HEADER DNA BINDING PROTEIN/DNA 31-MAR-24 9B8R TITLE CRYO-EM STRUCTURE OF S. CEREVISIAE POLE-CORE-DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRIMER DNA; COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TEMPLATE DNA; COMPND 7 CHAIN: T; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA POLYMERASE EPSILON CATALYTIC SUBUNIT; COMPND 11 CHAIN: E; COMPND 12 EC: 2.7.7.7; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: DNA MOLECULE; SOURCE 4 ORGANISM_TAXID: 2853804; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: DNA MOLECULE; SOURCE 8 ORGANISM_TAXID: 2853804; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 11 ORGANISM_COMMON: BREWER'S YEAST; SOURCE 12 ORGANISM_TAXID: 4932; SOURCE 13 GENE: POL2, GI527_G0004851; SOURCE 14 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 4932 KEYWDS POL2, DNA, REPLICATION, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Z.YUAN,R.GEORGESCU,M.O'DONNELL,H.LI REVDAT 2 16-OCT-24 9B8R 1 JRNL REVDAT 1 09-OCT-24 9B8R 0 JRNL AUTH Z.YUAN,R.GEORGESCU,N.Y.YAO,O.YURIEVA,M.E.O'DONNELL,H.LI JRNL TITL MECHANISM OF PCNA LOADING BY CTF18-RFC FOR LEADING-STRAND JRNL TITL 2 DNA SYNTHESIS. JRNL REF SCIENCE V. 385 2024 JRNL REFN ESSN 1095-9203 JRNL PMID 39088616 JRNL DOI 10.1126/SCIENCE.ADK5901 REMARK 2 REMARK 2 RESOLUTION. 3.50 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 121833 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 9B8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-APR-24. REMARK 100 THE DEPOSITION ID IS D_1000282885. 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 : POLE-CORE-DNA COMPLEX 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 : 7.40 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 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 6000.00 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, T, E 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 GLN E 89 REMARK 465 GLU E 90 REMARK 465 THR E 91 REMARK 465 LEU E 92 REMARK 465 SER E 93 REMARK 465 SER E 94 REMARK 465 GLY E 95 REMARK 465 SER E 96 REMARK 465 ASN E 97 REMARK 465 GLY E 98 REMARK 465 GLY E 99 REMARK 465 GLY E 100 REMARK 465 ASN E 101 REMARK 465 SER E 102 REMARK 465 ASN E 103 REMARK 465 ASP E 104 REMARK 465 GLY E 105 REMARK 465 GLU E 106 REMARK 465 ARG E 107 REMARK 465 VAL E 108 REMARK 465 THR E 109 REMARK 465 THR E 110 REMARK 465 ASN E 111 REMARK 465 GLN E 112 REMARK 465 ASN E 217 REMARK 465 VAL E 218 REMARK 465 GLN E 219 REMARK 465 ARG E 220 REMARK 465 ASN E 221 REMARK 465 ILE E 222 REMARK 465 TYR E 223 REMARK 465 ASN E 224 REMARK 465 VAL E 225 REMARK 465 ALA E 226 REMARK 465 ALA E 227 REMARK 465 ASN E 228 REMARK 465 GLY E 229 REMARK 465 SER E 230 REMARK 465 GLU E 231 REMARK 465 LYS E 232 REMARK 465 VAL E 233 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 DC P 10 O3' REMARK 470 TYR E 60 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE E 72 CG1 CG2 CD1 REMARK 470 LEU E 79 