HEADER DNA BINDING PROTEIN 01-AUG-22 8ALQ TITLE THE SOLUTION STRUCTURE OF THE TRIPLE MUTANT METHYL-CPG-BINDING DOMAIN TITLE 2 FROM MECP2 THAT BINDS TO ASYMMETRICALLY MODIFIED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MECP-2 PROTEIN,MECP2; COMPND 5 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: MECP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HMC-MC COMPLEX, GENE REGULATION, METHYL-CPG-BINDING DOMAIN (MBD) OF KEYWDS 2 MECP2, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR H.SINGH REVDAT 3 19-JUL-23 8ALQ 1 JRNL REVDAT 2 29-MAR-23 8ALQ 1 JRNL REVDAT 1 22-FEB-23 8ALQ 0 JRNL AUTH H.SINGH,C.K.DAS,B.C.BUCHMULLER,L.V.SCHAFER,D.SUMMERER, JRNL AUTH 2 R.LINSER JRNL TITL EPIGENETIC CPG DUPLEX MARKS PROBED BY AN EVOLVED DNA READER JRNL TITL 2 VIA A WELL-TEMPERED CONFORMATIONAL PLASTICITY. JRNL REF NUCLEIC ACIDS RES. V. 51 6495 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 36919612 JRNL DOI 10.1093/NAR/GKAD134 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.SINGH,C.K.DAS,B.C.BUCHMULLER,S.EPPMANN,L.V.SCHAFER, REMARK 1 AUTH 2 D.SUMMERER,R.LINSER REMARK 1 TITL EPIGENETIC CPG DUPLEX MARKS PROBED BY AN EVOLVED DNA READER REMARK 1 TITL 2 VIA A WELL-TEMPERED CONFORMATIONAL PLASTICITY REMARK 1 REF BIORXIV 2022 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2022.10.06.511192 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8ALQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1292124662. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 305 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-100% 13C; U-100% 15N] REMARK 210 METHYL-CPG-BINDING DOMAIN (MBD) REMARK 210 OF MECP2, 90% H2O/10% D2O; 0.6 REMARK 210 MM [U-100% 15N] METHYL-CPG- REMARK 210 BINDING DOMAIN (MBD) OF MECP2, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D CBCA(CO)NH; 3D HNCACB; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, CARA, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: 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 TYR A 9 -71.31 -142.34 REMARK 500 1 ASP A 10 -55.42 -147.93 REMARK 500 1 PRO A 66 20.53 -72.25 REMARK 500 1 THR A 72 -56.50 -165.48 REMARK 500 1 PRO A 79 40.44 -78.44 REMARK 500 1 GLN A 84 -73.46 67.51 REMARK 500 1 SER A 92 74.43 -166.22 REMARK 500 1 PRO A 93 36.67 -96.99 REMARK 500 1 LYS A 94 -80.92 -82.47 REMARK 500 2 LEU A 2 -78.81 -101.94 REMARK 500 2 TYR A 9 -64.12 -91.33 REMARK 500 2 PRO A 12 35.21 -77.96 REMARK 500 2 PRO A 66 4.33 -66.65 REMARK 500 2 THR A 72 -74.78 -167.52 REMARK 500 2 PRO A 79 40.90 -79.21 REMARK 500 2 LYS A 89 70.38 56.87 REMARK 500 2 SER A 92 72.01 -150.21 REMARK 500 2 PRO A 93 39.77 -88.17 REMARK 500 2 SER A 97 85.86 61.28 REMARK 500 3 LEU A 2 -41.61 -153.88 REMARK 500 3 TYR A 9 -64.59 -123.10 REMARK 500 3 ASP A 10 -72.33 -91.36 REMARK 500 3 PRO A 66 4.33 -64.50 REMARK 500 3 VAL A 73 -47.89 71.19 REMARK 500 3 PRO A 79 43.84 -77.58 REMARK 500 3 ARG