HEADER TRANSCRIPTION 03-OCT-17 5YI9 TITLE SOLUTION STRUCTURE OF THE LEDGF/P75 IBD - JPO2 (AA 56-91) COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PC4 AND SFRS1-INTERACTING PROTEIN,CELL DIVISION CYCLE- COMPND 3 ASSOCIATED 7-LIKE PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 345-442,UNP RESIDUES 345-442; COMPND 6 SYNONYM: CLL-ASSOCIATED ANTIGEN KW-7,DENSE FINE SPECKLES 70 KDA COMPND 7 PROTEIN,DFS 70,LENS EPITHELIUM-DERIVED GROWTH FACTOR,TRANSCRIPTIONAL COMPND 8 COACTIVATOR P75/P52,PROTEIN JPO2,TRANSCRIPTION FACTOR RAM2; COMPND 9 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: PSIP1, DFS70, LEDGF, PSIP2, CDCA7L, HR1, JPO2, R1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-PROTEIN COMPLEX, EPIGENETICS, LEUKEMIA, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 40 AUTHOR V.VEVERKA REVDAT 2 14-JUN-23 5YI9 1 REMARK REVDAT 1 15-AUG-18 5YI9 0 JRNL AUTH S.SHARMA,K.CERMAKOVA,J.DE RIJCK,J.DEMEULEMEESTER,M.FABRY, JRNL AUTH 2 S.EL ASHKAR,S.VAN BELLE,M.LEPSIK,P.TESINA,V.DUCHOSLAV, JRNL AUTH 3 P.NOVAK,M.HUBALEK,P.SRB,F.CHRIST,P.REZACOVA,H.C.HODGES, JRNL AUTH 4 Z.DEBYSER,V.VEVERKA JRNL TITL AFFINITY SWITCHING OF THE LEDGF/P75 IBD INTERACTOME IS JRNL TITL 2 GOVERNED BY KINASE-DEPENDENT PHOSPHORYLATION. JRNL REF PROC. NATL. ACAD. SCI. V. 115 E7053 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 29997176 JRNL DOI 10.1073/PNAS.1803909115 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : YASARA, CYANA REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5YI9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005255. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 200 REMARK 210 PRESSURE : ARBITRARY PA REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-13C; U-15N] LEDGF/P75 REMARK 210 IBD- JPO2 M2, 50 MM TRIS, 150 MM REMARK 210 SODIUM CHLORIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D HNCO; 3D HCCH REMARK 210 -TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 40 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 9 ARG A 351 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 372 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 351 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A 404 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 18 ARG A 459 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 19 ARG A 404 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 26 ARG A 351 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 26 ARG A 471 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 31 ARG A 404 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 33 ARG A 471 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 39 ARG A 404 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 39 ARG A 471 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 TRP A 344 -86.11 -87.70 REMARK 500 1 LEU A 363 44.03 -101.48 REMARK 500 1 ASN A 367 74.44 -153.19 REMARK 500 1 PHE A 406 91.27 -68.39 REMARK 500 1 VAL A 429 61.02 29.67 REMARK 500 1 SER A 434 32.87 -149.50 REMARK 500 1 ARG A 459 36.58 -147.08 REMARK 500 2 TRP A 344 166.07 63.55 REMARK 500 2 ASN A 367 77.29 -154.85 REMARK 500 2 HIS A 393 42.58 -84.07 REMARK 500 2 PHE A 406 