HEADER TRANSCRIPTION/DNA 04-JUN-12 4AWL TITLE THE NF-Y TRANSCRIPTION FACTOR IS STRUCTURALLY AND FUNCTIONALLY A TITLE 2 SEQUENCE SPECIFIC HISTONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 233-303; COMPND 5 SYNONYM: CCAAT BOX DNA-BINDING PROTEIN SUBUNIT A, CAAT BOX DNA- COMPND 6 BINDING PROTEIN SUBUNIT A, NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT A, COMPND 7 NF-YA; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: RESIDUES 51-143; COMPND 13 SYNONYM: CCAAT BOX DNA-BINDING PROTEIN SUBUNIT B, CAAT BOX DNA- COMPND 14 BINDING PROTEIN SUBUNIT B, NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B, COMPND 15 NF-YB; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: FRAGMENT NUMBERING 49-141 IS THE NUMBERING DEFINED IN COMPND 18 THE LITERATURE; COMPND 19 MOL_ID: 3; COMPND 20 MOLECULE: NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA; COMPND 21 CHAIN: C; COMPND 22 FRAGMENT: RESIDUES 27-120; COMPND 23 SYNONYM: CAAT BOX DNA-BINDING PROTEIN SUBUNIT C, CAAT BOX DNA-BINDING COMPND 24 PROTEIN SUBUNIT C, NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C, NF-YC, COMPND 25 TRANSACTIVATOR HSM-1/2; COMPND 26 ENGINEERED: YES; COMPND 27 MOL_ID: 4; COMPND 28 MOLECULE: HSP70 PROMOTER FRAGMENT; COMPND 29 CHAIN: I; COMPND 30 ENGINEERED: YES; COMPND 31 MOL_ID: 5; COMPND 32 MOLECULE: HSP70 PROMOTER FRAGMENT; COMPND 33 CHAIN: J; COMPND 34 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 22 ORGANISM_COMMON: HUMAN; SOURCE 23 ORGANISM_TAXID: 9606; SOURCE 24 MOL_ID: 5; SOURCE 25 SYNTHETIC: YES; SOURCE 26 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 27 ORGANISM_COMMON: HUMAN; SOURCE 28 ORGANISM_TAXID: 9606 KEYWDS TRANSCRIPTION-DNA COMPLEX, NF-Y, DNA-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.NARDINI,N.GNESUTTA,G.DONATI,R.GATTA,C.FORNI,A.FOSSATI,C.VONRHEIN, AUTHOR 2 D.MORAS,C.ROMIER,R.MANTOVANI,M.BOLOGNESI REVDAT 3 20-DEC-23 4AWL 1 REMARK REVDAT 2 08-MAY-19 4AWL 1 REMARK REVDAT 1 30-JAN-13 4AWL 0 JRNL AUTH M.NARDINI,N.GNESUTTA,G.DONATI,R.GATTA,C.FORNI,A.FOSSATI, JRNL AUTH 2 C.VONRHEIN,D.MORAS,C.ROMIER,M.BOLOGNESI,R.MANTOVANI JRNL TITL SEQUENCE-SPECIFIC TRANSCRIPTION FACTOR NF-Y DISPLAYS JRNL TITL 2 HISTONE-LIKE DNA BINDING AND H2B-LIKE UBIQUITINATION. JRNL REF CELL(CAMBRIDGE,MASS.) V. 152 132 2013 JRNL REFN ISSN 0092-8674 JRNL PMID 23332751 JRNL DOI 10.1016/J.CELL.2012.11.047 REMARK 2 REMARK 2 RESOLUTION. 3.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 8448 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 418 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.08 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 454 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2410 REMARK 3 BIN FREE R VALUE SET COUNT : 29 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1928 REMARK 3 NUCLEIC ACID ATOMS : 1019 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.15000 REMARK 3 B22 (A**2) : -0.55000 REMARK 3 B33 (A**2) : -7.60000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.462 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.413 