HEADER HYDROLASE 05-MAR-26 11NY TITLE CRYSTAL STRUCTURE OF VIRAL OTU DOMAIN PROTEASE FROM TACHENG TICK VIRUS TITLE 2 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-DIRECTED RNA POLYMERASE L; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LARGE STRUCTURAL PROTEIN,REPLICASE,TRANSCRIPTASE; COMPND 5 EC: 2.7.7.48; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORTHONAIROVIRUS TACHENGENSE; SOURCE 3 ORGANISM_TAXID: 3052536; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: T7 KEYWDS TTV1, L-PROTEIN, VIRAL OTU, DEUBIQUITINASE, DEISGLYASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.S.GONZALEZ,S.D.PEGAN REVDAT 1 05-AUG-26 11NY 0 JRNL AUTH D.S.GONZALEZ,A.JALF,V.MORESCO,J.GARCIA,L.JAROSZEWSKI, JRNL AUTH 2 D.MATTA,J.NGUYEN,B.TORRES,E.BERGERON,A.GODZIK,S.D.PEGAN JRNL TITL INSIGHTS INTO THE STRUCTURE AND FUNCTION OF THE OTU PROTEASE JRNL TITL 2 VIRULENCE FACTORS FROM EMERGING HUMAN NAIROVIRUSES. JRNL REF ACS INFECT DIS. 2026 JRNL REFN ESSN 2373-8227 JRNL PMID 42439547 JRNL DOI 10.1021/ACSINFECDIS.6C00320 REMARK 2 REMARK 2 RESOLUTION. 1.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 2.0_5936 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 34708 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1736 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 29.6300 - 3.1300 1.00 2981 177 0.1498 0.1852 REMARK 3 2 3.1300 - 2.4800 1.00 2892 137 0.1711 0.2018 REMARK 3 3 2.4800 - 2.1700 1.00 2850 138 0.1534 0.1962 REMARK 3 4 2.1700 - 1.9700 1.00 2823 154 0.1347 0.1717 REMARK 3 5 1.9700 - 1.8300 1.00 2779 172 0.1415 0.2146 REMARK 3 6 1.8300 - 1.7200 1.00 2805 146 0.1444 0.1799 REMARK 3 7 1.7200 - 1.6300 1.00 2795 162 0.1432 0.1870 REMARK 3 8 1.6300 - 1.5600 1.00 2801 123 0.1600 0.2089 REMARK 3 9 1.5600 - 1.5000 1.00 2795 153 0.1867 0.2541 REMARK 3 10 1.5000 - 1.4500 0.99 2732 141 0.2444 0.2888 REMARK 3 11 1.4500 - 1.4100 0.93 2585 120 0.2896 0.2888 REMARK 3 12 1.4100 - 1.3700 0.76 2134 113 0.3300 0.3974 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) : 21.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.012 1320 REMARK 3 ANGLE : 1.237 1810 REMARK 3 CHIRALITY : 0.109 202 REMARK 3 PLANARITY : 0.010 234 REMARK 3 DIHEDRAL : 13.596 476 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 11NY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAR-26. REMARK 100 THE DEPOSITION ID IS D_1000305729. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9201 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35646 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.366 REMARK 200 RESOLUTION RANGE LOW (A) : 29.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.7780 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M LITHIUM SULLFATE, 21 % PEG 3350, REMARK 280 0.1M BIS-TRIS PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 273K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 23.88350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.62800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.03500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.62800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.88350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.03500 REMARK 290 SMTRY3 4 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 REMARK 465 ARG A 4 REMARK 465 ARG A 5 REMARK 465 ARG A 6 REMARK 465 SER A 7 REMARK 465 LYS A 164 REMARK 465 GLU A 165 REMARK 465 GLY A 166 REMARK 465 THR A 167 REMARK 465 SER A 168 REMARK 465 GLY A 169 REMARK 465 SER A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 REMARK 465 HIS A 176 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 CYS A 48 -3.90 81.