HEADER IMMUNE SYSTEM 01-FEB-23 8CDT TITLE CRYSTAL STRUCTURE OF THE XNUP93-NB2T VHH ANTIBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: 15-NUP93 TRACKING 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 VHH ANTIBODY, NANOBODY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.GUTTLER,M.S.COLOM,D.GORLICH REVDAT 4 23-OCT-24 8CDT 1 REMARK REVDAT 3 12-JUN-24 8CDT 1 JRNL REVDAT 2 22-MAY-24 8CDT 1 JRNL REVDAT 1 21-FEB-24 8CDT 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. 1.41 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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 34216 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1674 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 32.7200 - 3.2300 1.00 2830 143 0.1528 0.1729 REMARK 3 2 3.2300 - 2.5600 1.00 2730 143 0.1682 0.2159 REMARK 3 3 2.5600 - 2.2400 1.00 2740 143 0.1614 0.2310 REMARK 3 4 2.2400 - 2.0300 1.00 2713 140 0.1463 0.1619 REMARK 3 5 2.0300 - 1.8900 1.00 2704 137 0.1431 0.1540 REMARK 3 6 1.8900 - 1.7800 1.00 2696 140 0.1422 0.1705 REMARK 3 7 1.7800 - 1.6900 1.00 2689 146 0.1470 0.1796 REMARK 3 8 1.6900 - 1.6100 1.00 2689 139 0.1487 0.1783 REMARK 3 9 1.6100 - 1.5500 1.00 2711 139 0.1500 0.1801 REMARK 3 10 1.5500 - 1.5000 1.00 2692 135 0.1554 0.1830 REMARK 3 11 1.5000 - 1.4500 1.00 2655 136 0.2210 0.2219 REMARK 3 12 1.4500 - 1.4100 1.00 2693 133 0.3566 0.3870 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) : 0.168 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.771 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.24 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 : 0.019 996 REMARK 3 ANGLE : 1.535 1353 REMARK 3 CHIRALITY : 0.113 147 REMARK 3 PLANARITY : 0.010 177 REMARK 3 DIHEDRAL : 12.435 384 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 8CDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128340. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.5 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 EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JAN 31, 2020 BUILT=20200417 REMARK 200 DATA SCALING SOFTWARE : XDS JAN 31, 2020 BUILT=20200417 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79377 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 43.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 19.80 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.81800 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 (%): 64.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CAPS (PH 10.5), 1.2 M SODIUM REMARK 280 PHOSPHATE, 0.8 M POTASSIUM PHOSPHATE, 0.2 M LITHIUM SULFATE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 15.35350 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 15.35350 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 15.35350 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 REMARK 465 SER A 123 REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 GOL A 202 DBREF 8CDT A 1 123 PDB 8CDT 8CDT 1 123 SEQRES 1 A 123 GLY ASP VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL SEQRES 2 A 123 GLN PRO GLY GLY SER LEU ARG LEU SER CYS VAL ALA SER SEQRES 3 A 123 GLY PHE THR PHE SER ARG VAL GLY MET GLY TRP VAL ARG SEQRES 4 A 123 GLN ALA PRO GLY LYS GLY LEU GLU TRP VAL SER ASP ILE SEQRES 5 A 123 ASN ALA SER GLY GLY THR GLY TYR ALA ASP SER VAL LYS SEQRES 6 A 123 GLY ARG PHE ALA ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 A 123 LEU TYR LEU GLN MET ASN ARG LEU LYS PRO GLU ASP THR SEQRES 8 A 123 ALA VAL TYR TYR CYS ALA LYS MET MET ASP THR ALA MET SEQRES 9 A 123 ILE GLU ALA GLY ILE ILE LYS PRO ALA GLY GLN GLY THR SEQRES 10 A 123 GLN VAL THR VAL SER SER HET GOL A 201 6 HET GOL A 202 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *125(H2 O) HELIX 1 AA1 ASP A 62 LYS A 65 5 4 HELIX 2 AA2 ASN A 74 LYS A 76 5 3 HELIX 3 AA3 LYS A 87 THR A 91 5 5 HELIX 4 AA4 ASP A 101 ALA A 107 1 7 SHEET 1 AA1 4 GLN A 4 SER A 8 0 SHEET 2 AA1 4 LEU A 19 SER A 26 -1 O SER A 22 N SER A 8 SHEET 3 AA1 4 THR A 78 MET A 83 -1 O MET A 83 N LEU A 19 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N ALA A 69 O GLN A 82 SHEET 1 AA2 6 GLY A 11 VAL A 13 0 SHEET 2 AA2 6 THR A 117 VAL A 121 1 O THR A 120 N GLY A 11 SHEET 3 AA2 6 ALA A 92 LYS A 98 -1 N TYR A 94 O THR A 117 SHEET 4 AA2 6 MET A 35 GLN A 40 -1 N VAL A 38 O TYR A 95 SHEET 5 AA2 6 LEU A 46 ILE A 52 -1 O ILE A 52 N MET A 35 SHEET 6 AA2 6 THR A 58 TYR A 60 -1 O GLY A 59 N ASP A 51 SSBOND 1 CYS A 23 CYS A 96 1555 1555 2.41 CRYST1 99.968 99.968 30.707 90.00 90.00 120.00 P 63 6 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 0.010003 0.005775 0.000000 0.00000 SCALE2 0.000000 0.011551 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032566 0.00000