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 43.765 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3099 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4379 ; 1.751 ; 2.382 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 231 ; 5.831 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 97 ;35.568 ;22.990 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 389 ;23.756 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;18.478 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 482 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1979 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1170 ; 0.420 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1887 ; 0.853 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1929 ; 1.183 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2492 ; 1.969 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 232 A 293 REMARK 3 ORIGIN FOR THE GROUP (A): 4.7418 -4.5547 -11.0834 REMARK 3 T TENSOR REMARK 3 T11: 0.0578 T22: 0.3199 REMARK 3 T33: 0.2037 T12: -0.0178 REMARK 3 T13: 0.0647 T23: -0.0244 REMARK 3 L TENSOR REMARK 3 L11: 2.4211 L22: 10.1407 REMARK 3 L33: 4.7595 L12: -0.6110 REMARK 3 L13: 0.4994 L23: -1.3938 REMARK 3 S TENSOR REMARK 3 S11: -0.0033 S12: 0.0272 S13: -0.0309 REMARK 3 S21: 0.1882 S22: 0.1026 S23: 0.8673 REMARK 3 S31: -0.3645 S32: -0.6517 S33: -0.0993 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 50 B 141 REMARK 3 ORIGIN FOR THE GROUP (A): 14.6984 5.4631 -18.0178 REMARK 3 T TENSOR REMARK 3 T11: 0.1914 T22: 0.1298 REMARK 3 T33: 0.3289 T12: -0.0566 REMARK 3 T13: 0.0048 T23: 0.0820 REMARK 3 L TENSOR REMARK 3 L11: 3.6264 L22: 6.8842 REMARK 3 L33: 11.1020 L12: -1.1813 REMARK 3 L13: 2.1437 L23: -3.0892 REMARK 3 S TENSOR REMARK 3 S11: -0.1970 S12: 0.6290 S13: 0.5963 REMARK 3 S21: -0.4932 S22: -0.2198 S23: -0.4506 REMARK 3 S31: -1.1906 S32: 0.3693 S33: 0.4168 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 40 C 119 REMARK 3 ORIGIN FOR THE GROUP (A): 14.0240 4.3378 -10.7036 REMARK 3 T TENSOR REMARK 3 T11: 0.0391 T22: 0.0565 REMARK 3 T33: 0.2714 T12: -0.1322 REMARK 3 T13: -0.0654 T23: 0.0692 REMARK 3 L TENSOR REMARK 3 L11: 3.0816 L22: 6.7140 REMARK 3 L33: 21.2583 L12: -1.3605 REMARK 3 L13: 4.4551 L23: -3.2749 REMARK 3 S TENSOR REMARK 3 S11: -0.2023 S12: 0.1441 S13: 0.4327 REMARK 3 S21: 0.3520 S22: 0.0613 S23: -0.2120 REMARK 3 S31: -1.2927 S32: -0.1826 S33: 0.1410 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : I 1 I 25 REMARK 3 ORIGIN FOR THE GROUP (A): 13.2061 -12.3674 -18.4462 REMARK 3 T TENSOR REMARK 3 T11: 0.2283 T22: 0.2451 REMARK 3 T33: 0.2342 T12: -0.0727 REMARK 3 T13: 0.0254 T23: -0.0255 REMARK 3 L TENSOR REMARK 3 L11: 2.1146 L22: 3.2313 REMARK 3 L33: 4.1345 L12: -0.7163 REMARK 3 L13: 1.4609 L23: -1.3295 REMARK 3 S TENSOR REMARK 3 S11: 0.0746 S12: 0.3310 S13: 0.0951 REMARK 3 S21: -0.7381 S22: -0.1236 S23: -0.1930 REMARK 3 S31: 0.8998 S32: 0.3327 S33: 0.0490 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : J -10 J -1 REMARK 3 ORIGIN FOR THE GROUP (A): 14.1637 -17.2582 4.8075 REMARK 3 T TENSOR