PDB Short entry for 2MV7 HEADER PROTEIN BINDING/TRANSFERASE 24-SEP-14 2MV7 TITLE SOLUTION NMR STRUCTURE OF DOT1L IN COMPLEX WITH AF9 (DOT1L-AF9) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN AF-9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 500-568; COMPND 5 SYNONYM: ALL1-FUSED GENE FROM CHROMOSOME 9 PROTEIN, MYELOID/LYMPHOID COMPND 6 OR MIXED-LINEAGE LEUKEMIA TRANSLOCATED TO CHROMOSOME 3 PROTEIN, YEATS COMPND 7 DOMAIN-CONTAINING PROTEIN 3; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: UNP RESIDUES 877-900; COMPND 13 SYNONYM: DOT1-LIKE PROTEIN, HISTONE H3-K79 METHYLTRANSFERASE, H3-K79- COMPND 14 HMTASE, LYSINE N-METHYLTRANSFERASE 4; COMPND 15 EC: 2.1.1.43; 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: AF9, MLLT3, YEATS3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PETDUET-1; SOURCE 10 OTHER_DETAILS: PETDUET-1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: DOT1L, KIAA1814, KMT4; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 DE3; SOURCE 19 EXPRESSION_SYSTEM_VECTOR: PETDUET-1; SOURCE 20 OTHER_DETAILS: PETDUET-1 KEYWDS MIXED LINEAGE LEUKEMIA, LEUKEMIA, PROTEIN BINDING-TRANSFERASE COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.KUNTIMADDI,J.H.BUSHWELLER REVDAT 3 14-JUN-23 2MV7 1 REMARK SEQADV REVDAT 2 17-JUN-15 2MV7 1 JRNL REVDAT 1 22-APR-15 2MV7 0 JRNL AUTH A.KUNTIMADDI,N.J.ACHILLE,J.THORPE,A.A.LOKKEN,R.SINGH, JRNL AUTH 2 C.S.HEMENWAY,M.ADLI,N.J.ZELEZNIK-LE,J.H.BUSHWELLER JRNL TITL DEGREE OF RECRUITMENT OF DOT1L TO MLL-AF9 DEFINES LEVEL OF JRNL TITL 2 H3K79 DI- AND TRI-METHYLATION ON TARGET GENES AND JRNL TITL 3 TRANSFORMATION POTENTIAL. JRNL REF CELL REP V. 11 808 2015 JRNL REFN ESSN 2211-1247 JRNL PMID 25921540 JRNL DOI 10.1016/J.CELREP.2015.04.004 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH_2.34, SPARKY REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJ (X-PLOR_NIH_2.34), REMARK 3 GODDARD (SPARKY) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FIRST ROUND OF STRUCTURE REMARK 3 CALCULATION/REFINEMENT WAS CONDUCTED WITH DISTANCE AND DIHEDRAL REMARK 3 ANGLE RESTRAINTS ONLY USING HIGH TEMPERATURE ANNEALING. FINAL REMARK 3 ROUND OF REFINEMENT INCLUDED RDCS USING LOW TEMPERATURE REMARK 3 ANNEALING., FIRST ROUND WITH DISTANCE AND DIHEDRAL ANGLE REMARK 3 RESTRAINTS ONLY WITH HIGH TEMPERATURE ANNEALING., FINAL ROUND OF REMARK 3 REFINEMENT WITH RDCS WITH LOW TEMPERATURE ANNEALING. REMARK 4 REMARK 4 2MV7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000104085. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 750 UM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN AF, 750 UM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N- REMARK 210 METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 MM BIS-TRIS, 15.8 REMARK 210 MM MES, 100 MM SODIUM CHLORIDE, 1 MM DTT, 95% H2O/5% D2O; 750 MM REMARK 210 [U-100% 13C; U-100% 15N] PROTEIN AF, 750 MM [U-100% 13C; U-100% REMARK 210 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, REMARK 210 9.3 MM BIS-TRIS, 15.8 MM MES, 100 MM SODIUM CHLORIDE, 1 MM DTT, REMARK 210 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % REMARK 210 ACRYLIC ACID, 750 MM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 MM REMARK 210 [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 REMARK 210 LYSINE-79 SPECIFIC, 9.3 MM BIS-TRIS, 15.8 MM MES, 100 MM SODIUM REMARK 210 CHLORIDE, 1 MM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM REMARK 210 CHLORIDE, 3.5 % ACRYLAMIDE, 95% H2O/5% D2O; 750 MM [U-100% 13C; REMARK 210 U-100% 15N] PROTEIN AF, 750 MM [U-100% 13C; U-100% 15N] HISTONE- REMARK 210 LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 MM BIS- REMARK 210 TRIS, 15.8 MM MES, 100 MM SODIUM CHLORIDE, 1 MM DTT, 3.5 % (3- REMARK 210 ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLIC ACID, REMARK 210 750 