CG CD1 CD2 REMARK 470 PHE E 119 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU E 122 CG CD1 CD2 REMARK 470 ASP E 123 CG OD1 OD2 REMARK 470 GLU E 125 CG CD OE1 OE2 REMARK 470 SER E 128 OG REMARK 470 VAL E 133 CG1 CG2 REMARK 470 LEU E 175 CG CD1 CD2 REMARK 470 HIS E 180 CG ND1 CD2 CE1 NE2 REMARK 470 LEU E 181 CG CD1 CD2 REMARK 470 ILE E 259 CG1 CG2 CD1 REMARK 470 LYS E 266 CG CD CE NZ REMARK 470 ILE E 273 CG1 CG2 CD1 REMARK 470 ASP E 275 CG OD1 OD2 REMARK 470 LEU E 298 CG CD1 CD2 REMARK 470 PHE E 300 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP E 368 CG OD1 OD2 REMARK 470 GLN E 468 CG CD OE1 NE2 REMARK 470 GLU E 472 CG CD OE1 OE2 REMARK 470 CYS E 516 SG REMARK 470 LYS E 534 CG CD CE NZ REMARK 470 GLU E 540 CG CD OE1 OE2 REMARK 470 THR E 552 OG1 CG2 REMARK 470 PHE E 566 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU E 570 CG CD1 CD2 REMARK 470 GLN E 655 CG CD OE1 NE2 REMARK 470 LYS E 660 CG CD CE NZ REMARK 470 ARG E 765 CG CD NE CZ NH1 NH2 REMARK 470 PHE E 777 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN E 820 CG CD OE1 NE2 REMARK 470 ILE E 826 CG1 CG2 CD1 REMARK 470 TYR E 831 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 MET E 835 CG SD CE REMARK 470 ARG E 836 CG CD NE CZ NH1 NH2 REMARK 470 ARG E 840 CG CD NE CZ NH1 NH2 REMARK 470 LYS E1096 CG CD CE NZ REMARK 470 ARG E1105 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DG P 3 C1' DG P 3 N9 -0.116 REMARK 500 DG T 5 O3' DG T 5 C3' -0.042 REMARK 500 DA T 10 O3' DA T 10 C3' -0.039 REMARK 500 GLU E 766 C ASN E 767 N 0.219 REMARK 500 PRO E 949 C TYR E 950 N 0.227 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 DA T 10 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 DA T 10 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG T 14 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 ARG E 148 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG E 243 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG E 252 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG E 325 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG E 361 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG E 361 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG E 367 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG E 424 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG E 653 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG E 672 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG E 672 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG E 679 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG E 738 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 GLU E 766 O - C - N ANGL. DEV. = -11.0 DEGREES REMARK 500 ARG E 913 NE - CZ - NH1 ANGL. DEV. = 4.8 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 ASP E 68 34.39 -98.68 REMARK 500 ASP E 123 162.55 61.06 REMARK 500 GLU E 125 -68.44 66.12 REMARK 500 SER E 128 162.70 163.06 REMARK 500 