HEADER DNA BINDING PROTEIN 28-MAR-24 8YV8 TITLE CRYO-EM STRUCTURE OF CDCA7 BOUND TO NUCLEOSOME INCLUDING TITLE 2 HEMIMETHYLATED CPG SITE IN WIDOM601 POSITIONING SEQUENCE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3.1; COMPND 3 CHAIN: A, E; COMPND 4 SYNONYM: HISTONE H3/A,HISTONE H3/B,HISTONE H3/C,HISTONE H3/D,HISTONE COMPND 5 H3/F,HISTONE H3/H,HISTONE H3/I,HISTONE H3/J,HISTONE H3/K,HISTONE COMPND 6 H3/L; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HISTONE H4; COMPND 10 CHAIN: B, F; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: HISTONE H2A TYPE 1-B/E; COMPND 14 CHAIN: C, G; COMPND 15 SYNONYM: HISTONE H2A.2,HISTONE H2A/A,HISTONE H2A/M; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: HISTONE H2B TYPE 1-K; COMPND 19 CHAIN: D, H; COMPND 20 SYNONYM: H2B K,HIRA-INTERACTING PROTEIN 1; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 5; COMPND 23 MOLECULE: DNA (132-MER); COMPND 24 CHAIN: I; COMPND 25 ENGINEERED: YES; COMPND 26 MOL_ID: 6; COMPND 27 MOLECULE: DNA (132-MER); COMPND 28 CHAIN: J; COMPND 29 ENGINEERED: YES; COMPND 30 MOL_ID: 7; COMPND 31 MOLECULE: CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7; COMPND 32 CHAIN: K; COMPND 33 SYNONYM: PROTEIN JPO1; COMPND 34 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: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC SOURCE 6 HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, SOURCE 7 HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, SOURCE 8 HIST1H3I, H3C12, H3FJ, HIST1H3J; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 GENE: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE; 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_COMMON: HUMAN; SOURCE 27 ORGANISM_TAXID: 9606; SOURCE 28 GENE: H2BC12, H2BFT, HIRIP1, HIST1H2BK; SOURCE 29 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 30 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 31 MOL_ID: 5; SOURCE 32 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 33 ORGANISM_TAXID: 32630; SOURCE 34 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 35 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 36 MOL_ID: 6; SOURCE 37 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 38 ORGANISM_TAXID: 32630; SOURCE 39 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 40 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 41 MOL_ID: 7; SOURCE 42 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 43 ORGANISM_COMMON: HUMAN; SOURCE 44 ORGANISM_TAXID: 9606; SOURCE 45 GENE: CDCA7, JPO1; SOURCE 46 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 47 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOSOME, DNA METHYLATION, CDCA7, DNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR A.KIKUCHI,R.SHIKIMACHI,A.NISHIYAMA,H.FUNABIKI,K.ARITA REVDAT 1 31-JUL-24 8YV8 0 JRNL AUTH I.WASSING,A.NISHIYAMA,K.ARITA,H.FUNABIKI JRNL TITL CDCA7 IS A HEMIMETHYLATED DNA ADAPTOR FOR THE NUCLEOSOME JRNL TITL 2 REMODELER HELLS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.000 REMARK 3 NUMBER OF PARTICLES : 257342 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8YV8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300046435. 