HEADER GENE REGULATION 05-NOV-23 8UW1 TITLE CRYO-EM STRUCTURE OF DNMT3A1 UDR IN COMPLEX WITH H2AK119UB-NUCLEOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3.2; COMPND 3 CHAIN: A, E; COMPND 4 SYNONYM: HISTONE H3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE H4; COMPND 8 CHAIN: B, F; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: HISTONE H2A; COMPND 12 CHAIN: C, G; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: HISTONE H2B 1.1; COMPND 16 CHAIN: D, H; COMPND 17 SYNONYM: H2B1.1; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 5; COMPND 20 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 3A; COMPND 21 CHAIN: K; COMPND 22 SYNONYM: DNMT3A,CYSTEINE METHYLTRANSFERASE DNMT3A,DNA COMPND 23 METHYLTRANSFERASE HSAIIIA,DNA MTASE HSAIIIA,M.HSAIIIA; COMPND 24 EC: 2.1.1.37,2.1.1.-; COMPND 25 ENGINEERED: YES; COMPND 26 MOL_ID: 6; COMPND 27 MOLECULE: DNA (146-MER); COMPND 28 CHAIN: I; COMPND 29 MOL_ID: 7; COMPND 30 MOLECULE: DNA (146-MER); COMPND 31 CHAIN: J SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 9 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 10 ORGANISM_TAXID: 8355; SOURCE 11 GENE: LOC121398084; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 16 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 17 ORGANISM_TAXID: 8355; SOURCE 18 GENE: H2AC14.L; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 21 MOL_ID: 4; SOURCE 22 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 23 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 24 ORGANISM_TAXID: 8355; SOURCE 25 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 26 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 27 MOL_ID: 5; SOURCE 28 SYNTHETIC: YES; SOURCE 29 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 30 ORGANISM_COMMON: HUMAN; SOURCE 31 ORGANISM_TAXID: 9606; SOURCE 32 MOL_ID: 6; SOURCE 33 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 34 ORGANISM_TAXID: 866768; SOURCE 35 MOL_ID: 7; SOURCE 36 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 37 ORGANISM_TAXID: 866768 KEYWDS DNMT3A1, CHROMATIN, H2A LYSINE 119 MONOUBIQUITINATION, DNA KEYWDS 2 METHYLTRANSFERASE, GENE REGULATION EXPDTA ELECTRON MICROSCOPY AUTHOR K.GRETARSSON,S.ABINI-AGBOMSON,K.-J.ARMACHE,C.LU REVDAT 1 11-SEP-24 8UW1 0 JRNL AUTH K.H.GRETARSSON,S.ABINI-AGBOMSON,S.L.GLOOR,D.N.WEINBERG, JRNL AUTH 2 J.L.MCCUISTON,V.U.S.KUMARY,A.R.HICKMAN,V.SAHU,R.LEE,X.XU, JRNL AUTH 3 N.LIPIETA,S.FLASHNER,O.A.ADELEKE,I.K.POPOVA,H.F.TAYLOR, JRNL AUTH 4 K.NOLL,C.L.WINDHAM,D.N.MARYANSKI,B.J.VENTERS,H.NAKAGAWA, JRNL AUTH 5 M.C.KEOGH,K.J.ARMACHE,C.LU JRNL TITL CANCER-ASSOCIATED DNA HYPERMETHYLATION OF POLYCOMB TARGETS JRNL TITL 2 REQUIRES DNMT3A DUAL RECOGNITION OF HISTONE H2AK119 JRNL TITL 3 UBIQUITINATION AND THE NUCLEOSOME ACIDIC PATCH. JRNL REF SCI ADV V. 10 P0975 2024 JRNL REFN ESSN 2375-2548 JRNL PMID 39196936 JRNL DOI 10.1126/SCIADV.ADP0975 REMARK 2 REMARK 2 RESOLUTION. 2.