HEADER NUCLEAR PROTEIN 09-JUN-25 9VEA TITLE THE MIDN CATCH-IRF4 (A8I) FUSION PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MIDNOLIN,INTERFERON REGULATORY FACTOR 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MIDBRAIN NUCLEOLAR PROTEIN,IRF-4,LYMPHOCYTE-SPECIFIC COMPND 5 INTERFERON REGULATORY FACTOR,LSIRF,MULTIPLE MYELOMA ONCOGENE 1,NF- COMPND 6 EM5; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: MIDNOLIN; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: MIDBRAIN NUCLEOLAR PROTEIN; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MIDN, IRF4, MUM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI (STRAIN B / BL21-DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: MIDN; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI (STRAIN B / BL21-DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MIDNOLIN, IRF4, PROTEASOME, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.DING,Z.CHEN,Y.ZHONG REVDAT 1 04-FEB-26 9VEA 0 JRNL AUTH J.DING,Z.CHEN,Y.ZHONG JRNL TITL THE MIDN CATCH-IRF4 (A8I) FUSION PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 3.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 2028 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 101 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 31.7400 - 3.6000 0.97 1927 101 0.2371 0.2718 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) : 0.367 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.306 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 105.0 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 105.4 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 : 0.003 911 REMARK 3 ANGLE : 0.645 1239 REMARK 3 CHIRALITY : 0.042 146 REMARK 3 PLANARITY : 0.004 159 REMARK 3 DIHEDRAL : 14.819 320 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 9VEA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 13-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1300060534. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-25 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2091 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.600 REMARK 200 RESOLUTION RANGE LOW (A) : 31.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.73 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 (%): 52.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM TARTRATE (PH 7.0) AND REMARK 280 12% (W/V) PEG 3,350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 46.52933 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 23.26467 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 34.89700 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 11.63233 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 58.16167 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 46.52933 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 23.26467 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 11.63233 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 34.89700 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 58.16167 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 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 162 REMARK 465 ASN A 163 REMARK 465 GLU A 178 REMARK 465 PRO B 265 REMARK 465 CYS B 292 REMARK 465 GLN B 293 REMARK 465 ASP B 294 REMARK 465 SER B 295 REMARK 465 SER B 296 REMARK 465 GLY B 297 REMARK 465 ARG B 298 REMARK 465 PRO B 299 REMARK 465 ARG B 300 REMARK 465 ARG B 331 REMARK 465 CYS B 332 REMARK 465 HIS B 333 REMARK 465 ALA B 334 REMARK 465 GLY B 335 REMARK 465 SER B 336 REMARK 465 GLY B 337 REMARK 465 SER B 338 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 ARG A 144 CG CD NE CZ NH1 NH2 DBREF 9VEA A 113 157 UNP Q504T8 MIDN_HUMAN 113 157 DBREF 9VEA A 158 178 UNP Q15306 IRF4_HUMAN 205 227 DBREF 9VEA B 265 334 UNP Q504T8 MIDN_HUMAN 265 334 SEQADV 9VEA A UNP Q15306 GLN 206 DELETION SEQADV 9VEA A UNP Q15306 GLY 207 DELETION SEQADV 9VEA ILE A 173 UNP Q15306 ALA 222 ENGINEERED MUTATION SEQADV 9VEA GLY B 335 UNP Q504T8 EXPRESSION TAG SEQADV 9VEA SER B 336 UNP Q504T8 EXPRESSION TAG SEQADV 9VEA GLY B 337 UNP Q504T8 EXPRESSION TAG SEQADV 9VEA SER B 338 UNP Q504T8 EXPRESSION TAG SEQRES 1 A 66 PRO GLU GLN SER VAL MET GLN ALA LEU GLU SER LEU THR SEQRES 2 A 66 GLU THR GLN VAL SER ASP PHE LEU SER GLY ARG SER PRO SEQRES 3 A 66 LEU THR LEU ALA LEU ARG VAL GLY ASP HIS MET MET PHE SEQRES 4 A 66 VAL GLN LEU GLN LEU ALA TRP PRO ALA CYS GLU ASN GLY SEQRES 5 A 66 CYS GLN VAL THR GLY THR PHE TYR ILE CYS ALA PRO PRO SEQRES 6 A 66 GLU SEQRES 1 B 74 PRO GLY ALA VAL ILE GLU SER PHE VAL ASN HIS ALA PRO SEQRES 2 B 74 GLY VAL PHE SER GLY THR PHE SER GLY THR LEU HIS PRO SEQRES 3 B 74 ASN CYS GLN ASP SER SER GLY ARG PRO ARG ARG ASP ILE SEQRES 4 B 74 GLY THR ILE LEU GLN ILE LEU ASN ASP LEU LEU SER ALA SEQRES 5 B 74 THR ARG HIS TYR GLN GLY MET PRO PRO SER LEU ALA GLN SEQRES 6 B 74 LEU ARG CYS HIS ALA GLY SER GLY SER HELIX 1 AA1 PRO A 113 GLU A 122 1 10 HELIX 2 AA2 THR A 125 GLY A 135 1 11 HELIX 3 AA3 ASP B 302 THR B 317 1 16 HELIX 4 AA4 ARG B 318 TYR B 320 5 3 HELIX 5 AA5 PRO B 324 LEU B 330 1 7 SHEET 1 AA1 5 LEU A 139 LEU A 141 0 SHEET 2 AA1 5 PHE A 151 LEU A 156 -1 O LEU A 154 N LEU A 139 SHEET 3 AA1 5 VAL A 167 CYS A 174 -1 O THR A 170 N GLN A 155 SHEET 4 AA1 5 VAL B 279 GLY B 286 -1 O PHE B 284 N GLY A 169 SHEET 5 AA1 5 VAL B 268 ILE B 269 -1 N VAL B 268 O SER B 285 SHEET 1 AA2 5 LEU A 139 LEU A 141 0 SHEET 2 AA2 5 PHE A 151 LEU A 156 -1 O LEU A 154 N LEU A 139 SHEET 3 AA2 5 VAL A 167 CYS A 174 -1 O THR A 170 N GLN A 155 SHEET 4 AA2 5 VAL B 279 GLY B 286 -1 O PHE B 284 N GLY A 169 SHEET 5 AA2 5 VAL B 273 ALA B 276 -1 N ALA B 276 O VAL B 279 SSBOND 1 CYS A 174 CYS A 174 1555 7554 2.02 CISPEP 1 TRP A 158 PRO A 159 0 -1.22 CRYST1 88.255 88.255 69.794 90.00 90.00 120.00 P 65 2 2 12 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 0.011331 0.006542 0.000000 0.00000 SCALE2 0.000000 0.013084 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014328 0.00000 MASTER 260 0 0 5 10 0 0 6 892 2 0 12 END