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 : CDCA7 BOUND TO 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 : 7.50 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 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) : 5140.00 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, I, J, REMARK 350 AND CHAINS: K 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 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 ALA A 135 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 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 120 REMARK 465 GLU C 121 REMARK 465 SER C 122 REMARK 465 HIS C 123 REMARK 465 HIS C 124 REMARK 465 LYS C 125 REMARK 465 ALA C 126 REMARK 465 LYS C 127 REMARK 465 GLY C 128 REMARK 465 LYS C 129 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 ALA 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 LYS D 122 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 ALA E 135 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 GLY F 102 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 ALA G 10 REMARK 465 ARG G 11 REMARK 465 ALA G 12 REMARK 465 LYS G 13 REMARK 465 ALA G 14 REMARK 465 LYS G 118 REMARK 465 LYS G 119 REMARK 465 THR G 120 REMARK 465 GLU G 121 REMARK 465 SER G 122 REMARK 465 HIS G 123 REMARK 465 HIS G 124 REMARK 465 LYS G 125 REMARK 465 ALA G 126 REMARK 465 LYS G 127 REMARK 465 GLY G 128 REMARK 465 LYS G 129 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 ALA 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 LYS H 27 REMARK 465 ARG H 28 REMARK 465 SER H 29 REMARK 465 LYS H 122 REMARK 465 DT I 60 REMARK 465 DA I 61 REMARK 465 DT I 62 REMARK 465 DA I 63 REMARK 465 DT I 64 REMARK 465 DA I 65 REMARK 465 DC I 66 REMARK 465 DA I 67 REMARK 465 DT I 68 REMARK 465 DC I 69 REMARK 465 DG I 70 REMARK 465 DA I 71 REMARK 465 DT I 72 REMARK 465 DA J -72 REMARK 465 DT J -71 REMARK 465 DC J -70 REMARK 465 DG J -69 REMARK 465 DA J -68 REMARK 465 DT J -67 REMARK 465 DG J -66 REMARK 465 DT J -65 REMARK 465 DA J -64 REMARK 465 DT J -63 REMARK 465 DA J -62 REMARK 465 DT J -61 REMARK 465 DA J -60 REMARK 465 PHE K 367 REMARK 465 GLU K 368 REMARK 465 MET K 369 REMARK 465 GLN K 370 REMARK 465 ALA K 371 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 N2 DG I -41 O2 DC J 41 2.12 REMARK 500 OG SER D 29 OP1 DT I 30 2.15 REMARK 500 OD2 ASP D 65 OH TYR F 98 2.16 REMARK 500 O2 DC I 0 N2 DG J 0 2.16 REMARK 500 OH TYR G 39 OE2 GLU H 68 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 ASP B 24 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 DT J 15 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT J 54 O4' - C1' - N1 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 LEU B 22 125.37 70.12 REMARK 500 ASP B 24 17.96 57.41 REMARK 500 ASN C 38 59.14 37.33 REMARK 500 ASP F 24 71.40 58.62 REMARK 500 ASN G 38 55.31 35.74 REMARK 500 GLN G 104 41.98 37.52 REMARK 500 ARG K 293 -9.17 -56.05 REMARK 500 SER K 339 -175.78 -69.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN K 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS K 270 SG REMARK 620 2 CYS K 273 SG 107.4 REMARK 620 3 CYS K 297 SG 94.3 110.2 REMARK 620 4 CYS K 300 SG 121.4 117.7 102.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN K 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS K 271 NE2 REMARK 620 2 CYS K 327 SG 100.9 REMARK 620 3 CYS K 329 SG 94.1 114.0 REMARK 620 4 CYS K 332 SG 123.8 113.2 109.