PDB Short entry for 2KQS HEADER TRANSCRIPTION, APOPTOSIS 17-NOV-09 2KQS TITLE PHOSPHORYLATION OF SUMO-INTERACTING MOTIF BY CK2 ENHANCES DAXX SUMO TITLE 2 BINDING ACTIVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: SMALL UBIQUITIN-RELATED MODIFIER 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SUMO-1, SENTRIN, UBIQUITIN-LIKE PROTEIN SMT3C, SMT3 HOMOLOG COMPND 5 3, UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1, UBIQUITIN-LIKE PROTEIN COMPND 6 UBL1, GAP-MODIFYING PROTEIN 1, GMP1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DEATH DOMAIN-ASSOCIATED PROTEIN 6; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 721-741; COMPND 12 SYNONYM: DAXX, HDAXX, FAS DEATH DOMAIN-ASSOCIATED PROTEIN, ETS1- COMPND 13 ASSOCIATED PROTEIN 1, EAP1; COMPND 14 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: OK/SW-CL.43, SMT3C, SMT3H3, SUMO1, UBL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-4T1; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 16 OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN) KEYWDS SUMO, SIM, DAXX, NUCLEUS, PHOSPHOPROTEIN, UBL CONJUGATION PATHWAY, KEYWDS 2 APOPTOSIS, TRANSCRIPTION, TRANSCRIPTION REGULATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.T.NAIK,T.H.HUANG,H.SHIH REVDAT 2 21-AUG-13 2KQS 1 JRNL VERSN REVDAT 1 01-DEC-10 2KQS 0 JRNL AUTH C.C.CHANG,M.T.NAIK,Y.S.HUANG,J.C.JENG,P.H.LIAO,H.Y.KUO, JRNL AUTH 2 C.C.HO,Y.L.HSIEH,C.H.LIN,N.J.HUANG,N.M.NAIK,C.C.KUNG, JRNL AUTH 3 S.Y.LIN,R.H.CHEN,K.S.CHANG,T.H.HUANG,H.M.SHIH JRNL TITL STRUCTURAL AND FUNCTIONAL ROLES OF DAXX SIM PHOSPHORYLATION JRNL TITL 2 IN SUMO PARALOG-SELECTIVE BINDING AND APOPTOSIS MODULATION. JRNL REF MOL.CELL V. 42 62 2011 JRNL REFN ISSN 1097-2765 JRNL PMID 21474068 JRNL DOI 10.1016/J.MOLCEL.2011.02.022 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2, ARIA 2.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARREN (CNS), REMARK 3 LINGE, O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KQS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-NOV-09. REMARK 100 THE RCSB ID CODE IS RCSB101457. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 290 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.27-0.5MM [U-100% 15N] SUMO1-1, REMARK 210 0-1.7MM DAXX20-2, 10MM POTASSIUM REMARK 210 PHOSPHATE-3, 100MM POTASSIUM REMARK 210 CHLORIDE-4, 2MM DTT-5, 0.1MM EDTA REMARK 210 -6, 0.001% SODIUM AZIDE-7, 90% REMARK 210 H2O/10% D2O; 0.5 MM [U-100% 13C; REMARK 210 U-100% 15N] SUMO1-8, 2MM DAXX20- REMARK 210 9, 10MM POTASSIUM PHOSPHATE-10, REMARK 210 100MM POTASSIUM CHLORIDE-11, 2MM REMARK 210 DTT-12, 0.1MM EDTA-13, 0.001% REMARK 210 SODIUM AZIDE-14, 90% H2O/10% D2O; REMARK 210 2 MM SUMO1-15, 0.5MM [U-100% 13C; REMARK 210 U-100% 15N] DAXX20-16, 10MM REMARK 210 POTASSIUM PHOSPHATE-17, 100MM REMARK 210 POTASSIUM CHLORIDE-18, 2MM DTT- REMARK 210 19, 0.1MM EDTA-20, 0.001% SODIUM REMARK 210 AZIDE-21, 90% H2O/10% D2O; 0.5MM REMARK 210 [U-100% 13C; U-100% 15N] SUMO1- REMARK 210 22, 0.5MM [U-100% 13C; U-100% REMARK 210 15N] DAXX20-23, 10MM POTASSIUM REMARK 210 PHOSPHATE-24, 100MM POTASSIUM REMARK 210 CHLORIDE-25, 2MM DTT-26, 0.1MM REMARK 210 EDTA-27, 0.001% SODIUM AZIDE-28, REMARK 210 0.0066 W/V PF1 PHAGE-29, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D HNCO; 3D 1H-15N TOCSY; 3D REMARK 210 HCCH-COSY; 3D CCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 3D 1H REMARK 210 -15N NOESY - F1 FILTERED; 3D 1H- REMARK 210 13C NOESY - F1 FILTERED; 3D HNHA; REMARK 210 2D 1H-15N HSQC - IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.2, ARIA 2.2, TOPSPIN 2.1, REMARK 210 SPARKY 3.113 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLY B 719 REMARK 465 SER B 720 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 HZ1 LYS A 