HEADER DNA BINDING PROTEIN 17-OCT-24 9E09 TITLE CRYO-EM STRUCTURE A SINGLE NUCLEOSOME (2) FOCUS OF HUMAN DNMT3A2- TITLE 2 DNMT3B3 COMPLEX BOUND TO DI-NUCLEOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3.2; COMPND 3 CHAIN: M, Q; COMPND 4 SYNONYM: H3-CLUSTERED HISTONE 13,H3-CLUSTERED HISTONE 14,H3-CLUSTERED COMPND 5 HISTONE 15,HISTONE H3/M,HISTONE H3/O; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HISTONE H4; COMPND 9 CHAIN: N, R; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HISTONE H2A; COMPND 13 CHAIN: O, S; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: HISTONE H2B; COMPND 17 CHAIN: P, T; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 5; COMPND 20 MOLECULE: DNA (156-MER); COMPND 21 CHAIN: I; COMPND 22 ENGINEERED: YES; COMPND 23 MOL_ID: 6; COMPND 24 MOLECULE: DNA (156-MER); COMPND 25 CHAIN: J; COMPND 26 ENGINEERED: YES; COMPND 27 MOL_ID: 7; COMPND 28 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 3B; COMPND 29 CHAIN: X; COMPND 30 SYNONYM: DNMT3B,DNA METHYLTRANSFERASE HSAIIIB,DNA MTASE HSAIIIB, COMPND 31 M.HSAIIIB; COMPND 32 EC: 2.1.1.37; COMPND 33 ENGINEERED: YES; COMPND 34 MOL_ID: 8; COMPND 35 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 3B; COMPND 36 CHAIN: V; COMPND 37 SYNONYM: DNMT3B,DNA METHYLTRANSFERASE HSAIIIB,DNA MTASE HSAIIIB, COMPND 38 M.HSAIIIB; COMPND 39 EC: 2.1.1.37; COMPND 40 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: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, SOURCE 13 H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, SOURCE 14 H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, SOURCE 15 H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, SOURCE 16 H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_TAXID: 9606; SOURCE 22 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 24 MOL_ID: 4; SOURCE 25 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 26 ORGANISM_TAXID: 9606; SOURCE 27 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 29 MOL_ID: 5; SOURCE 30 SYNTHETIC: YES; SOURCE 31 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 32 ORGANISM_TAXID: 9606; SOURCE 33 MOL_ID: 6; SOURCE 34 SYNTHETIC: YES; SOURCE 35 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 36 ORGANISM_TAXID: 9606; SOURCE 37 MOL_ID: 7; SOURCE 38 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 39 ORGANISM_COMMON: HUMAN; SOURCE 40 ORGANISM_TAXID: 9606; SOURCE 41 GENE: DNMT3B; SOURCE 42 EXPRESSION_SYSTEM: SPODOPTERA; SOURCE 43 EXPRESSION_SYSTEM_TAXID: 7106; SOURCE 44 MOL_ID: 8; SOURCE 45 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 46 ORGANISM_COMMON: HUMAN; SOURCE 47 ORGANISM_TAXID: 9606; SOURCE 48 GENE: DNMT3B; SOURCE 49 EXPRESSION_SYSTEM: SPODOPTERA; SOURCE 50 EXPRESSION_SYSTEM_TAXID: 7106 KEYWDS