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, LEGINON 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) : 2.880 REMARK 3 NUMBER OF PARTICLES : 55652 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 8UW1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000278914. 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 : DNMT3A1 UDR IN COMPLEX WITH REMARK 245 H2AK119UB-NUCLEOSOME REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.30 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.90 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 TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1300.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 5000.00 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: UNDECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, K, I, REMARK 350 AND CHAINS: J 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 MET A 0 REMARK 465 ALA A 1 REMARK 465 ARG A 2 REMARK 465 THR A 3 REMARK 465 LYS A 4 REMARK 465 GLN A 5 REMARK 465 THR A 6 REMARK 465 ALA A 7 REMARK 465 ARG A 8 REMARK 465 LYS A 9 REMARK 465 SER A 10 REMARK 465 THR A 11 REMARK 465 GLY A 12 REMARK 465 GLY A 13 REMARK 465 LYS A 14 REMARK 465 ALA A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 LYS A 18 REMARK 465 GLN A 19 REMARK 465 LEU A 20 REMARK 465 ALA A 21 REMARK 465 THR A 22 REMARK 465 LYS A 23 REMARK 465 ALA A 24 REMARK 465 ALA A 25 REMARK 465 ARG A 26 REMARK 465 LYS A 27 REMARK 465 SER A 28 REMARK 465 ALA A 29 REMARK 465 PRO A 30 REMARK 465 ALA A 31 REMARK 465 THR A 32 REMARK 465 GLY A 33 REMARK 465 GLY A 34 REMARK 465 VAL A 35 REMARK 465 LYS A 36 REMARK 465 LYS A 37 REMARK 465 PRO A 38 REMARK 465 HIS A 39 REMARK 465 MET B 0 REMARK 465 SER B 1 REMARK 465 GLY B 2 REMARK 465 ARG B 3 REMARK 465 GLY B 4 REMARK 465 LYS B 5 REMARK 465 GLY B 6 REMARK 465 GLY B 7 REMARK 465 LYS B 8 REMARK 465 GLY B 9 REMARK 465 LEU B 10 REMARK 465 GLY B 11 REMARK 465 LYS B 12 REMARK 465 GLY B 13 REMARK 465 GLY B 14 REMARK 465 ALA B 15 REMARK 465 LYS B 16 REMARK 465 ARG B 17 REMARK 465 HIS B 18 REMARK 465 ARG B 19 REMARK 465 LYS B 20 REMARK 465 VAL B 21 REMARK 465 LEU B 22 REMARK 465 ARG B 23 REMARK 465 MET C 0 REMARK 465 SER C 1 REMARK 465 GLY C 2 REMARK 465 ARG C 3 REMARK 465 GLY C 4 REMARK 465 LYS C 5 REMARK 465 GLN C 6 REMARK 465 GLY C 7 REMARK 465 GLY C 8 REMARK 465 LYS C 9 REMARK 465 THR C 10 REMARK 465 ARG C 11 REMARK 465 LYS C 118 REMARK 465 LYS C 119 REMARK 465 THR C 120 REMARK 465 GLU C 121 REMARK 465 SER C 122 REMARK 465 SER C 123 REMARK 465 LYS C 124 REMARK 465 SER C 125 REMARK 465 ALA C 126 REMARK 465 LYS C 127 REMARK 465 SER C 128 REMARK 465 LYS C 129 REMARK 465 MET D -3 REMARK 465 PRO D -2 REMARK 465 GLU D -1 REMARK 465 PRO D 0 REMARK 465 ALA D 1 REMARK 465 LYS D 2 REMARK 465 SER D 3 REMARK 465 ALA D 4 REMARK 465 PRO D 5 REMARK 465 ALA D 6 REMARK 465 PRO D 7 REMARK 465 LYS D 8 REMARK 465 LYS D 9 REMARK 465 GLY D 10 REMARK 465 SER D 11 REMARK 465 LYS D 12 REMARK 465 LYS D 13 REMARK 465 ALA D 14 REMARK 465 VAL D 15 REMARK 465 THR D 16 REMARK 465 LYS D 17 REMARK 465 THR D 