REMARK 3 T11: 0.2481 T22: 0.1216 REMARK 3 T33: 0.1323 T12: -0.0294 REMARK 3 T13: 0.0715 T23: 0.0831 REMARK 3 L TENSOR REMARK 3 L11: 1.4718 L22: 6.6598 REMARK 3 L33: 9.8097 L12: -0.0297 REMARK 3 L13: 2.7189 L23: 1.2144 REMARK 3 S TENSOR REMARK 3 S11: -0.0288 S12: -0.5150 S13: -0.3239 REMARK 3 S21: 1.0735 S22: -0.3196 S23: 0.1836 REMARK 3 S31: 1.0613 S32: -0.4786 S33: 0.3484 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. THE NF-YA MODEL COMPRISES RESIDUES 232-293. POOR REMARK 3 DENSITY IS PRESENT FOR THE 232-235 SEGMENT, WHILE NO REMARK 3 INTERPRETABLE ELECTRON DENSITY WAS PRESENT FOR THE 294-307 REMARK 3 SEGMENT. NF-YB AND NF-YC COMPRISE RESIDUES 50-141 AND 40-119, REMARK 3 RESPECTIVELY. FOR THE FIRST TWO NF-YB N-TERMINAL RESIDUES, THE REMARK 3 FIRST THIRTEEN NF-YC N-TERMINAL RESIDUES AND THE LAST NF-YC C- REMARK 3 TERMINAL RESIDUES NO ELECTRON DENSITY WAS AVAILABLE. FINAL REMARK 3 STRUCTURE HAS NO RESIDUES IN THE DISALLOWED REGION OF THE REMARK 3 RAMACHANDRAN PLOT AS DEFINED IN THE CCP4 PROCHECK PROGRAM. REMARK 4 REMARK 4 4AWL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1290052720. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9,1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8907 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.080 REMARK 200 RESOLUTION RANGE LOW (A) : 62.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 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: PDB ENTRY 1N1J REMARK 200 REMARK 200 REMARK: A 25 BP OLIGONUCLEOTIDE CUT FROM THE XENOPUS LAEVIS REMARK 200 NUCLEOSOME, PDB ENTRY 1AOI, WAS USED AS THE SEARCH MODEL FOR THE REMARK 200 DNA PART OF THE COMPLEX REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOUR DIFFUSION METHOD , HANGING REMARK 280 DROP, 20-24% PEG3350, 100 MM MES OR CACODYLATE BUFFER, PH 6.5, REMARK 280 50 MM NAF. T ROOM., VAPOR DIFFUSION, HANGING DROP 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 27.35000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.84000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.28000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.84000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.35000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.28000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -94.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, I, J 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 294 REMARK 465 LYS A 295 REMARK 465 ASP A 296 REMARK 465 SER A 297 REMARK 465 PRO A 298 REMARK 465 HIS A 299 REMARK 465 MET A 300 REMARK 465 GLN A 301 REMARK 465 ASP A 302 REMARK 465 PRO A 303 REMARK 465 GLY A 304 REMARK 465 SER A 305 REMARK 465 LEU A 306 REMARK 465 VAL A 307 REMARK 465 PRO A 308 REMARK 465 ARG A 309 REMARK 465 MET B 48 REMARK 465 SER B 49 REMARK 465 MET C 27 REMARK 465 GLU C 28 REMARK 465 GLU C 29 REMARK 465 ILE C 30 REMARK 465 ARG C 31 REMARK 465 ASN C 32 REMARK 465 LEU C 33 REMARK 465 THR C 34 REMARK 465 VAL C 35 REMARK 465 LYS C 36 REMARK 465 ASP C 37 REMARK 465 PHE C 38 REMARK 465 ARG C 39 REMARK 465 ARG C 120 