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN K 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS K 284 SG REMARK 620 2 CYS K 289 SG 94.8 REMARK 620 3 ARG K 293 NH1 134.3 118.5 REMARK 620 4 CYS K 320 SG 92.9 158.3 68.0 REMARK 620 5 CYS K 323 SG 65.6 133.7 68.8 67.8 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-39594 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF CDCA7 BOUND TO NUCLEOSOME INCLUDING REMARK 900 HEMIMETHYLATED CPG SITE IN WIDOM601 POSITIONING SEQUENCE. DBREF 8YV8 A 1 135 UNP P68431 H31_HUMAN 2 136 DBREF 8YV8 B 1 102 UNP P62805 H4_HUMAN 2 103 DBREF 8YV8 C 1 129 UNP P04908 H2A1B_HUMAN 2 130 DBREF 8YV8 D -2 122 UNP O60814 H2B1K_HUMAN 2 126 DBREF 8YV8 E 1 135 UNP P68431 H31_HUMAN 2 136 DBREF 8YV8 F 1 102 UNP P62805 H4_HUMAN 2 103 DBREF 8YV8 G 1 129 UNP P04908 H2A1B_HUMAN 2 130 DBREF 8YV8 H -2 122 UNP O60814 H2B1K_HUMAN 2 126 DBREF 8YV8 I -72 72 PDB 8YV8 8YV8 -72 72 DBREF 8YV8 J -72 72 PDB 8YV8 8YV8 -72 72 DBREF 8YV8 K 264 371 UNP Q9BWT1 CDCA7_HUMAN 264 371 SEQADV 8YV8 SER K 339 UNP Q9BWT1 CYS 339 ENGINEERED MUTATION SEQRES 1 A 135 ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 A 135 LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA ARG SEQRES 3 A 135 LYS SER ALA PRO ALA THR GLY GLY VAL LYS LYS PRO HIS SEQRES 4 A 135 ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU ILE ARG SEQRES 5 A 135 ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG LYS LEU SEQRES 6 A 135 PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN ASP PHE SEQRES 7 A 135 LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL MET ALA SEQRES 8 A 135 LEU GLN GLU ALA CYS GLU ALA TYR LEU VAL GLY LEU PHE SEQRES 9 A 135 GLU ASP THR ASN LEU CYS ALA ILE HIS ALA LYS ARG VAL SEQRES 10 A 135 THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG ARG ILE SEQRES 11 A 135 ARG GLY GLU ARG ALA SEQRES 1 B 102 SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 B 102 GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN ILE SEQRES 3 B 102 GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA ARG SEQRES 4 B 102 ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR GLU SEQRES 5 B 102 GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN VAL SEQRES 6 B 102 ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS ARG SEQRES 7 B 102 LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU LYS SEQRES 8 B 102 ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 C 129 SER GLY ARG GLY LYS GLN GLY GLY LYS ALA ARG ALA LYS SEQRES 2 C 129 ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE PRO SEQRES 3 C 129 VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN TYR SEQRES 4 C 129 SER GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU ALA SEQRES 5 C 129 ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU LEU SEQRES 6 C 129 ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG ILE SEQRES 7 C 129 ILE PRO ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP GLU SEQRES 8 C 129 GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA GLN SEQRES 9 C 129 GLY GLY VAL LEU PRO ASN ILE GLN ALA VAL LEU LEU PRO SEQRES 10 C 129 LYS LYS THR GLU SER HIS HIS LYS ALA LYS GLY LYS SEQRES 1 D 125 PRO GLU PRO ALA LYS SER ALA PRO ALA PRO LYS LYS GLY SEQRES 2 D 125 SER LYS LYS ALA VAL THR LYS ALA GLN LYS LYS ASP GLY SEQRES 3 D 125 LYS LYS ARG LYS ARG SER ARG LYS GLU SER TYR SER VAL SEQRES 4 D 125 TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP THR SEQRES 5 D 125 GLY ILE SER SER LYS ALA MET GLY ILE MET ASN SER PHE SEQRES 6 D 125 VAL ASN ASP ILE PHE GLU ARG ILE ALA GLY GLU ALA SER SEQRES 7 D 125 ARG LEU ALA HIS TYR ASN LYS ARG SER THR ILE THR SER SEQRES 8 D 125 ARG GLU ILE GLN THR ALA VAL ARG LEU LEU LEU PRO GLY SEQRES 9 D 125 GLU LEU ALA LYS HIS ALA VAL SER GLU GLY THR LYS ALA SEQRES 10 D 125 VAL THR LYS TYR THR SER ALA LYS SEQRES 1 E 135 ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 