LYS A 89 THR A 93 5 5 HELIX 3 AA3 VAL A 110 TYR A 114 5 5 SHEET 1 AA1 4 GLN A 5 SER A 9 0 SHEET 2 AA1 4 LEU A 20 SER A 27 -1 O SER A 23 N SER A 9 SHEET 3 AA1 4 MET A 80 MET A 85 -1 O MET A 85 N LEU A 20 SHEET 4 AA1 4 PHE A 70 ASP A 75 -1 N SER A 73 O TYR A 82 SHEET 1 AA2 6 VAL A 13 GLN A 15 0 SHEET 2 AA2 6 THR A 121 SER A 126 1 O SER A 126 N VAL A 14 SHEET 3 AA2 6 ALA A 94 ASP A 101 -1 N TYR A 96 O THR A 121 SHEET 4 AA2 6 ALA A 35 GLN A 41 -1 N PHE A 39 O PHE A 97 SHEET 5 AA2 6 GLU A 48 ILE A 53 -1 O ALA A 51 N TRP A 38 SHEET 6 AA2 6 ALA A 60 TYR A 62 -1 O ILE A 61 N ALA A 52 CRYST1 26.877 42.105 44.946 90.00 93.06 90.00 P 1 21 1 2 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 0.037207 0.000000 0.001986 0.00000 SCALE2 0.000000 0.023750 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022281 0.00000