CYS E 163 -23.28 -145.00 REMARK 500 GLU E 244 17.72 59.23 REMARK 500 ARG E 277 -2.63 -58.57 REMARK 500 ASP E 316 12.19 51.64 REMARK 500 PHE E 382 -71.53 -131.57 REMARK 500 TYR E 431 11.50 59.14 REMARK 500 LYS E 466 54.34 -151.86 REMARK 500 TYR E 488 -52.07 -128.96 REMARK 500 THR E 552 -163.80 -162.96 REMARK 500 ILE E 659 102.00 -35.11 REMARK 500 PRO E 691 1.09 -66.39 REMARK 500 HIS E 748 -1.05 58.02 REMARK 500 ASN E 767 119.68 -22.31 REMARK 500 PHE E 769 -34.90 -131.04 REMARK 500 ILE E 798 -173.44 -63.88 REMARK 500 HIS E 804 46.16 -149.48 REMARK 500 TYR E 833 -53.49 -14.40 REMARK 500 VAL E 834 2.11 -56.04 REMARK 500 TRP E 841 19.07 49.44 REMARK 500 SER E 843 60.18 -165.81 REMARK 500 GLU E 845 -99.99 -53.77 REMARK 500 MET E 846 -47.09 0.80 REMARK 500 THR E 876 -72.56 64.78 REMARK 500 GLU E 889 -108.20 -119.29 REMARK 500 GLU E 991 151.70 73.83 REMARK 500 MET E1036 42.01 -79.63 REMARK 500 LYS E1054 -163.55 -112.04 REMARK 500 SER E1095 144.26 141.89 REMARK 500 LYS E1096 -81.82 -128.50 REMARK 500 PHE E1098 -144.50 -120.45 REMARK 500 VAL E1102 -79.90 -55.98 REMARK 500 ILE E1137 -38.57 -35.35 REMARK 500 ASN E1169 99.29 -26.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG E 749 VAL E 750 -139.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG E 509 0.08 SIDE CHAIN REMARK 500 ARG E 567 0.10 SIDE CHAIN REMARK 500 ARG E 630 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN E 81 17.12 REMARK 500 ASP E 123 10.11 REMARK 500 GLU E 766 11.18 REMARK 500 PRO E 949 -13.61 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 SF4 E1401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 665 SG REMARK 620 2 SF4 E1401 S2 110.0 REMARK 620 3 SF4 E1401 S3 138.9 104.1 REMARK 620 4 SF4 E1401 S4 89.2 104.5 103.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 E1401 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 668 SG REMARK 620 2 SF4 E1401 S1 119.0 REMARK 620 3 SF4 E1401 S2 124.0 104.6 REMARK 620 4 SF4 E1401 S3 97.4 104.4 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 E1401 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 677 SG REMARK 620 2 SF4 E1401 S1 103.8 REMARK 620 3 SF4 E1401 S3 142.8 104.1 REMARK 620 4 SF4 E1401 S4 92.2 104.5 103.9 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-44356 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF S. CEREVISIAE POLE-CORE-DNA DBREF 9B8R P 1 10 PDB 9B8R 9B8R 1 10 DBREF 9B8R T 3 14 PDB 9B8R 9B8R 3 14 DBREF1 9B8R E 27 1186 UNP A0A8H4BWE7_YEASX DBREF2 9B8R E A0A8H4BWE7 27 1186 SEQRES 1 P 10 DC DT DG DT DT DG DC DT DG DC SEQRES 1 T 12 DT DA DG DC DA DG DC DA DA DC DA DG SEQRES 1 E 1160 SER ASN ASN TYR ALA LEU SER ALA GLN GLN LEU LEU ASN SEQRES 2 E 1160 ALA SER LYS ILE ASP ASP ILE ASP SER MET MET GLY PHE SEQRES 3 E 1160 GLU ARG TYR VAL PRO PRO GLN TYR ASN GLY ARG PHE ASP SEQRES 4 E 1160 ALA LYS ASP ILE ASP GLN ILE PRO GLY ARG VAL GLY TRP SEQRES 5 E 1160 LEU THR ASN MET HIS ALA THR LEU VAL SER GLN