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DA I 6 O3' DA I 6 C3' -0.042 REMARK 500 DA I 10 O3' DA I 10 C3' -0.041 REMARK 500 DA I 11 O3' DA I 11 C3' -0.049 REMARK 500 DC I 20 O3' DC I 20 C3' -0.041 REMARK 500 DA J -4 O3' DA J -4 C3' -0.055 REMARK 500 REMARK 500 REMARK: NULL 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 PHE A 289 CB - CA - C ANGL. DEV. = 19.1 DEGREES REMARK 500 PHE A 290 CB - CA - C ANGL. DEV. = 29.3 DEGREES REMARK 500 GLU C 42 CB - CA - C ANGL. DEV. = 13.3 DEGREES REMARK 500 VAL C 58 CB - CA - C ANGL. DEV. = -15.1 DEGREES REMARK 500 DT I 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC I 3 C3' - C2' - C1' ANGL. DEV. = -6.3 DEGREES REMARK 500 DA I 6 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 DC I 8 O4' - C1' - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA I 11 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC I 15 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 DA I 18 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC I 20 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT I 21 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG I 23 C3' - O3' - P ANGL. DEV. = 11.0 DEGREES REMARK 500 DA I 24 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT I 25 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT J -24 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 DC J -23 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 DC J -23 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA J -21 O4' - C1' - N9 ANGL. DEV. = -7.5 DEGREES REMARK 500 DC J -19 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC J -17 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 DG J -16 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG J -16 C3' - O3' - P ANGL. DEV. = 9.4 DEGREES REMARK 500 DT J -14 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG J -13 O4' - C1' - N9 ANGL. DEV. = -5.6 DEGREES REMARK 500 DA J -12 O4' - C1' - N9 ANGL. DEV. = -9.2 DEGREES REMARK 500 DT J -11 O4' - C1' - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 DG J -9 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DG J -9 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG J -8 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 DC J -7 O4' - C1' - N1 ANGL. DEV. = -5.3 DEGREES REMARK 500 DC J -5 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG J -3 O4' - C1' - N9 ANGL. DEV. = 2.1 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 GLU A 233 144.16 174.74 REMARK 500 PRO A 235 -138.94 -103.05 REMARK 500 GLU A 259 -86.91 -101.71 REMARK 500 PHE A 289 -72.87 -82.46 REMARK 500 PHE A 290 176.12 171.45 REMARK 500 PRO A 292 173.06 -55.64 REMARK 500 PHE B 139 -16.80 -168.