18 REMARK 465 GLN D 19 REMARK 465 LYS D 20 REMARK 465 LYS D 21 REMARK 465 ASP D 22 REMARK 465 GLY D 23 REMARK 465 LYS D 24 REMARK 465 LYS D 25 REMARK 465 ARG D 26 REMARK 465 ARG D 27 REMARK 465 LYS D 28 REMARK 465 THR D 29 REMARK 465 MET E 0 REMARK 465 ALA E 1 REMARK 465 ARG E 2 REMARK 465 THR E 3 REMARK 465 LYS E 4 REMARK 465 GLN E 5 REMARK 465 THR E 6 REMARK 465 ALA E 7 REMARK 465 ARG E 8 REMARK 465 LYS E 9 REMARK 465 SER E 10 REMARK 465 THR E 11 REMARK 465 GLY E 12 REMARK 465 GLY E 13 REMARK 465 LYS E 14 REMARK 465 ALA E 15 REMARK 465 PRO E 16 REMARK 465 ARG E 17 REMARK 465 LYS E 18 REMARK 465 GLN E 19 REMARK 465 LEU E 20 REMARK 465 ALA E 21 REMARK 465 THR E 22 REMARK 465 LYS E 23 REMARK 465 ALA E 24 REMARK 465 ALA E 25 REMARK 465 ARG E 26 REMARK 465 LYS E 27 REMARK 465 SER E 28 REMARK 465 ALA E 29 REMARK 465 PRO E 30 REMARK 465 ALA E 31 REMARK 465 THR E 32 REMARK 465 GLY E 33 REMARK 465 GLY E 34 REMARK 465 VAL E 35 REMARK 465 LYS E 36 REMARK 465 LYS E 37 REMARK 465 PRO E 38 REMARK 465 HIS E 39 REMARK 465 ARG E 40 REMARK 465 TYR E 41 REMARK 465 ARG E 42 REMARK 465 PRO E 43 REMARK 465 GLY E 44 REMARK 465 MET F 0 REMARK 465 SER F 1 REMARK 465 GLY F 2 REMARK 465 ARG F 3 REMARK 465 GLY F 4 REMARK 465 LYS F 5 REMARK 465 GLY F 6 REMARK 465 GLY F 7 REMARK 465 LYS F 8 REMARK 465 GLY F 9 REMARK 465 LEU F 10 REMARK 465 GLY F 11 REMARK 465 LYS F 12 REMARK 465 GLY F 13 REMARK 465 GLY F 14 REMARK 465 ALA F 15 REMARK 465 LYS F 16 REMARK 465 ARG F 17 REMARK 465 HIS F 18 REMARK 465 ARG F 19 REMARK 465 LYS F 20 REMARK 465 MET G 0 REMARK 465 SER G 1 REMARK 465 GLY G 2 REMARK 465 ARG G 3 REMARK 465 GLY G 4 REMARK 465 LYS G 5 REMARK 465 GLN G 6 REMARK 465 GLY G 7 REMARK 465 GLY G 8 REMARK 465 LYS G 9 REMARK 465 THR G 10 REMARK 465 ARG G 11 REMARK 465 THR G 120 REMARK 465 GLU G 121 REMARK 465 SER G 122 REMARK 465 SER G 123 REMARK 465 LYS G 124 REMARK 465 SER G 125 REMARK 465 ALA G 126 REMARK 465 LYS G 127 REMARK 465 SER G 128 REMARK 465 LYS G 129 REMARK 465 MET H -3 REMARK 465 PRO H -2 REMARK 465 GLU H -1 REMARK 465 PRO H 0 REMARK 465 ALA H 1 REMARK 465 LYS H 2 REMARK 465 SER H 3 REMARK 465 ALA H 4 REMARK 465 PRO H 5 REMARK 465 ALA H 6 REMARK 465 PRO H 7 REMARK 465 LYS H 8 REMARK 465 LYS H 9 REMARK 465 GLY H 10 REMARK 465 SER H 11 REMARK 465 LYS H 12 REMARK 465 LYS H 13 REMARK 465 ALA H 14 REMARK 465 VAL H 15 REMARK 465 THR H 16 REMARK 465 LYS H 17 REMARK 465 THR H 18 REMARK 465 GLN H 19 REMARK 465 LYS H 20 REMARK 465 LYS H 21 REMARK 465 ASP H 22 REMARK 465 GLY H 23 REMARK 465 LYS H 24 REMARK 465 LYS H 25 REMARK 465 ARG H 26 REMARK 465 ARG H 27 REMARK 465 HIS K 153 REMARK 465 HIS K 154 REMARK 465 HIS K 155 REMARK 465 HIS K 156 REMARK 465 HIS K 157 REMARK 465 HIS K 158 REMARK 465 GLU K 159 REMARK 465 SER K 160 REMARK 465 MET K 161 REMARK 465 LYS K 162 REMARK 465 MET K 163 REMARK 465 GLU K 164 REMARK 465 ILE K 198 REMARK 465 SER K 199 REMARK 465 LYS K 200 REMARK 465 ARG K 201 REMARK 465 LYS K 202 REMARK 465 ARG K 203 REMARK 465 ASP K 204 REMARK 