DNMT3A2, DNMT3B3, DNA METHYLATION, DI-NUCLEOSOME, DNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR X.XIE,X.E.ZHOU,E.J.WORDEN,P.A.JONES REVDAT 1 18-FEB-26 9E09 0 JRNL AUTH X.XIE,M.LIU,X.E.ZHOU,E.J.WORDEN,P.A.JONES JRNL TITL THE STRUCTURE BASIS FOR DE NOVO DNA METHYLATION IN CHROMATIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.720 REMARK 3 NUMBER OF PARTICLES : 211221 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9E09 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1000289211. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : DNMT3A/3B TETRAMER BOUND TO DI REMARK 245 -NUCLEOSOME REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.80 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1100.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6100.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: 12-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 12-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: M, N, O, P, Q, R, S, T, I, J, REMARK 350 AND CHAINS: X, V 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA M 1 REMARK 465 ARG M 2 REMARK 465 THR M 3 REMARK 465 LYS M 4 REMARK 465 GLN M 5 REMARK 465 THR M 6 REMARK 465 ALA M 7 REMARK 465 ARG M 8 REMARK 465 LYS M 9 REMARK 465 SER M 10 REMARK 465 THR M 11 REMARK 465 GLY M 12 REMARK 465 GLY M 13 REMARK 465 LYS M 14 REMARK 465 ALA M 15 REMARK 465 PRO M 16 REMARK 465 ARG M 17 REMARK 465 LYS M 18 REMARK 465 GLN M 19 REMARK 465 LEU M 20 REMARK 465 ALA M 21 REMARK 465 THR M 22 REMARK 465 LYS M 23 REMARK 465 ALA M 24 REMARK 465 ALA M 25 REMARK 465 ARG M 26 REMARK 465 LYS M 27 REMARK 465 SER M 28 REMARK 465 ALA M 29 REMARK 465 PRO M 30 REMARK 465 ALA M 31 REMARK 465 THR M 32 REMARK 465 GLY M 33 REMARK 465 GLY M 34 REMARK 465 VAL M 35 REMARK 465 ALA M 135 REMARK 465 MET N 0 REMARK 465 SER N 1 REMARK 465 GLY N 2 REMARK 465 ARG N 3 REMARK 465 GLY N 4 REMARK 465 LYS N 5 REMARK 465 GLY N 6 REMARK 465 GLY N 7 REMARK 465 LYS N 8 REMARK 465 GLY N 9 REMARK 465 LEU N 10 REMARK 465 GLY N 11 REMARK 465 LYS N 12 REMARK 465 GLY N 13 REMARK 465 GLY N 14 REMARK 465 ALA N 15 REMARK 465 LYS N 16 REMARK 465 ARG N 17 REMARK 465 HIS N 18 REMARK 465 ARG N 19 REMARK 465 LYS N 20 REMARK 465 VAL N 21 REMARK 465 LEU N 22 REMARK 465 ARG N 23 REMARK 465 GLY N 102 REMARK 465 SER O 1 REMARK 465 GLY O 2 REMARK 465 ARG O 3 REMARK 465 GLY O 4 REMARK 465 LYS O 5 REMARK 465 GLN O 6 REMARK 465 GLY O 7 REMARK 465 GLY O 8 REMARK 465 LYS O 9 REMARK 465 THR O 10 REMARK 465 ARG O 11 REMARK 465 ALA O 12 REMARK 465 LYS O 13 REMARK 465 GLN O 112 REMARK 465 SER O 113 REMARK 465 VAL O 114 REMARK 465 LEU O 115 REMARK 465 LEU O 116 REMARK 465 PRO O 117 REMARK 465 LYS O 118 REMARK 465 LYS O 119 REMARK 465 THR O 120 REMARK 465 GLU O 121 REMARK 465 SER O 122 