A 82 71.70 -114.66 REMARK 500 3 HIS A 99 76.77 -104.22 REMARK 500 3 HIS A 100 -64.91 -144.73 REMARK 500 4 GLU A 3 109.34 -59.45 REMARK 500 4 ASP A 10 -175.91 61.48 REMARK 500 4 THR A 72 -105.01 -142.59 REMARK 500 4 ARG A 81 78.55 59.19 REMARK 500 4 GLU A 83 -68.47 -101.20 REMARK 500 4 GLN A 84 83.84 52.71 REMARK 500 5 LEU A 2 -166.17 65.59 REMARK 500 5 GLU A 3 -159.93 66.96 REMARK 500 5 ASP A 4 47.93 -80.47 REMARK 500 5 ASP A 10 20.29 -166.01 REMARK 500 5 PRO A 41 -8.76 -59.22 REMARK 500 5 THR A 72 -64.03 177.73 REMARK 500 5 ARG A 82 49.67 -163.43 REMARK 500 5 GLN A 84 44.51 -145.74 REMARK 500 5 LYS A 85 114.39 -167.59 REMARK 500 5 PRO A 93 69.85 -69.54 REMARK 500 5 LYS A 94 -77.10 -104.21 REMARK 500 5 HIS A 98 60.72 70.92 REMARK 500 6 ASP A 4 44.10 -82.00 REMARK 500 6 TYR A 9 -77.77 -137.93 REMARK 500 6 ASP A 10 -64.76 176.13 REMARK 500 6 PRO A 12 31.88 -91.35 REMARK 500 REMARK 500 THIS ENTRY HAS 82 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34745 RELATED DB: BMRB REMARK 900 THE SOLUTION STRUCTURE OF THE TRIPLE MUTANT METHYL-CPG-BINDING REMARK 900 DOMAIN FROM MECP2 THAT BINDS TO ASYMMETRICALLY MODIFIED DNA DBREF1 8ALQ A 3 95 UNP A0A8C5LDB3_JACJA DBREF2 8ALQ A A0A8C5LDB3 101 193 SEQADV 8ALQ SER A 1 UNP A0A8C5LDB EXPRESSION TAG SEQADV 8ALQ LEU A 2 UNP A0A8C5LDB EXPRESSION TAG SEQADV 8ALQ GLU A 3 UNP A0A8C5LDB ARG 101 CONFLICT SEQADV 8ALQ THR A 23 UNP A0A8C5LDB LYS 121 CONFLICT SEQADV 8ALQ ALA A 36 UNP A0A8C5LDB VAL 134 CONFLICT SEQADV 8ALQ ASN A 48 UNP A0A8C5LDB SER 146 CONFLICT SEQADV 8ALQ LYS A 85 UNP A0A8C5LDB ARG 183 CONFLICT SEQADV 8ALQ PRO A 87 UNP A0A8C5LDB ALA 185 CONFLICT SEQADV 8ALQ THR A 96 UNP A0A8C5LDB EXPRESSION TAG SEQADV 8ALQ SER A 97 UNP A0A8C5LDB EXPRESSION TAG SEQADV 8ALQ HIS A 98 UNP A0A8C5LDB EXPRESSION TAG SEQADV 8ALQ HIS A 99 UNP A0A8C5LDB EXPRESSION TAG SEQADV 8ALQ HIS A 100 UNP A0A8C5LDB EXPRESSION TAG SEQADV 8ALQ HIS A 101 UNP A0A8C5LDB EXPRESSION TAG SEQADV 8ALQ HIS A 102 UNP A0A8C5LDB EXPRESSION TAG SEQADV 8ALQ HIS A 103 UNP A0A8C5LDB EXPRESSION TAG SEQADV 8ALQ HIS A 104 UNP A0A8C5LDB EXPRESSION TAG SEQRES 1 A 104 SER LEU GLU ASP ARG GLY PRO MET TYR ASP ASP PRO THR SEQRES 2 A 104 LEU PRO GLU GLY TRP THR ARG LYS LEU THR GLN ARG LYS SEQRES 3 A 104 SER GLY ARG SER ALA GLY LYS TYR ASP ALA TYR LEU ILE SEQRES 4 A 104 ASN PRO GLN GLY LYS ALA PHE ARG ASN LYS VAL GLU LEU SEQRES 5 A 104 ILE ALA TYR PHE GLU LYS VAL GLY ASP THR SER LEU ASP SEQRES 6 A 104 PRO ASN ASP PHE ASP PHE THR VAL THR GLY ARG GLY SER SEQRES 7 A 104 PRO SER ARG ARG GLU GLN LYS PRO PRO LYS LYS PRO LYS SEQRES 8 A 104 SER PRO LYS ALA THR SER HIS HIS HIS HIS HIS HIS HIS HELIX 1 AA1 LYS A 49 GLY A 60 1 12 HELIX 2 AA2 ASP A 65 PHE A 69 5 5 SHEET 1 AA1 3 THR A 19 GLN A 24 0 SHEET 2 AA1 3 TYR A 34 ILE A 39 -1 O TYR A 37 N LYS A 21 SHEET 3 AA1 3 ALA A 45 PHE A 46 -1 O PHE A 46 N LEU A 38 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