HEADER TRANSCRIPTION/DNA 26-JAN-18 5Z6Z TITLE CRYSTAL STRUCTURE OF HUMAN DUX4 HOMEODOMAINS BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOUBLE HOMEOBOX PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HOMEODOMAIN; COMPND 5 SYNONYM: DOUBLE HOMEOBOX PROTEIN 10; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*CP*CP*AP*CP*TP*AP*AP*CP*CP*TP*AP*AP*TP*CP*AP*CP*AP*CP*C)-3'); COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'- COMPND 14 D(*GP*GP*TP*GP*TP*GP*AP*TP*TP*AP*GP*GP*TP*TP*AP*GP*TP*GP*G)-3'); COMPND 15 CHAIN: E; 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: DUX4, DUX10; 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 HOMEODOMAINS, DUX4, COMPLEX, DNA RECOGNITION, TRANSCRIPTION-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.Y.LI,B.X.WU,J.H.GAN REVDAT 3 27-MAR-24 5Z6Z 1 REMARK REVDAT 2 14-NOV-18 5Z6Z 1 JRNL REVDAT 1 31-OCT-18 5Z6Z 0 JRNL AUTH Y.LI,B.WU,H.LIU,Y.GAO,C.YANG,X.CHEN,J.ZHANG,Y.CHEN,Y.GU, JRNL AUTH 2 J.LI,J.MA,J.GAN JRNL TITL STRUCTURAL BASIS FOR MULTIPLE GENE REGULATION BY HUMAN DUX4. JRNL REF BIOCHEM. BIOPHYS. RES. V. 505 1161 2018 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 30322619 JRNL DOI 10.1016/J.BBRC.2018.10.056 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 3 NUMBER OF REFLECTIONS : 14902 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.490 REMARK 3 FREE R VALUE TEST SET COUNT : 818 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 29.8401 - 4.1785 1.00 2839 173 0.1631 0.2002 REMARK 3 2 4.1785 - 3.3180 1.00 2733 129 0.1754 0.2190 REMARK 3 3 3.3180 - 2.8990 1.00 2626 210 0.2203 0.2667 REMARK 3 4 2.8990 - 2.6341 1.00 2662 135 0.2924 0.3495 REMARK 3 5 2.6341 - 2.4454 0.86 2286 114 0.3262 0.3100 REMARK 3 6 2.4454 - 2.3013 0.36 938 57 0.3436 0.3790 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.520 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 : 0.004 1907 REMARK 3 ANGLE : 0.614 2730 REMARK 3 CHIRALITY : 0.033 290 REMARK 3 PLANARITY : 0.004 227 REMARK 3 DIHEDRAL : 24.229 1022 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 70.0316 41.6642 12.8506 REMARK 3 T TENSOR REMARK 3 T11: 0.2645 T22: 0.1569 REMARK 3 T33: 0.2055 T12: 0.0006 REMARK 3 T13: 0.0032 T23: 0.0786 REMARK 3 L TENSOR REMARK 3 L11: 2.9879 L22: 3.2635 REMARK 3 L33: 2.9821 L12: 0.3697 REMARK 3 L13: -0.8234 L23: 1.0137 REMARK 3 S TENSOR REMARK 3 S11: 0.0372 S12: 0.1550 S13: 0.2988 REMARK 3 S21: 0.2359 S22: -0.0316 S23: -0.0969 REMARK 3 S31: -0.2690 S32: -0.0100 S33: 0.1085 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 5Z6Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1300006590. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JAN-18 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 : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18746 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 56.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 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: NULL 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 (%): 60.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2% V/V TACSIMATE PH 7.0, 0.1 M HEPES REMARK 280 PH 7.5, 20% W/V POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 101.38333 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 50.69167 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.69167 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 101.38333 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: 5670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, E 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 242 LIES ON A SPECIAL POSITION. 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 LEU A 3 REMARK 465 PRO A 4 REMARK 465 THR A 5 REMARK 465 PRO A 6 REMARK 465 SER A 7 REMARK 465 ASP A 8 REMARK 465 SER A 9 REMARK 465 THR A 10 REMARK 465 LEU A 11 REMARK 465 PRO A 12 REMARK 465 ALA A 13 REMARK 465 GLU A 14 REMARK 465 ALA A 15 REMARK 465 ARG A 16 REMARK 465 GLY A 17 REMARK 465 ARG A 18 REMARK 465 ARG A 83 REMARK 465 PRO A 84 REMARK 465 TRP A 85 REMARK 465 PRO A 86 REMARK 465 GLY A 87 REMARK 465 ARG A 88 REMARK 465 ARG A 89 REMARK 465 GLY A 90 REMARK 465 PRO A 91 REMARK 465 PRO A 150 REMARK 465 GLY A 151 REMARK 465 GLN A 152 REMARK 465 GLY A 153 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG E 11 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 41 98.31 -163.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 5Z6Z A 1 153 UNP Q9UBX2 DUX4_HUMAN 1 153 DBREF 5Z6Z D 1 19 PDB 5Z6Z 5Z6Z 1 19 DBREF 5Z6Z E 1 19 PDB 5Z6Z 5Z6Z 1 19 SEQRES 1 A 153 MET ALA LEU PRO THR PRO SER ASP SER THR LEU PRO ALA SEQRES 2 A 153 GLU ALA ARG GLY ARG GLY ARG ARG ARG ARG LEU VAL TRP SEQRES 3 A 153 THR PRO SER GLN SER GLU ALA LEU ARG ALA CYS PHE GLU SEQRES 4 A 153 ARG ASN PRO TYR PRO GLY ILE ALA THR ARG GLU ARG LEU SEQRES 5 A 153 ALA GLN ALA ILE GLY ILE PRO GLU PRO ARG VAL GLN ILE SEQRES 6 A 153 TRP PHE GLN ASN GLU ARG SER ARG GLN LEU ARG GLN HIS SEQRES 7 A 153 ARG ARG GLU SER ARG PRO TRP PRO GLY ARG ARG GLY PRO SEQRES 8 A 153 PRO GLU GLY ARG ARG LYS ARG THR ALA VAL THR GLY SER SEQRES 9 A 153 GLN THR ALA LEU LEU LEU ARG ALA PHE GLU LYS ASP ARG SEQRES 10 A 153 PHE PRO GLY ILE ALA ALA ARG GLU GLU LEU ALA ARG GLU SEQRES 11 A 153 THR GLY LEU PRO GLU SER ARG ILE GLN ILE TRP PHE GLN SEQRES 12 A 153 ASN ARG ARG ALA ARG HIS PRO GLY GLN GLY SEQRES 1 D 19 DC DC DA DC DT DA DA DC DC DT DA DA DT SEQRES 2 D 19 DC DA DC DA DC DC SEQRES 1 E 19 DG DG DT DG DT DG DA DT DT DA DG DG DT SEQRES 2 E 19 DT DA DG DT DG DG FORMUL 4 HOH *94(H2 O) HELIX 1 AA1 THR A 27 ASN A 41 1 15 HELIX 2 AA2 GLY A 45 GLY A 57 1 13 HELIX 3 AA3 PRO A 59 SER A 82 1 24 HELIX 4 AA4 THR A 102 ASP A 116 1 15 HELIX 5 AA5 GLY A 120 GLY A 132 1 13 HELIX 6 AA6 PRO A 134 HIS A 149 1 16 CRYST1 64.879 64.879 152.075 90.00 90.00 120.00 P 32 2 1 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 0.015413 0.008899 0.000000 0.00000 SCALE2 0.000000 0.017798 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006576 0.00000