HEADER PROTEIN BINDING 05-AUG-14 2MSR TITLE SOLUTION STRUCTURE OF LEDGF/P75 IBD IN COMPLEX WITH MLL1 PEPTIDE (140- TITLE 2 160) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE 2A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 140-160; COMPND 5 SYNONYM: LYSINE N-METHYLTRANSFERASE 2A, ALL-1, CXXC-TYPE ZINC FINGER COMPND 6 PROTEIN 7, MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA, COMPND 7 MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA PROTEIN 1, TRITHORAX-LIKE COMPND 8 PROTEIN, ZINC FINGER PROTEIN HRX, MLL CLEAVAGE PRODUCT N320, N- COMPND 9 TERMINAL CLEAVAGE PRODUCT OF 320 KDA, P320, MLL CLEAVAGE PRODUCT COMPND 10 C180, C-TERMINAL CLEAVAGE PRODUCT OF 180 KDA, P180; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 2; COMPND 13 MOLECULE: PC4 AND SFRS1-INTERACTING PROTEIN; COMPND 14 CHAIN: B; COMPND 15 FRAGMENT: UNP RESIDUES 344-425; COMPND 16 SYNONYM: CLL-ASSOCIATED ANTIGEN KW-7, DENSE FINE SPECKLES 70 KDA COMPND 17 PROTEIN, DFS 70, LENS EPITHELIUM-DERIVED GROWTH FACTOR, COMPND 18 TRANSCRIPTIONAL COACTIVATOR P75/P52; COMPND 19 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: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG7; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: PSIP1, DFS70, LEDGF, PSIP2; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS LEDGF/P75, MLL, MIXED LINEAGE LEUKEMIA, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.CERMAKOVA,P.TESINA,J.DEMEULEMEESTER,S.EL ASHKAR,H.MEREAU, AUTHOR 2 J.SCHWALLER,P.REZACOVA,V.VEVERKA,J.DE RIJCK REVDAT 4 15-MAY-24 2MSR 1 REMARK REVDAT 3 14-JUN-23 2MSR 1 REMARK SEQADV REVDAT 2 08-OCT-14 2MSR 1 JRNL REVDAT 1 20-AUG-14 2MSR 0 JRNL AUTH K.CERMAKOVA,P.TESINA,J.DEMEULEMEESTER,S.EL ASHKAR,H.MEREAU, JRNL AUTH 2 J.SCHWALLER,P.REZACOVA,V.VEVERKA,J.DE RIJCK JRNL TITL VALIDATION AND STRUCTURAL CHARACTERIZATION OF THE JRNL TITL 2 LEDGF/P75-MLL INTERFACE AS A NEW TARGET FOR THE TREATMENT OF JRNL TITL 3 MLL-DEPENDENT LEUKEMIA. JRNL REF CANCER RES. V. 74 5139 2014 JRNL REFN ISSN 0008-5472 JRNL PMID 25082813 JRNL DOI 10.1158/0008-5472.CAN-13-3602 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, YASARA, CYANA REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), YASARA (YASARA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MSR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000104003. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 125 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM MLL1_140, 0.5 MM [U-13C; REMARK 210 U-15N] IBD, 25 MM HEPES, 100 MM REMARK 210 SODIUM CHLORIDE, 0.05 % BETA- REMARK 210 MERCAPTOETHANOL, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D HCCH-TOCSY; 3D 1H-13C REMARK 210 NOESY; 3D 1H-15N NOESY; 2D 1H-1H REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, CYANA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 596 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8544 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.6 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 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 6 ARG A 158 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 13 ARG B 404 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 158 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 16 ARG A 158 