465 GLU K 205 REMARK 465 TRP K 206 REMARK 465 LEU K 207 REMARK 465 ALA K 208 REMARK 465 ARG K 209 REMARK 465 TRP K 210 REMARK 465 LYS K 211 REMARK 465 ARG K 212 REMARK 465 GLU K 213 REMARK 465 ALA K 214 REMARK 465 GLU K 215 REMARK 465 LYS K 216 REMARK 465 LYS K 217 REMARK 465 ALA K 218 REMARK 465 LYS K 219 REMARK 465 VAL K 220 REMARK 465 ILE K 221 REMARK 465 ALA K 222 REMARK 465 GLY K 223 REMARK 465 MET K 224 REMARK 465 ASN K 225 REMARK 465 ALA K 226 REMARK 465 VAL K 227 REMARK 465 GLU K 228 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 LYS G 118 CG CD CE NZ REMARK 470 LYS G 119 CG CD CE NZ REMARK 470 TYR K 196 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR K 197 CG CD1 CD2 CE1 CE2 CZ OH 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 DG I 6 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT I 27 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC I 47 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC I 78 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG J 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT J 58 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA J 71 C3' - O3' - P ANGL. DEV. = -9.3 DEGREES REMARK 500 DG J 72 C3' - O3' - P ANGL. DEV. = -9.4 DEGREES REMARK 500 DA J 73 C3' - O3' - P ANGL. DEV. = -9.7 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 ASN B 25 -9.69 72.15 REMARK 500 ALA C 14 23.52 -140.13 REMARK 500 LEU C 97 40.74 -108.80 REMARK 500 LYS H 82 60.39 60.77 REMARK 500 LEU K 174 -168.56 -79.64 REMARK 500 PRO K 195 46.87 -79.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-42636 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF DNMT3A1 UDR IN COMPLEX WITH H2AK119UB- REMARK 900 NUCLEOSOME DBREF 8UW1 A 0 135 UNP P84233 H32_XENLA 1 136 DBREF1 8UW1 B 0 102 UNP A0A8J1LTD2_XENLA DBREF2 8UW1 B A0A8J1LTD2 14 116 DBREF 8UW1 C 0 129 UNP Q6AZJ8 Q6AZJ8_XENLA 1 130 DBREF 8UW1 D -3 122 UNP P02281 H2B11_XENLA 1 126 DBREF 8UW1 E 0 135 UNP P84233 H32_XENLA 1 136 DBREF1 8UW1 F 0 102 UNP A0A8J1LTD2_XENLA DBREF2 8UW1 F A0A8J1LTD2 14 116 DBREF 8UW1 G 0 129 UNP Q6AZJ8 Q6AZJ8_XENLA 1 130 DBREF 8UW1 H -3 122 UNP P02281 H2B11_XENLA 1 126 DBREF 8UW1 K 159 228 UNP Q9Y6K1 DNM3A_HUMAN 159 228 DBREF 8UW1 I 2 147 PDB 8UW1 8UW1 2 147 DBREF 8UW1 J 1 146 PDB 8UW1 8UW1 1 146 SEQADV 8UW1 THR D 29 UNP P02281 SER 33 CONFLICT SEQADV 8UW1 THR H 29 UNP P02281 SER 33 CONFLICT SEQADV 8UW1 HIS K 153 UNP Q9Y6K1 EXPRESSION TAG SEQADV 8UW1 HIS K 154 UNP Q9Y6K1 EXPRESSION TAG SEQADV 8UW1 HIS K 155 UNP Q9Y6K1 EXPRESSION TAG SEQADV 8UW1 HIS K 156 UNP Q9Y6K1 EXPRESSION TAG SEQADV 8UW1 HIS K 157 UNP Q9Y6K1 EXPRESSION TAG SEQADV 8UW1 HIS K 158 UNP Q9Y6K1 EXPRESSION TAG SEQRES 1 A 136 MET ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY SEQRES 2 A 136 GLY LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA SEQRES 3 A 136 ARG LYS SER ALA PRO ALA THR GLY GLY VAL LYS LYS PRO SEQRES 4 A 136 HIS ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU ILE SEQRES 5 A 136 ARG ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG LYS SEQRES 6 A 136 LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN ASP SEQRES 7 A 136 PHE LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL MET SEQRES 8 A 136 ALA LEU GLN GLU ALA SER GLU ALA TYR LEU VAL GLY LEU SEQRES 9 A 136 PHE GLU ASP THR ASN LEU CYS ALA ILE HIS ALA LYS ARG SEQRES 10 A 136 VAL THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG ARG SEQRES 11 A 136 ILE ARG GLY GLU ARG ALA SEQRES 1 B 103 MET SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS SEQRES 2 B 103 GLY GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN SEQRES 3 B 103 ILE GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA SEQRES 4 B 103 ARG ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR SEQRES 5 B 103 GLU GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN SEQRES 6 B 103 VAL ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS SEQRES 7 B 103 ARG LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU SEQRES 8 B 103 LYS ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 C 130 MET SER GLY ARG GLY LYS GLN GLY GLY LYS THR ARG ALA SEQRES 2 C 130 LYS ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE SEQRES 3 C 130 PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN SEQRES 4 C 130 TYR ALA GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU SEQRES 5 C 130 ALA ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU SEQRES 6 C 130 LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG SEQRES 7 C 130 ILE ILE PRO ARG HIS LEU GLN LEU ALA VAL ARG ASN ASP SEQRES 8 C 130 GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA SEQRES 9 C 130 GLN GLY GLY VAL LEU PRO ASN ILE GLN SER VAL LEU LEU SEQRES 10 C 130 PRO LYS LYS THR GLU SER SER LYS SER ALA LYS SER LYS SEQRES 1 D 126 MET PRO GLU PRO ALA LYS SER ALA PRO ALA PRO LYS LYS SEQRES 2 D 126 GLY SER LYS LYS ALA VAL THR LYS THR GLN LYS LYS ASP SEQRES 3 D 126 GLY LYS LYS ARG ARG LYS THR ARG LYS GLU SER TYR ALA SEQRES 4 D 126 ILE TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP SEQRES 5 D 126 THR GLY ILE SER SER LYS ALA MET SER ILE MET ASN SER SEQRES 6 D 126 PHE VAL ASN ASP VAL PHE GLU ARG ILE ALA GLY GLU ALA SEQRES 7 D 126 SER ARG LEU ALA HIS TYR ASN LYS ARG SER THR ILE THR SEQRES 8 D 126 SER ARG GLU ILE GLN THR ALA VAL ARG LEU LEU LEU PRO SEQRES 9 D 126 GLY GLU LEU ALA LYS HIS ALA VAL SER GLU GLY THR LYS SEQRES 10 D 126 ALA VAL THR LYS TYR THR SER ALA LYS SEQRES 1 E 136 MET ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY SEQRES 2 E 136 GLY LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA SEQRES 3 E 136 ARG LYS SER ALA PRO ALA THR GLY GLY VAL LYS LYS PRO SEQRES 4 E 136 HIS ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU ILE SEQRES 5 E 136 ARG ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG LYS SEQRES 6 E 136 LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN ASP SEQRES 7 E 136 PHE LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL MET SEQRES 8 E 136 ALA LEU GLN GLU ALA SER