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1N1J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE NF-YB/NF-YC HISTONE PAIR REMARK 999 REMARK 999 SEQUENCE REMARK 999 FOREIGN SEQUENCE PRESENT IN THE NF-YA RECOMBINANT PROTEIN REMARK 999 THAT WERE ADDED FOR EXPRESSION-PURIFICATION PURPOSES N- REMARK 999 TERMINAL MET C-TERMINAL GLY-SER-LEU-VAL-PRO-ARG REMARK 999 FOREIGN SEQUENCE PRESENT IN THE NF-YB RECOMBINANT PROTEIN REMARK 999 THAT WERE ADDED FOR EXPRESSION-PURIFICATION PURPOSES N- REMARK 999 TERMINAL MET DBREF 4AWL A 233 303 UNP P23511 NFYA_HUMAN 233 303 DBREF 4AWL B 49 141 UNP P25208 NFYB_HUMAN 51 143 DBREF 4AWL C 27 120 UNP Q13952 NFYC_HUMAN 27 120 DBREF 4AWL I 1 25 PDB 4AWL 4AWL 1 25 DBREF 4AWL J -25 -1 PDB 4AWL 4AWL -25 -1 SEQADV 4AWL MET A 232 UNP P23511 EXPRESSION TAG SEQADV 4AWL GLY A 304 UNP P23511 EXPRESSION TAG SEQADV 4AWL SER A 305 UNP P23511 EXPRESSION TAG SEQADV 4AWL LEU A 306 UNP P23511 EXPRESSION TAG SEQADV 4AWL VAL A 307 UNP P23511 EXPRESSION TAG SEQADV 4AWL PRO A 308 UNP P23511 EXPRESSION TAG SEQADV 4AWL ARG A 309 UNP P23511 EXPRESSION TAG SEQADV 4AWL MET B 48 UNP P25208 EXPRESSION TAG SEQRES 1 A 78 MET GLU GLU PRO LEU TYR VAL ASN ALA LYS GLN TYR HIS SEQRES 2 A 78 ARG ILE LEU LYS ARG ARG GLN ALA ARG ALA LYS LEU GLU SEQRES 3 A 78 ALA GLU GLY LYS ILE PRO LYS GLU ARG ARG LYS TYR LEU SEQRES 4 A 78 HIS GLU SER ARG HIS ARG HIS ALA MET ALA ARG LYS ARG SEQRES 5 A 78 GLY GLU GLY GLY ARG PHE PHE SER PRO LYS GLU LYS ASP SEQRES 6 A 78 SER PRO HIS MET GLN ASP PRO GLY SER LEU VAL PRO ARG SEQRES 1 B 94 MET SER PHE ARG GLU GLN ASP ILE TYR LEU PRO ILE ALA SEQRES 2 B 94 ASN VAL ALA ARG ILE MET LYS ASN ALA ILE PRO GLN THR SEQRES 3 B 94 GLY LYS ILE ALA LYS ASP ALA LYS GLU CYS VAL GLN GLU SEQRES 4 B 94 CYS VAL SER GLU PHE ILE SER PHE ILE THR SER GLU ALA SEQRES 5 B 94 SER GLU ARG CYS HIS GLN GLU LYS ARG LYS THR ILE ASN SEQRES 6 B 94 GLY GLU ASP ILE LEU PHE ALA MET SER THR LEU GLY PHE SEQRES 7 B 94 ASP SER TYR VAL GLU PRO LEU LYS LEU TYR LEU GLN LYS SEQRES 8 B 94 PHE ARG GLU SEQRES 1 C 94 MET GLU GLU ILE ARG ASN LEU THR VAL LYS ASP PHE ARG SEQRES 2 C 94 VAL GLN GLU LEU PRO LEU ALA ARG ILE LYS LYS ILE MET SEQRES 3 C 94 LYS LEU ASP GLU ASP VAL LYS MET ILE SER ALA GLU ALA SEQRES 4 C 94 PRO VAL LEU PHE ALA LYS ALA ALA GLN ILE PHE ILE THR SEQRES 5 C 94 GLU LEU THR LEU ARG ALA TRP ILE HIS THR GLU ASP ASN SEQRES 6 C 94 LYS ARG ARG THR LEU GLN ARG ASN ASP ILE ALA MET ALA SEQRES 7 C 94 ILE THR LYS PHE ASP GLN PHE ASP PHE LEU ILE ASP ILE SEQRES 8 C 94 VAL PRO ARG SEQRES 1 I 25 DT DT DC DT DG DA DG DC DC DA DA DT DC SEQRES 2 I 25 DA DC DC DG DA DG DC DT DC DG DA DT SEQRES 1 J 25 DA DT DC DG DA DG DC DT DC DG DG DT DG SEQRES 2 J 25 DA DT DT DG DG DC DT DC DA DG DA DA FORMUL 6 HOH *2(H2 O) HELIX 1 1 TYR A 243 ALA A 258 1 16 HELIX 2 2 GLU A 272 ALA A 280 1 9 HELIX 3 3 ILE B 59 ASN B 68 1 10 HELIX 4 4 LYS B 78 GLN B 105 1 28 HELIX 5 5 GLY B 113 THR B 122 1 10 HELIX 6 6 VAL B 129 TYR B 135 1 7 HELIX 7 7 LEU C 45 MET C 52 1 8 HELIX 8 8 GLU C 64 ASP C 90 1 27 HELIX 9 11 ARG C 98 ILE C 105 1 8 SHEET 1 BA 2 LYS B 75 ILE B 76 0 SHEET 2 BA 2 THR C 95 LEU C 96 1 N LEU C 96 O LYS B 75 SHEET 1 BB 2 THR B 110 ILE B 111 0 SHEET 2 BB 2 MET C 60 ILE C 61 1 O MET C 60 N ILE B 111 CRYST1 54.700 62.560 139.680 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 0.018282 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015985 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007159 0.00000