REMARK 465 SER O 123 REMARK 465 LYS O 124 REMARK 465 SER O 125 REMARK 465 ALA O 126 REMARK 465 LYS O 127 REMARK 465 SER O 128 REMARK 465 LYS O 129 REMARK 465 MET P 0 REMARK 465 ALA P 1 REMARK 465 LYS P 2 REMARK 465 SER P 3 REMARK 465 ALA P 4 REMARK 465 PRO P 5 REMARK 465 ALA P 6 REMARK 465 PRO P 7 REMARK 465 LYS P 8 REMARK 465 LYS P 9 REMARK 465 GLY P 10 REMARK 465 SER P 11 REMARK 465 LYS P 12 REMARK 465 LYS P 13 REMARK 465 ALA P 14 REMARK 465 VAL P 15 REMARK 465 THR P 16 REMARK 465 LYS P 17 REMARK 465 THR P 18 REMARK 465 GLN P 19 REMARK 465 LYS P 20 REMARK 465 LYS P 21 REMARK 465 ASP P 22 REMARK 465 GLY P 23 REMARK 465 LYS P 24 REMARK 465 LYS P 25 REMARK 465 ARG P 26 REMARK 465 ARG P 27 REMARK 465 LYS P 28 REMARK 465 THR P 29 REMARK 465 ARG P 30 REMARK 465 LYS P 122 REMARK 465 ALA Q 1 REMARK 465 ARG Q 2 REMARK 465 THR Q 3 REMARK 465 LYS Q 4 REMARK 465 GLN Q 5 REMARK 465 THR Q 6 REMARK 465 ALA Q 7 REMARK 465 ARG Q 8 REMARK 465 LYS Q 9 REMARK 465 SER Q 10 REMARK 465 THR Q 11 REMARK 465 GLY Q 12 REMARK 465 GLY Q 13 REMARK 465 LYS Q 14 REMARK 465 ALA Q 15 REMARK 465 PRO Q 16 REMARK 465 ARG Q 17 REMARK 465 LYS Q 18 REMARK 465 GLN Q 19 REMARK 465 LEU Q 20 REMARK 465 ALA Q 21 REMARK 465 THR Q 22 REMARK 465 LYS Q 23 REMARK 465 ALA Q 24 REMARK 465 ALA Q 25 REMARK 465 ARG Q 26 REMARK 465 LYS Q 27 REMARK 465 SER Q 28 REMARK 465 ALA Q 29 REMARK 465 PRO Q 30 REMARK 465 ALA Q 31 REMARK 465 THR Q 32 REMARK 465 GLY Q 33 REMARK 465 GLY Q 34 REMARK 465 VAL Q 35 REMARK 465 LYS Q 36 REMARK 465 LYS Q 37 REMARK 465 PRO Q 38 REMARK 465 HIS Q 39 REMARK 465 ALA Q 135 REMARK 465 MET R 0 REMARK 465 SER R 1 REMARK 465 GLY R 2 REMARK 465 ARG R 3 REMARK 465 GLY R 4 REMARK 465 LYS R 5 REMARK 465 GLY R 6 REMARK 465 GLY R 7 REMARK 465 LYS R 8 REMARK 465 GLY R 9 REMARK 465 LEU R 10 REMARK 465 GLY R 11 REMARK 465 LYS R 12 REMARK 465 GLY R 13 REMARK 465 GLY R 14 REMARK 465 ALA R 15 REMARK 465 LYS R 16 REMARK 465 ARG R 17 REMARK 465 HIS R 18 REMARK 465 ARG R 19 REMARK 465 LYS R 20 REMARK 465 VAL R 21 REMARK 465 LEU R 22 REMARK 465 ARG R 23 REMARK 465 GLY R 102 REMARK 465 SER S 1 REMARK 465 GLY S 2 REMARK 465 ARG S 3 REMARK 465 GLY S 4 REMARK 465 LYS S 5 REMARK 465 GLN S 6 REMARK 465 GLY S 7 REMARK 465 GLY S 8 REMARK 465 LYS S 9 REMARK 465 THR S 10 REMARK 465 ARG S 11 REMARK 465 ALA S 12 REMARK 465 LYS S 13 REMARK 465 GLN S 112 REMARK 465 SER S 113 REMARK 465 VAL S 114 REMARK 465 LEU S 115 REMARK 465 LEU S 116 REMARK 465 PRO S 117 REMARK 465 LYS S 118 REMARK 465 LYS S 119 REMARK 465 THR S 120 REMARK 465 GLU S 121 REMARK 465 SER S 122 REMARK 465 SER S 123 REMARK 465 LYS S 124 REMARK 465 SER S 125 REMARK 465 ALA S 126 REMARK 465 LYS S 127 REMARK 465 SER S 128 REMARK 465 LYS S 129 REMARK 465 MET T 0 REMARK 465 ALA T 1 REMARK 465 LYS T 2 