GLU THR SEQRES 6 E 1160 LEU SER SER GLY SER ASN GLY GLY GLY ASN SER ASN ASP SEQRES 7 E 1160 GLY GLU ARG VAL THR THR ASN GLN GLY ILE SER GLY VAL SEQRES 8 E 1160 ASP PHE TYR PHE LEU ASP GLU GLU GLY GLY SER PHE LYS SEQRES 9 E 1160 SER THR VAL VAL TYR ASP PRO TYR PHE PHE ILE ALA CYS SEQRES 10 E 1160 ASN ASP GLU SER ARG VAL ASN ASP VAL GLU GLU LEU VAL SEQRES 11 E 1160 LYS LYS TYR LEU GLU SER CYS LEU LYS SER LEU GLN ILE SEQRES 12 E 1160 ILE ARG LYS GLU ASP LEU THR MET ASP ASN HIS LEU LEU SEQRES 13 E 1160 GLY LEU GLN LYS THR LEU ILE LYS LEU SER PHE VAL ASN SEQRES 14 E 1160 SER ASN GLN LEU PHE GLU ALA ARG LYS LEU LEU ARG PRO SEQRES 15 E 1160 ILE LEU GLN ASP ASN ALA ASN ASN ASN VAL GLN ARG ASN SEQRES 16 E 1160 ILE TYR ASN VAL ALA ALA ASN GLY SER GLU LYS VAL ASP SEQRES 17 E 1160 ALA LYS HIS LEU ILE GLU ASP ILE ARG GLU TYR ASP VAL SEQRES 18 E 1160 PRO TYR HIS VAL ARG VAL SER ILE ASP LYS ASP ILE ARG SEQRES 19 E 1160 VAL GLY LYS TRP TYR LYS VAL THR GLN GLN GLY PHE ILE SEQRES 20 E 1160 GLU ASP THR ARG LYS ILE ALA PHE ALA ASP PRO VAL VAL SEQRES 21 E 1160 MET ALA PHE ASP ILE GLU THR THR LYS PRO PRO LEU LYS SEQRES 22 E 1160 PHE PRO ASP SER ALA VAL ASP GLN ILE MET MET ILE SER SEQRES 23 E 1160 TYR MET ILE ASP GLY GLU GLY PHE LEU ILE THR ASN ARG SEQRES 24 E 1160 GLU ILE ILE SER GLU ASP ILE GLU ASP PHE GLU TYR THR SEQRES 25 E 1160 PRO LYS PRO GLU TYR PRO GLY PHE PHE THR ILE PHE ASN SEQRES 26 E 1160 GLU ASN ASP GLU VAL ALA LEU LEU GLN ARG PHE PHE GLU SEQRES 27 E 1160 HIS ILE ARG ASP VAL ARG PRO THR VAL ILE SER THR PHE SEQRES 28 E 1160 ASN GLY ASP PHE PHE ASP TRP PRO PHE ILE HIS ASN ARG SEQRES 29 E 1160 SER LYS ILE HIS GLY LEU ASP MET PHE ASP GLU ILE GLY SEQRES 30 E 1160 PHE ALA PRO ASP ALA GLU GLY GLU TYR LYS SER SER TYR SEQRES 31 E 1160 CYS SER HIS MET ASP CYS PHE ARG TRP VAL LYS ARG ASP SEQRES 32 E 1160 SER TYR LEU PRO GLN GLY SER GLN GLY LEU LYS ALA VAL SEQRES 33 E 1160 THR GLN SER LYS LEU GLY TYR ASN PRO ILE GLU LEU ASP SEQRES 34 E 1160 PRO GLU LEU MET THR PRO TYR ALA PHE GLU LYS PRO GLN SEQRES 35 E 1160 HIS LEU SER GLU TYR SER VAL SER ASP ALA VAL ALA THR SEQRES 36 E 1160 TYR TYR LEU TYR MET LYS TYR VAL HIS PRO PHE ILE PHE SEQRES 37 E 1160 SER LEU CYS THR ILE ILE PRO LEU ASN PRO ASP GLU THR SEQRES 38 E 1160 LEU ARG LYS GLY THR GLY THR LEU CYS GLU MET LEU LEU SEQRES 39 E 1160 MET VAL GLN ALA TYR GLN HIS ASN ILE LEU LEU PRO ASN SEQRES 40 E 1160 LYS HIS THR ASP PRO ILE GLU ARG PHE TYR ASP GLY HIS SEQRES 41 E 1160 LEU LEU GLU SER GLU THR TYR VAL GLY GLY HIS VAL GLU SEQRES 42 E 1160 SER LEU GLU ALA GLY VAL PHE ARG SER ASP LEU LYS ASN SEQRES 43 E 1160 GLU PHE LYS ILE ASP PRO SER ALA ILE ASP GLU LEU LEU SEQRES 44 E 1160 GLN GLU LEU PRO GLU ALA LEU LYS PHE SER VAL GLU VAL SEQRES 45 E 1160 GLU ASN LYS SER SER VAL ASP LYS VAL THR ASN PHE GLU SEQRES 46 E 1160 GLU ILE LYS ASN GLN ILE THR GLN LYS LEU LEU GLU LEU SEQRES 47 E 1160 LYS GLU ASN ASN ILE ARG ASN GLU LEU PRO LEU ILE TYR