HEADER GENE REGULATION 23-NOV-21 7SXI TITLE SOLUTION STRUCTURE OF SDS3 CAPPED TUDOR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIN3 HISTONE DEACETYLASE COREPRESSOR COMPLEX COMPONENT COMPND 3 SDS3; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: SUPPRESSOR OF DEFECTIVE SILENCING 3 PROTEIN HOMOLOG; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SUDS3, SDS3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTIONAL COREPRESSOR, TUDOR DOMAIN, NUCLEIC ACID BINDING, G- KEYWDS 2 QUADRUPLEX BINDING, GENE REGULATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.D.MARCUM,I.RADHAKRISHNAN REVDAT 3 14-JUN-23 7SXI 1 REMARK REVDAT 2 09-FEB-22 7SXI 1 JRNL REVDAT 1 19-JAN-22 7SXI 0 JRNL AUTH R.D.MARCUM,J.HSIEH,M.GILJEN,E.JUSTICE,N.DAFFERN,Y.ZHANG, JRNL AUTH 2 I.RADHAKRISHNAN JRNL TITL A CAPPED TUDOR DOMAIN WITHIN A CORE SUBUNIT OF THE JRNL TITL 2 SIN3L/RPD3L HISTONE DEACETYLASE COMPLEX BINDS TO NUCLEIC JRNL TITL 3 ACID G-QUADRUPLEXES. JRNL REF J.BIOL.CHEM. V. 298 01558 2022 JRNL REFN ESSN 1083-351X JRNL PMID 34979096 JRNL DOI 10.1016/J.JBC.2021.101558 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7SXI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1000261277. 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 : 0.07 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.35 MM [U-100% 15N] SDS3 CTD, REMARK 210 90% H2O/10% D2O; 0.35 MM [U-100% REMARK 210 13C; U-100% 15N] SDS3 CTD, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 2D 1H-1H NOESY; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D HCCH- REMARK 210 COSY; 3D HCCH-TOCSY; 3D C(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DIRECT DRIVE REMARK 210 SPECTROMETER MANUFACTURER : AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, NMRFAM-SPARKY, CNS 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: 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 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 ASP A 259 24.22 49.94 REMARK 500 2 ASP A 265 86.31 46.53 REMARK 500 2 LYS A 266 -6.16 70.84 REMARK 500 2 ASN A 282 -18.24 77.22 REMARK 500 2 ASP A 304 -32.88 -130.65 REMARK 500 3 ARG A 325 78.00 -108.48 REMARK 500 4 LYS A 266 -5.86 68.44 REMARK 500 4 GLN A 283 -155.66 59.46 REMARK 500 5 ASN A 249 -45.16 71.21 REMARK 500 5 ASN A 295 -37.69 -140.02 REMARK 500 5 ARG A 325 88.47 -151.33 REMARK 500 6 ASN A 249 -68.69 -104.60 REMARK 500 6 ALA A 250 38.33 -169.44 REMARK 500 6 ASP A 265 70.75 49.72 REMARK 500 6 LYS A 284 79.93 -112.66 REMARK 500 6 ASN A 295 -11.50 -149.31 REMARK 500 7 ASP A 265 77.80 55.54 REMARK 500 7 LYS A 266 -0.57 63.27 REMARK 500 7 ASP A 281 64.49 -118.67 REMARK 500 7 ASN A 282 -62.62 72.25 REMARK 500 8 LYS A 284 105.78 -56.82 REMARK 500 9 ASN A 282 60.20 60.34 REMARK 500 10 GLN A 251 122.92 70.23 REMARK 500 10 ASN A 282 -23.76 75.85 REMARK 500 10 SER A 305 -3.51 72.60 REMARK 500 11 ALA A 250 -174.03 67.08 REMARK 500 11 ASP A 265 76.92 50.36 REMARK 500 11 SER A 272 3.03 -68.12 REMARK 500 12 ASN A 249 104.66 -176.73 REMARK 500 12 ALA A 250 83.85 49.93 REMARK 500 13 ASN A 295 11.80 -140.09 REMARK 500 14 ASN A 249 71.42 62.74 REMARK 500 14 ASP A 265 78.40 48.02 REMARK 500 14 LYS A 266 -0.46 65.51 REMARK 500 14 ARG A 325 132.91 -173.23 REMARK 500 16 ASP A 265 82.88 40.32 REMARK 500 16 LYS A 266 -6.17 74.60 REMARK 500 16 GLN A 283 -173.66 71.17 REMARK 500 17 ASN A 249 -58.32 69.74 REMARK 500 18 ASN A 282 89.65 64.01 REMARK 500 18 GLN A 283 127.10 -176.28 REMARK 500 19 SER A 272 0.87 -69.31 REMARK 500 20 ASN A 249 97.38 64.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30969 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF SDS3 CAPPED TUDOR DOMAIN DBREF 7SXI A 250 326 UNP Q8BR65 SDS3_MOUSE 250 326 SEQADV 7SXI SER A 248 UNP Q8BR65 EXPRESSION TAG SEQADV 7SXI ASN A 249 UNP Q8BR65 EXPRESSION TAG SEQRES 1 A 79 SER ASN ALA GLN ARG PHE GLU ALA ARG ILE GLU ASP GLY SEQRES 2 A 79 LYS LEU TYR TYR ASP LYS ARG TRP TYR HIS LYS SER GLN SEQRES 3 A 79 ALA ILE TYR LEU GLU SER LYS ASP ASN GLN LYS LEU SER SEQRES 4 A 79 CYS VAL ILE SER SER VAL GLY ALA ASN GLU ILE TRP VAL SEQRES 5 A 79 ARG LYS THR SER ASP SER THR LYS MET ARG ILE TYR VAL SEQRES 6 A 79 GLY GLN LEU GLN ARG GLY LEU PHE VAL ILE ARG ARG ARG SEQRES 7 A 79 SER HELIX 1 AA1 VAL A 312 GLY A 318 1 7 SHEET 1 AA1 3 ALA A 255 GLU A 258 0 SHEET 2 AA1 3 LYS A 261 TYR A 264 -1 O TYR A 263 N ARG A 256 SHEET 3 AA1 3 ARG A 267 TYR A 269 -1 O TYR A 269 N LEU A 262 SHEET 1 AA2 5 LYS A 307 TYR A 311 0 SHEET 2 AA2 5 GLU A 296 LYS A 301 -1 N VAL A 299 O MET A 308 SHEET 3 AA2 5 LEU A 285 VAL A 292 -1 N SER A 290 O TRP A 298 SHEET 4 AA2 5 ALA A 274 GLU A 278 -1 N ILE A 275 O CYS A 287 SHEET 5 AA2 5 VAL A 321 ARG A 325 -1 O ARG A 323 N TYR A 276 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