GLU ALA TYR LEU VAL GLY LEU SEQRES 9 E 136 PHE GLU ASP THR ASN LEU CYS ALA ILE HIS ALA LYS ARG SEQRES 10 E 136 VAL THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG ARG SEQRES 11 E 136 ILE ARG GLY GLU ARG ALA SEQRES 1 F 103 MET SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS SEQRES 2 F 103 GLY GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN SEQRES 3 F 103 ILE GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA SEQRES 4 F 103 ARG ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR SEQRES 5 F 103 GLU GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN SEQRES 6 F 103 VAL ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS SEQRES 7 F 103 ARG LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU SEQRES 8 F 103 LYS ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 G 130 MET SER GLY ARG GLY LYS GLN GLY GLY LYS THR ARG ALA SEQRES 2 G 130 LYS ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE SEQRES 3 G 130 PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN SEQRES 4 G 130 TYR ALA GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU SEQRES 5 G 130 ALA ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU SEQRES 6 G 130 LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG SEQRES 7 G 130 ILE ILE PRO ARG HIS LEU GLN LEU ALA VAL ARG ASN ASP SEQRES 8 G 130 GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA SEQRES 9 G 130 GLN GLY GLY VAL LEU PRO ASN ILE GLN SER VAL LEU LEU SEQRES 10 G 130 PRO LYS LYS THR GLU SER SER LYS SER ALA LYS SER LYS SEQRES 1 H 126 MET PRO GLU PRO ALA LYS SER ALA PRO ALA PRO LYS LYS SEQRES 2 H 126 GLY SER LYS LYS ALA VAL THR LYS THR GLN LYS LYS ASP SEQRES 3 H 126 GLY LYS LYS ARG ARG LYS THR ARG LYS GLU SER TYR ALA SEQRES 4 H 126 ILE TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP SEQRES 5 H 126 THR GLY ILE SER SER LYS ALA MET SER ILE MET ASN SER SEQRES 6 H 126 PHE VAL ASN ASP VAL PHE GLU ARG ILE ALA GLY GLU ALA SEQRES 7 H 126 SER ARG LEU ALA HIS TYR ASN LYS ARG SER THR ILE THR SEQRES 8 H 126 SER ARG GLU ILE GLN THR ALA VAL ARG LEU LEU LEU PRO SEQRES 9 H 126 GLY GLU LEU ALA LYS HIS ALA VAL SER GLU GLY THR LYS SEQRES 10 H 126 ALA VAL THR LYS TYR THR SER ALA LYS SEQRES 1 K 76 HIS HIS HIS HIS HIS HIS GLU SER MET LYS MET GLU GLY SEQRES 2 K 76 SER ARG GLY ARG LEU ARG GLY GLY LEU GLY TRP GLU SER SEQRES 3 K 76 SER LEU ARG GLN ARG PRO MET PRO ARG LEU THR PHE GLN SEQRES 4 K 76 ALA GLY ASP PRO TYR TYR ILE SER LYS ARG LYS ARG ASP SEQRES 5 K 76 GLU TRP LEU ALA ARG TRP LYS ARG GLU ALA GLU LYS LYS SEQRES 6 K 76 ALA LYS VAL ILE ALA GLY MET ASN ALA VAL GLU SEQRES 1 I 146 DT DC DG DA DG DA DA DT DC DC DC DG DG SEQRES 2 I 146 DT DG DC DC DG DA DG DG DC DC DG DC DT SEQRES 3 I 146 DC DA DA DT DT DG DG DT DC DG DT DA DG SEQRES 4 I 146 DA DC DA DG DC DT DC DT DA DG DC DA DC SEQRES 5 I 146 DC DG DC DT DT DA DA DA DC DG DC DA DC SEQRES 6 I 146 DG DT DA DC DG DG DA DT DT DC DT DC DC SEQRES 7 I 146 DC DC DC DG DC DG DT DT DT DT DA DA DC SEQRES 8 I 146 DC DG DC DC DA DA DG