MM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 MM [U-100% 13C; REMARK 210 U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 REMARK 210 SPECIFIC, 9.3 MM BIS-TRIS, 15.8 MM MES, 100 MM SODIUM CHLORIDE, REMARK 210 1 MM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, REMARK 210 3.5 % ACRYLAMIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HCCH-TOCSY; 3D HNHA; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 3D REMARK 210 HNCO IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR_NIH_2.34, CYANA_2.1, REMARK 210 SPARKY, NMRPIPE, TOPSPIN, MOLMOL, REMARK 210 VNMRJ REMARK 210 METHOD USED : SIMULATED ANNEALING, SIMULATED REMARK 210 ANNEALING, SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H1 ASP A 500 H LYS A 501 1.27 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 519 95.19 -46.66 REMARK 500 1 GLU A 563 44.98 -77.82 REMARK 500 1 THR A 564 -179.06 -49.47 REMARK 500 1 SER A 565 -155.61 -165.70 REMARK 500 1 ASN B 877 38.57 -73.40 REMARK 500 1 SER B 892 48.49 -160.80 REMARK 500 1 ARG B 893 -86.55 -79.43 REMARK 500 1 SER B 899 70.25 55.18 REMARK 500 2 ASN A 540 -99.84 41.93 REMARK 500 2 THR A 541 75.65 -152.04 REMARK 500 2 TYR A 561 -18.97 -46.21 REMARK 500 2 SER A 565 173.26 52.04 REMARK 500 2 ASN B 877 38.30 -78.72 REMARK 500 2 SER B 892 -88.79 -47.69 REMARK 500 2 ARG B 893 70.18 48.48 REMARK 500 2 ALA B 894 57.03 -162.93 REMARK 500 2 ARG B 896 -130.12 -171.83 REMARK 500 2 ALA B 897 96.56 -160.32 REMARK 500 2 SER B 899 77.46 45.93 REMARK 500 3 GLU A 519 82.58 -54.70 REMARK 500 3 ASN A 540 -97.23 44.16 REMARK 500 3 THR A 541 76.89 -151.45 REMARK 500 3 SER A 565 -135.93 47.84 REMARK 500 3 ASN B 877 38.34 -78.21 REMARK 500 3 PRO B 891 167.51 -41.81 REMARK 500 3 SER B 892 -64.75 -160.10 REMARK 500 3 ALA B 894 107.27 54.48 REMARK 500 3 SER B 899 117.02 58.39 REMARK 500 4 HIS A 535 63.67 163.64 REMARK 500 4 ASN A 540 -98.18 42.25 REMARK 500 4 THR A 541 76.82 -151.76 REMARK 500 4 GLU A 563 78.38 -158.04 REMARK 500 4 SER A 565 -170.31 -68.93 REMARK 500 4 THR A 567 -74.64 60.71 REMARK 500 4 ASN B 877 38.85 -74.59 REMARK 500 4 ARG B 896 -170.30 -174.28 REMARK 500 4 ALA B 897 14.08 57.07 REMARK 500 4 ARG B 898 106.35 -47.86 REMARK 500 5 ASN A 540 -97.06 44.26 REMARK 500 5 THR A 541 77.30 -151.70 REMARK 500 5 TYR A 561 -16.05 -47.84 REMARK 500 5 GLU A 563 48.01 -88.44 REMARK 500 5 SER A 565 -151.12 -72.11 REMARK 500 5 ASN B 877 38.47 -73.16 REMARK 500 5 SER B 892 173.18 56.50 REMARK 500 5 ARG B 893 87.34 -171.30 REMARK 500 5 ALA B 894 95.74 53.18 REMARK 500 5 ALA B 897 99.06 49.98 REMARK 500 5 SER B 899 -71.15 -55.60 REMARK 500 6 GLU A 519 86.84 -50.16 REMARK 500 REMARK 500 THIS ENTRY HAS 105 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LM0 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF THE AF4-AF9 COMPLEX REMARK 900 RELATED ID: 19516 RELATED DB: BMRB DBREF 2MV7 A 500 568 UNP P42568 AF9_HUMAN 500 568 DBREF 2MV7 B 877 900 UNP Q8TEK3 DOT1L_HUMAN 877 900 SEQADV 2MV7 THR B 876 UNP Q8TEK3 EXPRESSION TAG SEQRES 1 A 69 ASP LYS ALA TYR LEU ASP GLU LEU VAL GLU LEU HIS ARG SEQRES 2 A 69 ARG LEU MET THR LEU ARG GLU ARG HIS ILE LEU GLN GLN SEQRES 3 A 69 ILE VAL ASN LEU ILE GLU GLU THR GLY HIS PHE HIS ILE SEQRES 4 A 69 THR ASN THR THR PHE ASP PHE ASP LEU CYS SER LEU ASP SEQRES 5 A 69 LYS THR THR VAL ARG LYS LEU GLN SER TYR LEU GLU THR SEQRES 6 A 69 SER GLY THR SER SEQRES 1 B 25 THR ASN LYS LEU PRO VAL SER ILE PRO LEU ALA SER VAL SEQRES 2 B 25 VAL LEU PRO SER ARG ALA GLU ARG ALA ARG SER THR HELIX 1 1 ASP A 500 LEU A 517 1 18 HELIX 2 2 GLU A 519 GLY A 534 1 16 HELIX 3 3 CYS A 548 LEU A 550 5 3 HELIX 4 4 ASP A 551 GLU A 563 1 13 SHEET 1 A 3 HIS A 537 THR A 539 0 SHEET 2 A 3 THR A 542 ASP A 546 -1 O ASP A 544 N HIS A 537 SHEET 3 A 3 PRO B 880 SER B 882 -1 O VAL B 881 N PHE A 545 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