SEQRES 48 E 1160 HIS VAL ASP VAL ALA SER MET TYR PRO ASN ILE MET THR SEQRES 49 E 1160 THR ASN ARG LEU GLN PRO ASP SER ILE LYS ALA GLU ARG SEQRES 50 E 1160 ASP CYS ALA SER CYS ASP PHE ASN ARG PRO GLY LYS THR SEQRES 51 E 1160 CYS ALA ARG LYS LEU LYS TRP ALA TRP ARG GLY GLU PHE SEQRES 52 E 1160 PHE PRO SER LYS MET ASP GLU TYR ASN MET ILE LYS ARG SEQRES 53 E 1160 ALA LEU GLN ASN GLU THR PHE PRO ASN LYS ASN LYS PHE SEQRES 54 E 1160 SER LYS LYS LYS VAL LEU THR PHE ASP GLU LEU SER TYR SEQRES 55 E 1160 ALA ASP GLN VAL ILE HIS ILE LYS LYS ARG LEU THR GLU SEQRES 56 E 1160 TYR SER ARG LYS VAL TYR HIS ARG VAL LYS VAL SER GLU SEQRES 57 E 1160 ILE VAL GLU ARG GLU ALA ILE VAL CYS GLN ARG GLU ASN SEQRES 58 E 1160 PRO PHE TYR VAL ASP THR VAL LYS SER PHE ARG ASP ARG SEQRES 59 E 1160 ARG TYR GLU PHE LYS GLY LEU ALA LYS THR TRP LYS GLY SEQRES 60 E 1160 ASN LEU SER LYS ILE ASP PRO SER ASP LYS HIS ALA ARG SEQRES 61 E 1160 ASP GLU ALA LYS LYS MET ILE VAL LEU TYR ASP SER LEU SEQRES 62 E 1160 GLN LEU ALA HIS LYS VAL ILE LEU ASN SER PHE TYR GLY SEQRES 63 E 1160 TYR VAL MET ARG LYS GLY SER ARG TRP TYR SER MET GLU SEQRES 64 E 1160 MET ALA GLY ILE THR CYS LEU THR GLY ALA THR ILE ILE SEQRES 65 E 1160 GLN MET ALA ARG ALA LEU VAL GLU ARG VAL GLY ARG PRO SEQRES 66 E 1160 LEU GLU LEU ASP THR ASP GLY ILE TRP CYS ILE LEU PRO SEQRES 67 E 1160 LYS SER PHE PRO GLU THR TYR PHE PHE THR LEU GLU ASN SEQRES 68 E 1160 GLY LYS LYS LEU TYR LEU SER TYR PRO CYS SER MET LEU SEQRES 69 E 1160 ASN TYR ARG VAL HIS GLN LYS PHE THR ASN HIS GLN TYR SEQRES 70 E 1160 GLN GLU LEU LYS ASP PRO LEU ASN TYR ILE TYR GLU THR SEQRES 71 E 1160 HIS SER GLU ASN THR ILE PHE PHE GLU VAL ASP GLY PRO SEQRES 72 E 1160 TYR LYS ALA MET ILE LEU PRO SER SER LYS GLU GLU GLY SEQRES 73 E 1160 LYS GLY ILE LYS LYS ARG TYR ALA VAL PHE ASN GLU ASP SEQRES 74 E 1160 GLY SER LEU ALA GLU LEU LYS GLY PHE GLU LEU LYS ARG SEQRES 75 E 1160 ARG GLY GLU LEU GLN LEU ILE LYS ASN PHE GLN SER ASP SEQRES 76 E 1160 ILE PHE LYS VAL PHE LEU GLU GLY ASP THR LEU GLU GLY SEQRES 77 E 1160 CYS TYR SER ALA VAL ALA SER VAL CYS ASN ARG TRP LEU SEQRES 78 E 1160 ASP VAL LEU ASP SER HIS GLY LEU MET LEU GLU ASP GLU SEQRES 79 E 1160 ASP LEU VAL SER LEU ILE CYS GLU ASN ARG SER MET SER SEQRES 80 E 1160 LYS THR LEU LYS GLU TYR GLU GLY GLN LYS SER THR SER SEQRES 81 E 1160 ILE THR THR ALA ARG ARG LEU GLY ASP PHE LEU GLY GLU SEQRES 82 E 1160 ASP MET VAL LYS ASP LYS GLY LEU GLN CYS LYS TYR ILE SEQRES 83 E 1160 ILE SER SER LYS PRO PHE ASN ALA PRO VAL THR GLU ARG SEQRES 84 E 1160 ALA ILE PRO VAL ALA ILE PHE SER ALA ASP ILE PRO ILE SEQRES 85 E 1160 LYS ARG SER PHE LEU ARG ARG TRP THR LEU ASP PRO SER SEQRES 86 E 1160 LEU GLU ASP LEU ASP ILE ARG THR ILE ILE ASP TRP GLY SEQRES 87 E 1160 TYR TYR ARG GLU ARG LEU GLY SER ALA ILE GLN LYS ILE SEQRES 88 E 1160 ILE THR ILE PRO ALA ALA LEU GLN GLY VAL SER ASN PRO SEQRES 89 E 1160 VAL PRO ARG VAL GLU HIS PRO ASP TRP LEU LYS ARG LYS SEQRES 90 