DG DG DG DA DT DT SEQRES 9 I 146 DA DC DT DC DC DC DT DA DG DT DC DT DC SEQRES 10 I 146 DC DA DG DG DC DA DC DG DT DG DT DC DA SEQRES 11 I 146 DG DA DT DA DT DA DT DA DC DA DT DC DC SEQRES 12 I 146 DG DA DT SEQRES 1 J 146 DA DT DC DG DG DA DT DG DT DA DT DA DT SEQRES 2 J 146 DA DT DC DT DG DA DC DA DC DG DT DG DC SEQRES 3 J 146 DC DT DG DG DA DG DA DC DT DA DG DG DG SEQRES 4 J 146 DA DG DT DA DA DT DC DC DC DC DT DT DG SEQRES 5 J 146 DG DC DG DG DT DT DA DA DA DA DC DG DC SEQRES 6 J 146 DG DG DG DG DG DA DG DA DA DT DC DC DG SEQRES 7 J 146 DT DA DC DG DT DG DC DG DT DT DT DA DA SEQRES 8 J 146 DG DC DG DG DT DG DC DT DA DG DA DG DC SEQRES 9 J 146 DT DG DT DC DT DA DC DG DA DC DC DA DA SEQRES 10 J 146 DT DT DG DA DG DC DG DG DC DC DT DC DG SEQRES 11 J 146 DG DC DA DC DC DG DG DG DA DT DT DC DT SEQRES 12 J 146 DC DG DA HELIX 1 AA1 GLY A 44 SER A 57 1 14 HELIX 2 AA2 ARG A 63 GLN A 76 1 14 HELIX 3 AA3 GLN A 85 ALA A 114 1 30 HELIX 4 AA4 MET A 120 ARG A 131 1 12 HELIX 5 AA5 THR B 30 GLY B 41 1 12 HELIX 6 AA6 LEU B 49 ALA B 76 1 28 HELIX 7 AA7 THR B 82 ARG B 92 1 11 HELIX 8 AA8 THR C 16 GLY C 22 1 7 HELIX 9 AA9 PRO C 26 GLY C 37 1 12 HELIX 10 AB1 ALA C 45 ASN C 73 1 29 HELIX 11 AB2 ILE C 79 ASP C 90 1 12 HELIX 12 AB3 ASP C 90 LEU C 97 1 8 HELIX 13 AB4 TYR D 34 HIS D 46 1 13 HELIX 14 AB5 SER D 52 ASN D 81 1 30 HELIX 15 AB6 THR D 87 LEU D 99 1 13 HELIX 16 AB7 GLY D 101 ALA D 121 1 21 HELIX 17 AB8 VAL E 46 SER E 57 1 12 HELIX 18 AB9 ARG E 63 LYS E 79 1 17 HELIX 19 AC1 GLN E 85 ALA E 114 1 30 HELIX 20 AC2 MET E 120 ARG E 131 1 12 HELIX 21 AC3 ASP F 24 ILE F 29 5 6 HELIX 22 AC4 THR F 30 GLY F 41 1 12 HELIX 23 AC5 LEU F 49 ALA F 76 1 28 HELIX 24 AC6 THR F 82 GLN F 93 1 12 HELIX 25 AC7 THR G 16 GLY G 22 1 7 HELIX 26 AC8 PRO G 26 GLY G 37 1 12 HELIX 27 AC9 GLY G 46 ASN G 73 1 28 HELIX 28 AD1 ILE G 79 ASN G 89 1 11 HELIX 29 AD2 ASP G 90 LEU G 97 1 8 HELIX 30 AD3 TYR H 34 HIS H 46 1 13 HELIX 31 AD4 SER H 52 ASN H 81 1 30 HELIX 32 AD5 THR H 87 LEU H 99 1 13 HELIX 33 AD6 PRO H 100 SER H 120 1 21 SHEET 1 AA1 2 ARG A 83 PHE A 84 0 SHEET 2 AA1 2 THR B 80 VAL B 81 1 O VAL B 81 N ARG A 83 SHEET 1 AA2 2 THR A 118 ILE A 119 0 SHEET 2 AA2 2 ARG B 45 ILE B 46 1 O ARG B 45 N ILE A 119 SHEET 1 AA3 2 THR B 96 TYR B 98 0 SHEET 2 AA3 2 VAL G 100 ILE G 102 1 O THR G 101 N TYR B 98 SHEET 1 AA4 2 ARG C 42 VAL C 43 0 SHEET 2 AA4 2 THR D 85 ILE D 86 1 O ILE D 86 N ARG C 42 SHEET 1 AA5 2 ARG C 77 ILE C 78 0 SHEET 2 AA5 2 GLY D 50 ILE D 51 1 O GLY D 50 N ILE C 78 SHEET 1 AA6 2 VAL C 100 ILE C 102 0 SHEET 2 AA6 2 THR F 96 TYR F 98 1 O THR F 96 N THR C 101 SHEET 1 AA7 2 ARG E 83 PHE E 84 0 SHEET 2 AA7 2 THR F 80 VAL F 81 1 O VAL F 81 N ARG E 83 SHEET 1 AA8 2 THR E 118 ILE E 119 0 SHEET 2 AA8 2 ARG F 45 ILE F 46 1 O ARG F 45 N ILE E 119 SHEET 1 AA9 2 ARG G 42 VAL G 43 0 SHEET 2 AA9 2 THR H 85 ILE H 86 1 O ILE H 86 N ARG G 42 SHEET 1 AB1 2 ARG G 77 ILE G 78 0 SHEET 2 AB1 2 GLY H 50 ILE H 51 1 O GLY H 50 N ILE G 78 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