E 135 LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA ARG SEQRES 3 E 135 LYS SER ALA PRO ALA THR GLY GLY VAL LYS LYS PRO HIS SEQRES 4 E 135 ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU ILE ARG SEQRES 5 E 135 ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG LYS LEU SEQRES 6 E 135 PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN ASP PHE SEQRES 7 E 135 LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL MET ALA SEQRES 8 E 135 LEU GLN GLU ALA CYS GLU ALA TYR LEU VAL GLY LEU PHE SEQRES 9 E 135 GLU ASP THR ASN LEU CYS ALA ILE HIS ALA LYS ARG VAL SEQRES 10 E 135 THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG ARG ILE SEQRES 11 E 135 ARG GLY GLU ARG ALA SEQRES 1 F 102 SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 F 102 GLY ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN ILE SEQRES 3 F 102 GLN GLY ILE THR LYS PRO ALA ILE ARG ARG LEU ALA ARG SEQRES 4 F 102 ARG GLY GLY VAL LYS ARG ILE SER GLY LEU ILE TYR GLU SEQRES 5 F 102 GLU THR ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN VAL SEQRES 6 F 102 ILE ARG ASP ALA VAL THR TYR THR GLU HIS ALA LYS ARG SEQRES 7 F 102 LYS THR VAL THR ALA MET ASP VAL VAL TYR ALA LEU LYS SEQRES 8 F 102 ARG GLN GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 G 129 SER GLY ARG GLY LYS GLN GLY GLY LYS ALA ARG ALA LYS SEQRES 2 G 129 ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE PRO SEQRES 3 G 129 VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN TYR SEQRES 4 G 129 SER GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU ALA SEQRES 5 G 129 ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU LEU SEQRES 6 G 129 ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG ILE SEQRES 7 G 129 ILE PRO ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP GLU SEQRES 8 G 129 GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA GLN SEQRES 9 G 129 GLY GLY VAL LEU PRO ASN ILE GLN ALA VAL LEU LEU PRO SEQRES 10 G 129 LYS LYS THR GLU SER HIS HIS LYS ALA LYS GLY LYS SEQRES 1 H 125 PRO GLU PRO ALA LYS SER ALA PRO ALA PRO LYS LYS GLY SEQRES 2 H 125 SER LYS LYS ALA VAL THR LYS ALA GLN LYS LYS ASP GLY SEQRES 3 H 125 LYS LYS ARG LYS ARG SER ARG LYS GLU SER TYR SER VAL SEQRES 4 H 125 TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP THR SEQRES 5 H 125 GLY ILE SER SER LYS ALA MET GLY ILE MET ASN SER PHE SEQRES 6 H 125 VAL ASN ASP ILE PHE GLU ARG ILE ALA GLY GLU ALA SER SEQRES 7 H 125 ARG LEU ALA HIS TYR ASN LYS ARG SER THR ILE THR SER SEQRES 8 H 125 ARG GLU ILE GLN THR ALA VAL ARG LEU LEU LEU PRO GLY SEQRES 9 H 125 GLU LEU ALA LYS HIS ALA VAL SER GLU GLY THR LYS ALA SEQRES 10 H 125 VAL THR LYS TYR THR SER ALA LYS SEQRES 1 I 145 DA DT DC DA DG DA DA DT DC DC DC DG DG SEQRES 2 I 145 DT 5CM DG DC DG DA DG DG DC DC DG DC DT SEQRES 3 I 145 DC DA DA DT DT DG DG DT DC DG DT DA DG SEQRES 4 I 145 DA DC DA DG DC DT DC DT DA DG DC DA DC SEQRES 5 I 145 DC DG DC DT DT DA DA DA DC DG DC DA DC SEQRES 6 I 145 DG DT DA DC DG DC DG DC DT DG DT DC DC SEQRES 7 I 145 DC DC DC DG DC DG DT DT DT DT DA DA DC SEQRES 8 I 145 DC DG DC DC DA DA DG DG DG DG DA DT DT SEQRES 9 I 145 DA DC DT DC DC DC DT DA DG DT DC DT DC SEQRES 10 I 145 DC DA DG DG DC DA DC DG DT DG DT DC DA SEQRES 11 I 145 DG DA DT DA DT DA DT DA DC DA DT DC DG SEQRES 12 I 145 DA DT SEQRES 1 J 145 DA DT DC DG DA DT DG DT DA DT DA DT DA SEQRES 2 J 145 DT DC DT DG DA DC DA DC DG DT DG DC DC SEQRES 3 J 145 DT DG DG DA DG DA DC DT DA DG DG DG DA SEQRES 4 J 145 DG DT DA DA DT DC DC