REMARK 465 SER T 3 REMARK 465 ALA T 4 REMARK 465 PRO T 5 REMARK 465 ALA T 6 REMARK 465 PRO T 7 REMARK 465 LYS T 8 REMARK 465 LYS T 9 REMARK 465 GLY T 10 REMARK 465 SER T 11 REMARK 465 LYS T 12 REMARK 465 LYS T 13 REMARK 465 ALA T 14 REMARK 465 VAL T 15 REMARK 465 THR T 16 REMARK 465 LYS T 17 REMARK 465 THR T 18 REMARK 465 GLN T 19 REMARK 465 LYS T 20 REMARK 465 LYS T 21 REMARK 465 ASP T 22 REMARK 465 GLY T 23 REMARK 465 LYS T 24 REMARK 465 LYS T 25 REMARK 465 ARG T 26 REMARK 465 ARG T 27 REMARK 465 LYS T 28 REMARK 465 THR T 29 REMARK 465 LYS T 122 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN S 73 CG OD1 ND2 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 DT I 9 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG I 155 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG J 4 O4' - C1' - N9 ANGL. DEV. = 1.9 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 ARG O 99 54.54 -91.65 REMARK 500 PRO O 109 80.79 -68.49 REMARK 500 THR T 49 -61.32 -101.01 REMARK 500 MET V 738 57.19 -94.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-47344 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-47349 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-47353 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE A SINGLE NUCLEOSOME (2) FOCUS OF HUMAN DNMT3A2- REMARK 900 DNMT3B3 COMPLEX BOUND TO DI-NUCLEOSOME DBREF 9E09 M 1 135 UNP Q71DI3 H32_HUMAN 2 136 DBREF 9E09 N 0 102 UNP P62805 H4_HUMAN 1 103 DBREF 9E09 O 1 129 PDB 9E09 9E09 1 129 DBREF 9E09 P 0 122 PDB 9E09 9E09 0 122 DBREF 9E09 Q 1 135 UNP Q71DI3 H32_HUMAN 2 136 DBREF 9E09 R 0 102 UNP P62805 H4_HUMAN 1 103 DBREF 9E09 S 1 129 PDB 9E09 9E09 1 129 DBREF 9E09 T 0 122 PDB 9E09 9E09 0 122 DBREF 9E09 I 2 157 PDB 9E09 9E09 2 157 DBREF 9E09 J 1 156 PDB 9E09 9E09 1 156 DBREF 9E09 X 736 747 UNP Q9UBC3 DNM3B_HUMAN 819 830 DBREF 9E09 V 736 746 UNP Q9UBC3 DNM3B_HUMAN 819 829 SEQADV 9E09 ALA M 102 UNP Q71DI3 GLY 103 CONFLICT SEQADV 9E09 ALA Q 102 UNP Q71DI3 GLY 103 CONFLICT SEQADV 9E09 ALA X 739 UNP Q9UBC3 GLY 822 CONFLICT SEQADV 9E09 ALA V 739 UNP Q9UBC3 GLY 822 CONFLICT SEQRES 1 M 135 ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 M 135 LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA ARG SEQRES 3 M 135 LYS SER ALA PRO ALA THR GLY GLY VAL LYS LYS PRO HIS SEQRES 4 M 135 ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU ILE ARG SEQRES 5 M 135 ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG LYS LEU SEQRES 6 M 135 PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN ASP PHE SEQRES 7 M 135 LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL MET ALA SEQRES 8 M 135 LEU GLN GLU ALA SER GLU ALA TYR LEU VAL ALA LEU PHE SEQRES 9 M 135 GLU ASP THR ASN LEU CYS ALA ILE HIS ALA LYS ARG VAL SEQRES 10 M 135 THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG ARG ILE SEQRES 11 M 135 ARG GLY GLU ARG ALA SEQRES 1 N 103 MET SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS SEQRES 2 N 103 GLY GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN SEQRES 3 N 103 ILE GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA SEQRES 4 N 103 ARG ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR SEQRES 5 N 103 GLU GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN SEQRES 6 N 103 VAL ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS SEQRES 7 N 103 ARG LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU SEQRES 8 N 103 LYS ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 O 129 SER GLY ARG GLY LYS GLN GLY GLY LYS THR ARG ALA LYS SEQRES 2 O 129 ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE PRO SEQRES 3 O 129 VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN TYR SEQRES 4 O 129 ALA GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU ALA SEQRES 5 O 129 ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU LEU SEQRES 6 O 129 ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG ILE SEQRES 7 O 129 ILE PRO ARG HIS LEU GLN LEU ALA VAL ARG ASN ASP GLU SEQRES 8 O 129 GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA GLN SEQRES 9 O 129 GLY GLY VAL LEU PRO ASN ILE GLN SER VAL LEU LEU PRO SEQRES 10 O 129 LYS LYS THR GLU SER SER LYS SER ALA LYS SER LYS SEQRES 1 P 123 MET ALA LYS SER ALA PRO ALA PRO LYS LYS GLY SER LYS SEQRES 2 P 123 LYS ALA VAL THR LYS THR GLN LYS LYS ASP GLY LYS LYS SEQRES 3 P 123 ARG ARG LYS THR ARG LYS GLU SER TYR ALA ILE TYR VAL SEQRES 4 P 123 TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP THR GLY ILE SEQRES 5 P 123 SER SER LYS ALA MET SER ILE MET ASN SER PHE VAL ASN SEQRES 6 P 123 ASP VAL PHE GLU ARG ILE ALA GLY GLU ALA SER ARG LEU SEQRES 7 P 123 ALA HIS TYR ASN LYS ARG SER THR ILE THR SER ARG GLU SEQRES 8 P 123 ILE GLN THR ALA VAL ARG LEU LEU LEU PRO GLY GLU LEU SEQRES 9 P 123 ALA LYS HIS ALA VAL SER GLU GLY THR LYS ALA VAL THR SEQRES 10 P 123 LYS TYR THR SER ALA LYS SEQRES 1 Q 135 ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 Q 135 LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA ARG SEQRES 3 Q 135 LYS SER ALA PRO ALA THR GLY GLY VAL LYS LYS PRO HIS SEQRES 4 Q 135 ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU ILE ARG SEQRES 5 Q 135 ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG LYS LEU SEQRES 6 Q 135 PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN ASP PHE SEQRES 7 Q 135 LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL MET ALA SEQRES 8 Q 135 LEU GLN GLU ALA SER GLU ALA TYR LEU VAL ALA LEU PHE SEQRES 9 Q 135 GLU ASP THR ASN LEU CYS ALA ILE HIS ALA LYS ARG VAL SEQRES 10 Q 135 THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG ARG ILE SEQRES 11 Q 135 ARG GLY GLU ARG ALA SEQRES 1 R 103 MET SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS SEQRES 2 R 103 GLY GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN SEQRES 3 R 103 ILE GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA SEQRES 4 R 103 ARG ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR SEQRES 5 R 103 GLU GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN SEQRES 6 R 103 VAL ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS SEQRES 7 R 103 ARG LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU SEQRES 8 R 103 LYS ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 S 129 SER GLY ARG GLY LYS GLN GLY GLY LYS THR ARG ALA LYS SEQRES 2 S 129 ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE PRO SEQRES 3 S 129 VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN TYR SEQRES 4 S 129 ALA GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU ALA SEQRES 5 S 129 ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU LEU SEQRES 6 S 129 ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG ILE SEQRES 7 S 129 ILE PRO ARG HIS LEU GLN LEU ALA VAL ARG ASN ASP GLU SEQRES 8 S 129 GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA GLN SEQRES 9 S 129 GLY GLY VAL LEU PRO ASN ILE GLN SER VAL LEU LEU PRO SEQRES 10 S 129 LYS LYS THR GLU SER SER LYS SER ALA LYS SER LYS SEQRES 1 T 123 MET ALA LYS SER ALA PRO ALA PRO LYS LYS GLY SER LYS SEQRES 2 T 123 LYS ALA VAL THR LYS THR GLN LYS LYS ASP GLY LYS LYS SEQRES 3 T 123 ARG ARG LYS THR ARG LYS GLU SER TYR ALA ILE TYR VAL SEQRES 4 T 123 TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP THR GLY ILE SEQRES 5 T 123 SER SER LYS ALA MET SER ILE MET ASN SER PHE VAL ASN SEQRES 6 T 123 ASP VAL PHE GLU ARG ILE ALA GLY GLU ALA SER ARG LEU SEQRES 7 T 123 ALA HIS TYR ASN LYS ARG SER THR ILE THR SER ARG GLU SEQRES 8 T 123 ILE GLN THR ALA VAL ARG LEU LEU LEU PRO GLY GLU LEU SEQRES 9 T 123 ALA LYS HIS ALA VAL SER GLU GLY THR LYS ALA VAL THR SEQRES 10 T 123 LYS TYR THR SER ALA LYS SEQRES 1 I 156 DC DA DG DG DA DT DG DT DA DT DA DT DA SEQRES 2 I 156 DT DC DT DG DA DC DA DC DG DT DG DC DC SEQRES 3 I 156 DT DG DG DA DG DA DC DT DA DG DG DG DA SEQRES 4 I 156 DG DT DA DA DT DC DC DC DC DT DT DG DG SEQRES 5 I 156 DC DG DG DT DT DA DA DA DA DC DG DC DG SEQRES 6 I 156 DG DG DG DG DA DC DA DG DC DG DC DG DT SEQRES 7 I 156 DA DC DG DT DG DC DG DT DT DT DA DA DG SEQRES 8 I 156 DC DG DG DT DG DC DT DA DG DA DG DC DT SEQRES 9 I 156 DG DT DC DT DA DC DG DA DC DC DA DA DT SEQRES 10 I 156 DT DG DA DG DC DG DG DC DC DT DC DG DG SEQRES 11 I 156 DC DA DC DC DG DG DG DA DT DT DC DT DC SEQRES 12 I 156 DC DA DG DG DG DC DG DG DC DC DG DA DT SEQRES 1 J 156 DA DT DC DG DG DC DC DG DC DC DC DT DG SEQRES 2 J 156 DG