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 530 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 531 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 532 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH A 533 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A 534 DISTANCE = 7.76 ANGSTROMS REMARK 525 HOH A 535 DISTANCE = 9.59 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 11NQ RELATED DB: PDB REMARK 900 RELATED ID: 11NS RELATED DB: PDB DBREF1 11NY A 1 167 UNP A0A0B5KXW6_9VIRU DBREF2 11NY A A0A0B5KXW6 1 167 SEQADV 11NY SER A 168 UNP A0A0B5KXW EXPRESSION TAG SEQADV 11NY GLY A 169 UNP A0A0B5KXW EXPRESSION TAG SEQADV 11NY SER A 170 UNP A0A0B5KXW EXPRESSION TAG SEQADV 11NY HIS A 171 UNP A0A0B5KXW EXPRESSION TAG SEQADV 11NY HIS A 172 UNP A0A0B5KXW EXPRESSION TAG SEQADV 11NY HIS A 173 UNP A0A0B5KXW EXPRESSION TAG SEQADV 11NY HIS A 174 UNP A0A0B5KXW EXPRESSION TAG SEQADV 11NY HIS A 175 UNP A0A0B5KXW EXPRESSION TAG SEQADV 11NY HIS A 176 UNP A0A0B5KXW EXPRESSION TAG SEQRES 1 A 176 MET ALA GLY ARG ARG ARG SER SER ASN LEU SER GLU SER SEQRES 2 A 176 LEU ILE SER ASP CYS ASP ASN LEU GLY ASN PHE TYR ARG SEQRES 3 A 176 GLY PRO ILE VAL LEU ASP ILE ASN LYS GLU PHE THR ILE SEQRES 4 A 176 GLU ASP VAL PRO GLY ASP GLY ASP CYS PHE PHE HIS CYS SEQRES 5 A 176 LEU ALA LYS GLN LEU PRO GLU VAL SER VAL SER ARG LEU SEQRES 6 A 176 LYS GLY ILE ILE THR SER TYR ALA LEU ARG ASN TRP ASP SEQRES 7 A 176 THR LEU THR GLU ALA PRO ARG PHE TYR SER ASP PRO LYS SEQRES 8 A 176 ASP TYR GLU ARG GLU LEU ASN ARG ALA GLY TYR TRP GLY SEQRES 9 A 176 GLY THR THR GLU ALA GLU ILE ILE ASN HIS SER PHE GLY SEQRES 10 A 176 VAL PRO VAL VAL ILE TRP THR THR GLU ASP LYS LYS LEU SEQRES 11 A 176 THR SER ALA VAL GLN VAL TRP THR ARG LYS HIS GLY ASN SEQRES 12 A 176 LEU PRO GLU LEU HIS LEU LEU HIS THR GLY THR HIS PHE SEQRES 13 A 176 MET CYS LEU ALA PRO ILE VAL LYS GLU GLY THR SER GLY SEQRES 14 A 176 SER HIS HIS HIS HIS HIS HIS HET SO4 A 201 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *235(H2 O) HELIX 1 AA1 LEU A 10 ILE A 15 1 6 HELIX 2 AA2 SER A 16 CYS A 18 5 3 HELIX 3 AA3 ASP A 32 GLU A 36 1 5 HELIX 4 AA4 CYS A 48 LEU A 57 1 10 HELIX 5 AA5 SER A 61 TRP A 77 1 17 HELIX 6 AA6 ASP A 78 LEU A 80 5 3 HELIX 7 AA7 THR A 81 TYR A 87 1 7 HELIX 8 AA8 ASP A 89 ASN A 98 1 10 HELIX 9 AA9 GLY A 105 GLY A 117 1 13 SHEET 1 AA1 7 ASP A 19 ASN A 20 0 SHEET 2 AA1 7 TYR A 25 PRO A 28 -1 O ARG A 26 N ASP A 19 SHEET 3 AA1 7 THR A 131 TRP A 137 -1 O VAL A 136 N TYR A 25 SHEET 4 AA1 7 VAL A 120 THR A 125 -1 N THR A 124 O ALA A 133 SHEET 5 AA1 7 LEU A 147 THR A 152 1 O HIS A 151 N TRP A 123 SHEET 6 AA1 7 HIS A 155 PRO A 161 -1 O MET A 157 N LEU A 150 SHEET 7 AA1 7 PHE A 37 GLU A 40 -1 N THR A 38 O ALA A 160 CRYST1 47.767 58.070 59.256 90.00 90.00 90.00 P 21 21 21 4 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 0.020935 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017221 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016876 0.00000 CONECT 1279 1280 1281 1282 1283 CONECT 1280 1279 CONECT 1281 1279 CONECT 1282 1279 CONECT 1283 1279 MASTER 266 0 1 9 7 0 0 6 1483 1 5 14 END