HEADER DNA BINDING PROTEIN 11-AUG-25 9WA7 TITLE CRYSTAL STRUCTURE OF HUMAN NFIX IN COMPLEX WITH TGGCA(N3)TGCCA TITLE 2 PALINDROMIC DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR FACTOR 1 X-TYPE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NF1-X,NUCLEAR FACTOR 1/X,CCAAT-BOX-BINDING TRANSCRIPTION COMPND 5 FACTOR,CTF,NUCLEAR FACTOR I/X,NF-I/X,NFI-X,TGGCA-BINDING PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*AP*GP*TP*TP*GP*GP*CP*AP*AP*GP*AP*TP*GP*CP*CP*AP*TP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'- COMPND 14 D(*GP*AP*TP*GP*GP*CP*AP*TP*CP*TP*TP*GP*CP*CP*AP*AP*CP*T)-3'); COMPND 15 CHAIN: C; COMPND 16 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: NFIX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS NFIX, TRANSCRIPTION FACTOR, SKELETAL MUSCLE DEVELOPMENT, DNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.ZHU,X.CHEN,C.QIN,H.SONG REVDAT 1 11-MAR-26 9WA7 0 JRNL AUTH C.ZHU,S.LIU,X.CHEN,C.QIN,Y.WANG,C.XUE,L.LI,W.DU,X.CHEN,X.LI, JRNL AUTH 2 J.SHEN,H.SONG JRNL TITL MECHANISTIC INSIGHTS INTO NFIX-MEDIATED DNA RECOGNITION AND JRNL TITL 2 TRANSCRIPTIONAL REGULATION IN SKELETAL MUSCLE. JRNL REF SMART MED V. 5 70027 2026 JRNL REFN ISSN 2751-1871 JRNL PMID 41623611 JRNL DOI 10.1002/SMMD.70027 REMARK 2 REMARK 2 RESOLUTION. 2.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 13756 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.250 REMARK 3 FREE R VALUE TEST SET COUNT : 997 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 31.1800 - 4.4200 1.00 1952 152 0.1900 0.2078 REMARK 3 2 4.4100 - 3.5100 1.00 1835 144 0.2046 0.2409 REMARK 3 3 3.5100 - 3.0600 1.00 1841 143 0.2218 0.2496 REMARK 3 4 3.0600 - 2.7800 1.00 1801 141 0.2795 0.3658 REMARK 3 5 2.7800 - 2.5800 1.00 1800 141 0.2845 0.3224 REMARK 3 6 2.5800 - 2.4300 1.00 1798 140 0.2880 0.3671 REMARK 3 7 2.4300 - 2.3100 0.97 1732 136 0.2916 0.3470 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) : 0.348 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.975 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.75 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 2193 REMARK 3 ANGLE : 0.522 3110 REMARK 3 CHIRALITY : 0.036 340 REMARK 3 PLANARITY : 0.004 271 REMARK 3 DIHEDRAL : 25.024 903 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 9WA7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1300062540. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-24 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 : 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-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13804 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 120.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 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: 7QQD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.04 M POTASSIUM PHOSPHATE MONOBASIC, REMARK 280 16% (W/V) PEG 8000, AND 20% (V/V) GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 -X+1/2,Y+1/2,-Z 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 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 -1.000000 0.000000 0.000000 38.50650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.67050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.50650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.67050 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 174 REMARK 465 LEU A 175 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 PHE A 26 -6.13 72.92 REMARK 500 ASP A 109 -169.75 -75.35 REMARK 500 ASP A 146 31.90 -97.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 103 SG REMARK 620 2 CYS A 156 SG 109.0 REMARK 620 3 CYS A 162 SG 114.3 110.6 REMARK 620 4 HIS A 167 ND1 99.1 125.3 98.2 REMARK 620 N 1 2 3 DBREF 9WA7 A 13 175 UNP Q14938 NFIX_HUMAN 13 175 DBREF 9WA7 B 1 18 PDB 9WA7 9WA7 1 18 DBREF 9WA7 C 1 18 PDB 9WA7 9WA7 1 18 SEQRES 1 A 163 HIS PRO PHE ILE GLU ALA LEU LEU PRO HIS VAL ARG ALA SEQRES 2 A 163 PHE SER TYR THR TRP PHE ASN LEU GLN ALA ARG LYS ARG SEQRES 3 A 163 LYS TYR PHE LYS LYS HIS GLU LYS ARG MET SER LYS ASP SEQRES 4 A 163 GLU GLU ARG ALA VAL LYS ASP GLU LEU LEU GLY GLU LYS SEQRES 5 A 163 PRO GLU ILE LYS GLN LYS TRP ALA SER ARG LEU LEU ALA SEQRES 6 A 163 LYS LEU ARG LYS ASP ILE ARG PRO GLU PHE ARG GLU ASP SEQRES 7 A 163 PHE VAL LEU THR ILE THR GLY LYS LYS PRO PRO CYS CYS SEQRES 8 A 163 VAL LEU SER ASN PRO ASP GLN LYS GLY LYS ILE ARG ARG SEQRES 9 A 163 ILE ASP CYS LEU ARG GLN ALA ASP LYS VAL TRP ARG LEU SEQRES 10 A 163 ASP LEU VAL MET VAL ILE LEU PHE LYS GLY ILE PRO LEU SEQRES 11 A 163 GLU SER THR ASP GLY GLU ARG LEU TYR LYS SER PRO GLN SEQRES 12 A 163 CYS SER ASN PRO GLY LEU CYS VAL GLN PRO HIS HIS ILE SEQRES 13 A 163 GLY VAL THR ILE LYS GLU LEU SEQRES 1 B 18 DA DG DT DT DG DG DC DA DA DG DA DT DG SEQRES 2 B 18 DC DC DA DT DC SEQRES 1 C 18 DG DA DT DG DG DC DA DT DC DT DT DG DC SEQRES 2 C 18 DC DA DA DC DT HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *105(H2 O) HELIX 1 AA1 HIS A 13 LEU A 20 1 8 HELIX 2 AA2 PHE A 26 GLU A 45 1 20 HELIX 3 AA3 SER A 49 GLY A 62 1 14 HELIX 4 AA4 LYS A 64 ILE A 83 1 20 HELIX 5 AA5 ARG A 84 THR A 96 1 13 HELIX 6 AA6 LEU A 129 GLY A 139 1 11 HELIX 7 AA7 ASP A 146 GLU A 148 5 3 HELIX 8 AA8 GLN A 164 HIS A 166 5 3 SHEET 1 AA1 2 ARG A 116 ILE A 117 0 SHEET 2 AA1 2 TRP A 127 ARG A 128 -1 O TRP A 127 N ILE A 117 SHEET 1 AA2 2 LEU A 150 LYS A 152 0 SHEET 2 AA2 2 ILE A 168 VAL A 170 -1 O GLY A 169 N TYR A 151 LINK SG CYS A 103 ZN ZN A 201 1555 1555 2.32 LINK SG CYS A 156 ZN ZN A 201 1555 1555 2.32 LINK SG CYS A 162 ZN ZN A 201 1555 1555 2.32 LINK ND1 HIS A 167 ZN ZN A 201 1555 1555 2.09 CRYST1 77.013 93.341 41.895 90.00 90.00 90.00 P 21 21 2 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 0.012985 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023869 0.00000 CONECT 781 2076 CONECT 1215 2076 CONECT 1254 2076 CONECT 1294 2076 CONECT 2076 781 1215 1254 1294 MASTER 241 0 1 8 4 0 0 6 2168 3 5 17 END