DA DG DA DA DT DC DC DC DG DG DT DG SEQRES 3 J 156 DC DC DG DA DG DG DC DC DG DC DT DC DA SEQRES 4 J 156 DA DT DT DG DG DT DC DG DT DA DG DA DC SEQRES 5 J 156 DA DG DC DT DC DT DA DG DC DA DC DC DG SEQRES 6 J 156 DC DT DT DA DA DA DC DG DC DA DC DG DT SEQRES 7 J 156 DA DC DG DC DG DC DT DG DT DC DC DC DC SEQRES 8 J 156 DC DG DC DG DT DT DT DT DA DA DC DC DG SEQRES 9 J 156 DC DC DA DA DG DG DG DG DA DT DT DA DC SEQRES 10 J 156 DT DC DC DC DT DA DG DT DC DT DC DC DA SEQRES 11 J 156 DG DG DC DA DC DG DT DG DT DC DA DG DA SEQRES 12 J 156 DT DA DT DA DT DA DC DA DT DC DC DT DG SEQRES 1 X 12 SER ASN MET ALA ARG GLY ALA ARG GLN LYS LEU LEU SEQRES 1 V 11 SER ASN MET ALA ARG GLY ALA ARG GLN LYS LEU HELIX 1 AA1 GLY M 44 SER M 57 1 14 HELIX 2 AA2 ARG M 63 ASP M 77 1 15 HELIX 3 AA3 GLN M 85 ALA M 114 1 30 HELIX 4 AA4 MET M 120 ARG M 131 1 12 HELIX 5 AA5 THR N 30 GLY N 42 1 13 HELIX 6 AA6 LEU N 49 ALA N 76 1 28 HELIX 7 AA7 THR N 82 ARG N 92 1 11 HELIX 8 AA8 THR O 16 ALA O 21 1 6 HELIX 9 AA9 PRO O 26 ASN O 38 1 13 HELIX 10 AB1 GLY O 46 ASN O 73 1 28 HELIX 11 AB2 ILE O 79 ASN O 89 1 11 HELIX 12 AB3 ASP O 90 LEU O 97 1 8 HELIX 13 AB4 TYR P 34 HIS P 46 1 13 HELIX 14 AB5 SER P 52 ASN P 81 1 30 HELIX 15 AB6 THR P 87 LEU P 99 1 13 HELIX 16 AB7 PRO P 100 SER P 120 1 21 HELIX 17 AB8 GLY Q 44 GLN Q 55 1 12 HELIX 18 AB9 ARG Q 63 LYS Q 79 1 17 HELIX 19 AC1 GLN Q 85 ALA Q 114 1 30 HELIX 20 AC2 MET Q 120 ARG Q 131 1 12 HELIX 21 AC3 ASN R 25 ILE R 29 5 5 HELIX 22 AC4 THR R 30 GLY R 42 1 13 HELIX 23 AC5 LEU R 49 ALA R 76 1 28 HELIX 24 AC6 THR R 82 ARG R 92 1 11 HELIX 25 AC7 THR S 16 GLY S 22 1 7 HELIX 26 AC8 PRO S 26 GLY S 37 1 12 HELIX 27 AC9 ALA S 45 ASN S 73 1 29 HELIX 28 AD1 ILE S 79 ASP S 90 1 12 HELIX 29 AD2 ASP S 90 LEU S 97 1 8 HELIX 30 AD3 TYR T 34 HIS T 46 1 13 HELIX 31 AD4 SER T 52 ASN T 81 1 30 HELIX 32 AD5 THR T 87 LEU T 99 1 13 HELIX 33 AD6 GLY T 101 THR T 119 1 19 HELIX 34 AD7 GLY X 741 LEU X 746 1 6 HELIX 35 AD8 GLY V 741 LEU V 746 1 6 SHEET 1 AA1 2 ARG M 83 PHE M 84 0 SHEET 2 AA1 2 THR N 80 VAL N 81 1 O VAL N 81 N ARG M 83 SHEET 1 AA2 2 THR M 118 ILE M 119 0 SHEET 2 AA2 2 ARG N 45 ILE N 46 1 O ARG N 45 N ILE M 119 SHEET 1 AA3 2 LEU N 97 TYR N 98 0 SHEET 2 AA3 2 THR S 101 ILE S 102 1 O THR S 101 N TYR N 98 SHEET 1 AA4 2 ARG O 42 VAL O 43 0 SHEET 2 AA4 2 THR P 85 ILE P 86 1 O ILE P 86 N ARG O 42 SHEET 1 AA5 2 VAL O 100 ILE O 102 0 SHEET 2 AA5 2 THR R 96 TYR R 98 1 O TYR R 98 N THR O 101 SHEET 1 AA6 2 ARG Q 83 PHE Q 84 0 SHEET 2 AA6 2 THR R 80 VAL R 81 1 O VAL R 81 N ARG Q 83 SHEET 1 AA7 2 ARG S 42 VAL S 43 0 SHEET 2 AA7 2 THR T 85 ILE T 86 1 O ILE T 86 N ARG S 42 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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 MASTER 410 0 0 35 14 0 0 612355 12 0 104 END