46 OE1 GLU A 49 1.59 REMARK 500 HZ2 LYS A 39 OD2 ASP B 740 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 7 TYR A 91 CE1 TYR A 91 CZ -0.082 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 GLN A 4 -91.92 -125.79 REMARK 500 1 ASP A 12 -59.70 -128.17 REMARK 500 1 LYS A 16 -95.39 -74.94 REMARK 500 1 LYS A 17 -94.60 -114.35 REMARK 500 1 SER A 31 -0.89 74.54 REMARK 500 1 PRO B 730 -149.17 -85.92 REMARK 500 2 GLN A 4 32.91 -99.41 REMARK 500 2 PRO A 8 37.48 -88.60 REMARK 500 2 LYS A 16 -80.54 -116.02 REMARK 500 2 LYS A 17 -93.48 -101.05 REMARK 500 2 GLU A 18 -172.54 -179.39 REMARK 500 2 GLN A 94 -159.03 -131.39 REMARK 500 3 SER A 2 -80.67 -84.30 REMARK 500 3 GLN A 4 -87.05 -113.25 REMARK 500 3 GLU A 5 -68.92 -110.00 REMARK 500 3 PRO A 8 31.31 -79.63 REMARK 500 3 ASP A 12 32.99 -93.84 REMARK 500 3 SER A 31 -15.22 68.53 REMARK 500 3 GLN A 94 -159.48 -140.67 REMARK 500 4 ASP A 3 -76.92 -129.42 REMARK 500 4 PRO A 8 43.54 -72.34 REMARK 500 4 GLU A 11 24.93 -76.48 REMARK 500 4 LYS A 17 -71.92 -96.43 REMARK 500 4 GLN A 94 -157.12 -132.69 REMARK 500 4 PRO B 730 -165.78 -61.03 REMARK 500 5 SER A 2 -95.09 -76.15 REMARK 500 5 PRO A 8 32.88 -81.81 REMARK 500 5 LYS A 17 -75.39 -87.12 REMARK 500 5 ARG A 70 109.18 -58.48 REMARK 500 5 PRO B 730 -159.82 -75.38 REMARK 500 6 LYS A 7 118.37 -38.06 REMARK 500 6 SER A 9 11.48 -140.41 REMARK 500 6 THR A 10 -68.61 -137.37 REMARK 500 6 LYS A 17 -62.74 -102.00 REMARK 500 6 SER A 31 -0.62 71.97 REMARK 500 6 GLN A 94 -169.23 -120.91 REMARK 500 7 PRO A 8 46.46 -73.38 REMARK 500 7 LYS A 17 -94.78 -102.14 REMARK 500 7 SER A 31 -5.87 72.53 REMARK 500 7 GLN A 94 -160.92 -114.12 REMARK 500 7 PRO B 730 -156.21 -78.24 REMARK 500 8 ASP A 3 -77.31 -111.28 REMARK 500 8 GLN A 4 -55.60 -125.88 REMARK 500 8 ASP A 12 32.43 -90.45 REMARK 500 8 LYS A 16 -82.94 -88.19 REMARK 500 8 SER A 31 -11.58 71.78 REMARK 500 9 THR A 10 -75.41 -80.55 REMARK 500 9 ASP A 15 -51.69 -125.92 REMARK 500 9 LYS A 17 -87.18 -90.57 REMARK 500 9 GLN A 94 -155.56 -163.50 REMARK 500 REMARK 500 THIS ENTRY HAS 113 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 19 TYR A 51 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ASQ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF COMPLEX BETWEEN SUMO-1 AND SIM FROM REMARK 900 PIASX REMARK 900 RELATED ID: 2RPQ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF COMPLEX BETWEEN SUMO-3 AND SIM FROM REMARK 900 MCAF1 REMARK 900 RELATED ID: 16611 RELATED DB: BMRB DBREF 2KQS A 1 97 UNP P63165 SUMO1_HUMAN 1 97 DBREF 2KQS B 721 740 UNP Q9UER7 DAXX_HUMAN 721 740 SEQADV 2KQS GLY A -1 UNP P63165 EXPRESSION TAG SEQADV 2KQS SER A 0 UNP P63165 EXPRESSION TAG SEQADV 2KQS GLY B 719 UNP Q9UER7 EXPRESSION TAG SEQADV 2KQS SER B 720 UNP Q9UER7 EXPRESSION TAG SEQRES 1 A 99 GLY SER MET SER ASP GLN GLU ALA LYS PRO SER THR GLU SEQRES 2 A 99 ASP LEU GLY ASP LYS LYS GLU GLY GLU TYR ILE LYS LEU SEQRES 3 A 99 LYS VAL ILE GLY GLN ASP SER SER GLU ILE HIS PHE LYS SEQRES 4 A 99 VAL LYS MET THR THR HIS LEU LYS LYS LEU LYS GLU SER SEQRES 5 A 99 TYR CYS GLN ARG GLN GLY VAL PRO MET ASN SER LEU ARG SEQRES 6 A 99 PHE LEU PHE GLU GLY GLN ARG ILE ALA ASP ASN HIS THR SEQRES 7 A 99 PRO LYS GLU LEU GLY MET GLU GLU GLU ASP VAL ILE GLU SEQRES 8 A 99 VAL TYR GLN GLU GLN THR GLY GLY SEQRES 1 B 22 GLY SER LYS THR SER VAL ALA THR GLN CYS ASP PRO GLU SEQRES 2 B 22 GLU ILE ILE VAL LEU SER ASP SER ASP HELIX 1 1 HIS A 43 GLY A 56 1 14 HELIX 2 2 THR A 76 GLY A 81 1 6 SHEET 1 A 5 GLU A 33 VAL A 38 0 SHEET 2 A 5 ILE A 22 ILE A 27 -1 N VAL A 26 O ILE A 34 SHEET 3 A 5 ASP A 86 GLN A 92 1 O ILE A 88 N LYS A 25 SHEET 4 A 5 LEU A 62 PHE A 66 -1 N ARG A 63 O TYR A 91 SHEET 5 A 5 GLN A 69 ARG A 70 -1 O GLN A 69 N PHE A 66 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