95.65 -58.27 REMARK 500 2 VAL A 429 74.73 22.82 REMARK 500 2 GLU A 431 -44.60 68.79 REMARK 500 3 TRP A 344 -51.43 -144.23 REMARK 500 3 ASN A 367 58.93 -148.00 REMARK 500 3 HIS A 393 43.88 -88.58 REMARK 500 3 THR A 437 -25.36 60.22 REMARK 500 4 ASN A 367 66.89 -152.09 REMARK 500 4 HIS A 393 42.64 -90.21 REMARK 500 4 SER A 434 52.41 -149.84 REMARK 500 4 VAL A 439 119.49 71.04 REMARK 500 4 LEU A 440 -111.38 37.91 REMARK 500 5 HIS A 393 41.14 -92.80 REMARK 500 5 PHE A 406 90.85 -69.69 REMARK 500 5 LEU A 440 12.01 45.36 REMARK 500 5 ASN A 441 47.37 -84.80 REMARK 500 5 GLU A 475 52.85 38.11 REMARK 500 6 ASN A 367 74.35 -153.83 REMARK 500 6 HIS A 393 42.28 -92.77 REMARK 500 6 PHE A 406 97.09 -57.62 REMARK 500 6 GLU A 431 -168.91 61.38 REMARK 500 6 HIS A 461 -173.09 65.86 REMARK 500 7 ALA A 341 170.30 60.66 REMARK 500 7 ASN A 367 73.76 -155.57 REMARK 500 7 HIS A 393 43.51 -89.46 REMARK 500 7 PHE A 406 96.50 -69.04 REMARK 500 7 GLN A 456 -158.82 67.25 REMARK 500 7 ASP A 476 -40.94 -172.93 REMARK 500 7 SER A 490 -0.16 69.64 REMARK 500 8 SER A 343 16.86 -148.90 REMARK 500 8 ASN A 367 77.97 -153.82 REMARK 500 8 ARG A 459 39.14 -149.50 REMARK 500 8 ASP A 476 -43.65 -161.06 REMARK 500 8 SER A 479 -6.94 -58.64 REMARK 500 9 ASN A 367 72.11 -155.26 REMARK 500 9 HIS A 393 42.34 -82.37 REMARK 500 9 VAL A 429 54.05 32.49 REMARK 500 9 SER A 434 55.71 -155.05 REMARK 500 9 THR A 437 -126.96 55.93 REMARK 500 9 VAL A 439 78.55 42.98 REMARK 500 REMARK 500 THIS ENTRY HAS 291 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36120 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE LEDGF/P75 IBD - JPO2 (AA 56-91) COMPLEX DBREF 5YI9 A 345 442 UNP O75475 PSIP1_HUMAN 345 442 DBREF 5YI9 A 456 491 UNP Q96GN5 CDA7L_HUMAN 56 91 SEQADV 5YI9 SER A 339 UNP O75475 EXPRESSION TAG SEQADV 5YI9 ASN A 340 UNP O75475 EXPRESSION TAG SEQADV 5YI9 ALA A 341 UNP O75475 EXPRESSION TAG SEQADV 5YI9 ALA A 342 UNP O75475 EXPRESSION TAG SEQADV 5YI9 SER A 343 UNP O75475 EXPRESSION TAG SEQADV 5YI9 TRP A 344 UNP O75475 EXPRESSION TAG SEQRES 1 A 140 SER ASN ALA ALA SER TRP GLU THR SER MET ASP SER ARG SEQRES 2 A 140 LEU GLN ARG ILE HIS ALA GLU ILE LYS ASN SER LEU LYS SEQRES 3 A 140 ILE ASP ASN LEU ASP VAL ASN ARG CYS ILE GLU ALA LEU SEQRES 4 A 140 ASP GLU LEU ALA SER LEU GLN VAL THR MET GLN GLN ALA SEQRES 5 A 140 GLN LYS HIS THR GLU MET ILE THR THR LEU LYS LYS ILE SEQRES 6 A 140 ARG ARG PHE LYS VAL SER GLN VAL ILE MET GLU LYS SER SEQRES 7 A 140 THR MET LEU TYR ASN LYS PHE LYS ASN MET PHE LEU VAL SEQRES 8 A 140 GLY GLU GLY ASP SER VAL ILE THR GLN VAL LEU ASN LYS SEQRES 9 A 140 GLN ASP VAL ARG PHE HIS SER LYS TYR PHE THR GLU GLU SEQRES 10 A 140 LEU ARG ARG ILE PHE ILE GLU ASP THR ASP SER GLU THR SEQRES 11 A 140 GLU ASP PHE ALA GLY PHE THR GLN SER ASP HELIX 1 AA1 THR A 346 SER A 362 1 17 HELIX 2 AA2 ASP A 369 GLN A 384 1 16 HELIX 3 AA3 THR A 386 GLN A 391 1 6 HELIX 4 AA4 HIS A 393 ARG A 404 1 12 HELIX 5 AA5 SER A 409 VAL A 429 1 21 HELIX 6 AA6 THR A 466 ILE A 474 1 9 HELIX 7 AA7 THR A 477 GLU A 482 5 6 SHEET 1 AA1 2 LEU A 363 LYS A 364 0 SHEET 2 AA1 2 ASN A 367 LEU A 368 -1 O ASN A 367 N LYS A 364 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