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 20 ARG A 160 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 20 ARG B 372 NE - CZ - NH1 ANGL. DEV. = 3.0 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 1 GLU A 144 42.02 -157.86 REMARK 500 1 ASP A 154 41.75 -145.10 REMARK 500 1 ALA B 341 -77.78 -145.40 REMARK 500 1 SER B 343 -3.72 -140.23 REMARK 500 1 ARG B 344 -42.14 -142.39 REMARK 500 1 GLU B 345 16.45 58.26 REMARK 500 1 THR B 346 -137.96 53.97 REMARK 500 1 SER B 347 -163.59 53.60 REMARK 500 2 PHE A 148 84.11 40.28 REMARK 500 2 PHE A 151 17.00 57.38 REMARK 500 2 SER A 153 -160.69 -77.96 REMARK 500 2 VAL A 159 150.90 71.43 REMARK 500 2 ASN B 340 46.07 -79.65 REMARK 500 2 THR B 346 0.71 49.51 REMARK 500 2 ASP B 369 71.60 -108.83 REMARK 500 2 HIS B 393 43.70 -106.04 REMARK 500 3 LEU B 363 41.71 -107.30 REMARK 500 3 ASN B 367 62.22 -158.39 REMARK 500 3 HIS B 393 42.72 -93.77 REMARK 500 4 SER A 142 -135.21 55.86 REMARK 500 4 ASP A 154 -36.95 64.49 REMARK 500 4 GLU A 155 16.74 58.82 REMARK 500 4 ARG A 158 36.94 -81.10 REMARK 500 4 SER B 343 35.77 -72.01 REMARK 500 5 GLU A 155 11.36 58.63 REMARK 500 5 VAL A 159 23.74 -70.87 REMARK 500 5 ALA B 342 -118.36 -148.36 REMARK 500 5 GLU B 345 171.96 62.87 REMARK 500 5 SER B 347 94.07 -64.69 REMARK 500 5 ASN B 367 111.98 -164.22 REMARK 500 5 HIS B 393 42.94 -90.79 REMARK 500 6 SER A 142 17.37 -143.09 REMARK 500 6 ASP A 145 48.91 -87.48 REMARK 500 6 GLU A 146 55.62 35.47 REMARK 500 6 LEU A 149 27.71 48.96 REMARK 500 6 PHE A 151 84.38 -154.48 REMARK 500 6 ASP A 154 36.10 -84.80 REMARK 500 6 ALA B 341 162.29 68.09 REMARK 500 6 ARG B 344 -30.93 -161.45 REMARK 500 6 LEU B 363 35.41 -99.37 REMARK 500 6 ASN B 367 76.58 -158.68 REMARK 500 6 HIS B 393 42.28 -109.02 REMARK 500 7 SER A 142 -153.52 59.83 REMARK 500 7 GLU A 144 -179.76 63.59 REMARK 500 7 ASN B 340 -154.73 59.86 REMARK 500 7 LEU B 363 41.75 -104.92 REMARK 500 7 ASP B 369 77.88 -101.62 REMARK 500 7 HIS B 393 44.67 -94.76 REMARK 500 8 PHE A 148 73.94 -107.98 REMARK 500 8 SER A 153 -31.60 -142.04 REMARK 500 REMARK 500 THIS ENTRY HAS 127 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25130 RELATED DB: BMRB DBREF 2MSR A 140 160 UNP Q03164 KMT2A_HUMAN 140 160 DBREF 2MSR B 344 426 UNP O75475 PSIP1_HUMAN 344 426 SEQADV 2MSR SER B 339 UNP O75475 EXPRESSION TAG SEQADV 2MSR ASN B 340 UNP O75475 EXPRESSION TAG SEQADV 2MSR ALA B 341 UNP O75475 EXPRESSION TAG SEQADV 2MSR ALA B 342 UNP O75475 EXPRESSION TAG SEQADV 2MSR SER B 343 UNP O75475 EXPRESSION TAG SEQRES 1 A 21 GLY GLY SER GLY GLU ASP GLU GLN PHE LEU GLY PHE GLY SEQRES 2 A 21 SER ASP GLU GLU VAL ARG VAL ARG SEQRES 1 B 88 SER ASN ALA ALA SER ARG GLU THR SER MET ASP SER ARG SEQRES 2 B 88 LEU GLN ARG ILE HIS ALA GLU ILE LYS ASN SER LEU LYS SEQRES 3 B 88 ILE ASP ASN LEU ASP VAL ASN ARG CYS ILE GLU ALA LEU SEQRES 4 B 88 ASP GLU LEU ALA SER LEU GLN VAL THR MET GLN GLN ALA SEQRES 5 B 88 GLN LYS HIS THR GLU MET ILE THR THR LEU LYS LYS ILE SEQRES 6 B 88 ARG ARG PHE LYS VAL SER GLN VAL ILE MET GLU LYS SER SEQRES 7 B 88 THR MET LEU TYR ASN LYS PHE LYS ASN MET HELIX 1 1 MET B 348 LEU B 363 1 16 HELIX 2 2 ASP B 369 LEU B 383 1 15 HELIX 3 3 THR B 386 HIS B 393 1 8 HELIX 4 4 HIS B 393 ARG B 404 1 12 HELIX 5 5 SER B 409 MET B 426 1 18 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1