DC DC DT DT DG DG SEQRES 5 J 145 DC DG DG DT DT DA DA DA DA DC DG DC DG SEQRES 6 J 145 DG DG DG DG DA DC DA DG DC DG DC DG DT SEQRES 7 J 145 DA DC DG DT DG DC DG DT DT DT DA DA DG SEQRES 8 J 145 DC DG DG DT DG DC DT DA DG DA DG DC DT SEQRES 9 J 145 DG DT DC DT DA DC DG DA DC DC DA DA DT SEQRES 10 J 145 DT DG DA DG DC DG DG DC DC DT DC DG DC SEQRES 11 J 145 DG DA DC DC DG DG DG DA DT DT DC DT DG SEQRES 12 J 145 DA DT SEQRES 1 K 108 ARG SER LEU GLY SER THR CYS HIS GLN CYS ARG GLN LYS SEQRES 2 K 108 THR ILE ASP THR LYS THR ASN CYS ARG ASN PRO ASP CYS SEQRES 3 K 108 TRP GLY VAL ARG GLY GLN PHE CYS GLY PRO CYS LEU ARG SEQRES 4 K 108 ASN ARG TYR GLY GLU GLU VAL ARG ASP ALA LEU LEU ASP SEQRES 5 K 108 PRO ASN TRP HIS CYS PRO PRO CYS ARG GLY ILE CYS ASN SEQRES 6 K 108 CYS SER PHE CYS ARG GLN ARG ASP GLY ARG SER ALA THR SEQRES 7 K 108 GLY VAL LEU VAL TYR LEU ALA LYS TYR HIS GLY PHE GLY SEQRES 8 K 108 ASN VAL HIS ALA TYR LEU LYS SER LEU LYS GLN GLU PHE SEQRES 9 K 108 GLU MET GLN ALA HET 5CM I -58 20 HET ZN K 401 1 HET ZN K 402 1 HET ZN K 403 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION FORMUL 9 5CM C10 H16 N3 O7 P FORMUL 12 ZN 3(ZN 2+) HELIX 1 AA1 GLY A 44 SER A 57 1 14 HELIX 2 AA2 ARG A 63 ASP A 77 1 15 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 ASP B 24 ILE B 29 5 6 HELIX 6 AA6 THR B 30 GLY B 42 1 13 HELIX 7 AA7 LEU B 49 ALA B 76 1 28 HELIX 8 AA8 THR B 82 GLN B 93 1 12 HELIX 9 AA9 THR C 16 GLY C 22 1 7 HELIX 10 AB1 PRO C 26 GLY C 37 1 12 HELIX 11 AB2 GLY C 46 ASP C 72 1 27 HELIX 12 AB3 PRO C 80 ARG C 88 1 9 HELIX 13 AB4 ASP C 90 LEU C 97 1 8 HELIX 14 AB5 TYR D 34 VAL D 41 1 8 HELIX 15 AB6 SER D 52 ASN D 81 1 30 HELIX 16 AB7 THR D 87 LEU D 99 1 13 HELIX 17 AB8 PRO D 100 ALA D 121 1 22 HELIX 18 AB9 GLY E 44 SER E 57 1 14 HELIX 19 AC1 ARG E 63 LYS E 79 1 17 HELIX 20 AC2 GLN E 85 ALA E 114 1 30 HELIX 21 AC3 MET E 120 GLY E 132 1 13 HELIX 22 AC4 ASN F 25 ILE F 29 5 5 HELIX 23 AC5 THR F 30 GLY F 41 1 12 HELIX 24 AC6 LEU F 49 ALA F 76 1 28 HELIX 25 AC7 THR F 82 ARG F 92 1 11 HELIX 26 AC8 THR G 16 GLY G 22 1 7 HELIX 27 AC9 VAL G 27 GLY G 37 1 11 HELIX 28 AD1 ALA G 45 ASN G 73 1 29 HELIX 29 AD2 ILE G 79 ASP G 90 1 12 HELIX 30 AD3 ASP G 90 LEU G 97 1 8 HELIX 31 AD4 TYR H 34 HIS H 46 1 13 HELIX 32 AD5 SER H 52 ASN H 81 1 30 HELIX 33 AD6 THR H 87 LEU H 99 1 13 HELIX 34 AD7 GLY H 101 ALA H 121 1 21 HELIX 35 AD8 CYS K 297 TYR K 305 1 9 HELIX 36 AD9 GLU K 308 ASP K 315 1 8 HELIX 37 AE1 CYS K 329 ASP K 336 1 8 HELIX 38 AE2 LEU K 344 HIS K 351 1 8 HELIX 39 AE3 ASN K 355 GLU K 366 1 12 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 THR B 96 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 SHEET 1 AB2 2 SER K 268 THR K 269 0 SHEET 2 AB2 2 LYS K 276 THR K 277 -1 O THR K 277 N SER K 268 LINK O3' DT I -59 P 5CM I -58 1555 1555 1.61 LINK O3' 5CM I -58 P DG I -57 1555 1555 1.62 LINK SG CYS K 270 ZN ZN K 401 1555 1555 2.35 LINK NE2 HIS K 271 ZN ZN K 403 1555 1555 2.02 LINK SG CYS K 273 ZN ZN K 401 1555 1555 2.32 LINK SG CYS K 284 ZN ZN K 402 1555 1555 2.30 LINK SG CYS K 289 ZN ZN K 402 1555 1555 2.30 LINK NH1 ARG K 293 ZN ZN K 402 1555 1555 2.52 LINK SG CYS K 297 ZN ZN K 401 1555 1555 2.23 LINK SG CYS K 300 ZN ZN K 401 1555 1555 2.32 LINK SG CYS K 320 ZN ZN K 402 1555 1555 2.30 LINK SG CYS K 323 ZN ZN K 402 1555 1555 2.32 LINK SG CYS K 327 ZN ZN K 403 1555 1555 2.39 LINK SG CYS K 329 ZN ZN K 403 1555 1555 2.22 LINK SG CYS K 332 ZN ZN K 403 1555 1555 2.28 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