E 1160 ILE ALA THR HET SF4 E1401 8 HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 4 SF4 FE4 S4 HELIX 1 AA1 SER E 27 MET E 50 1 24 HELIX 2 AA2 ASP E 65 ILE E 69 5 5 HELIX 3 AA3 ASP E 145 SER E 147 5 3 HELIX 4 AA4 ARG E 148 LEU E 160 1 13 HELIX 5 AA5 ASN E 179 GLY E 183 5 5 HELIX 6 AA6 ASN E 195 ASN E 216 1 22 HELIX 7 AA7 ASP E 234 HIS E 237 5 4 HELIX 8 AA8 PRO E 248 LYS E 257 1 10 HELIX 9 AA9 ASP E 354 ARG E 370 1 17 HELIX 10 AB1 PHE E 382 HIS E 394 1 13 HELIX 11 AB2 ASP E 397 GLY E 403 1 7 HELIX 12 AB3 CYS E 422 ASP E 429 1 8 HELIX 13 AB4 PRO E 433 GLN E 437 5 5 HELIX 14 AB5 GLY E 438 LEU E 447 1 10 HELIX 15 AB6 ASP E 455 LYS E 466 1 12 HELIX 16 AB7 LYS E 466 TYR E 488 1 23 HELIX 17 AB8 TYR E 488 THR E 498 1 11 HELIX 18 AB9 ASN E 503 LYS E 510 1 8 HELIX 19 AC1 GLY E 511 HIS E 527 1 17 HELIX 20 AC2 ASP E 577 VAL E 598 1 22 HELIX 21 AC3 SER E 603 VAL E 607 5 5 HELIX 22 AC4 ASN E 609 ASN E 627 1 19 HELIX 23 AC5 SER E 643 ARG E 653 1 11 HELIX 24 AC6 ALA E 661 CYS E 668 1 8 HELIX 25 AC7 LYS E 693 ASN E 706 1 14 HELIX 26 AC8 SER E 727 TYR E 747 1 21 HELIX 27 AC9 PHE E 769 ILE E 798 1 30 HELIX 28 AD1 ARG E 806 VAL E 834 1 29 HELIX 29 AD2 SER E 843 GLY E 869 1 27 HELIX 30 AD3 TYR E 905 THR E 919 1 15 HELIX 31 AD4 GLN E 993 PHE E 1003 1 11 HELIX 32 AD5 LYS E 1004 GLU E 1008 5 5 HELIX 33 AD6 THR E 1011 SER E 1032 1 22 HELIX 34 AD7 GLU E 1038 CYS E 1047 1 10 HELIX 35 AD8 THR E 1055 GLU E 1060 5 6 HELIX 36 AD9 SER E 1064 GLY E 1078 1 15 HELIX 37 AE1 GLU E 1079 LYS E 1083 5 5 HELIX 38 AE2 ALA E 1110 ALA E 1114 5 5 HELIX 39 AE3 ASP E 1115 LEU E 1128 1 14 HELIX 40 AE4 ASP E 1136 ILE E 1141 1 6 HELIX 41 AE5 ASP E 1142 ILE E 1158 1 17 HELIX 42 AE6 ILE E 1158 GLN E 1165 1 8 HELIX 43 AE7 PRO E 1177 ILE E 1184 1 8 SHEET 1 AA1 3 ARG E 75 TRP E 78 0 SHEET 2 AA1 3 TRP E 264 THR E 268 -1 O TYR E 265 N GLY E 77 SHEET 3 AA1 3 GLY E 271 ASP E 275 -1 O ASP E 275 N TRP E 264 SHEET 1 AA2 3 ASN E 81 VAL E 87 0 SHEET 2 AA2 3 ILE E 114 PHE E 121 -1 O TYR E 120 N ASN E 81 SHEET 3 AA2 3 PHE E 129 VAL E 134 -1 O SER E 131 N PHE E 119 SHEET 1 AA3 4 SER E 166 LYS E 172 0 SHEET 2 AA3 4 LYS E 186 SER E 192 -1 O LYS E 190 N GLN E 168 SHEET 3 AA3 4 TYR E 138 CYS E 143 -1 N PHE E 139 O LEU E 191 SHEET 4 AA3 4 ILE E 239 ARG E 243 -1 O ASP E 241 N ALA E 142 SHEET 1 AA4 7 PHE E 335 GLU E 336 0 SHEET 2 AA4 7 PHE E 346 GLU E 352 -1 O PHE E 347 N PHE E 335 SHEET 3 AA4 7 GLU E 318 ASN E 324 1 N LEU E 321 O PHE E 350 SHEET 4 AA4 7 ILE E 308 ILE E 315 -1 N TYR E 313 O PHE E 320 SHEET 5 AA4 7 VAL E 286 THR E 293 -1 N GLU E 292 O MET E 309 SHEET 6 AA4 7 VAL E 373 THR E 376 1 O SER E 375 N MET E 287 SHEET 7 AA4 7 SER E 418 ASP E 421 1 O MET E 420 N ILE E 374 SHEET 1 AA5 2 ALA E 405 PRO E 406 0 SHEET 2 AA5 2 TYR E 412 LYS E 413 -1 O LYS E 413 N ALA E 405 SHEET 1 AA6 4 PHE E 542 TYR E 543 0 SHEET 2 AA6 4 HIS E 546 TYR E 553 -1 O HIS E 546 N TYR E 543 SHEET 3 AA6 4 ALA E 678 PHE E 689 -1 O ARG E 686 N THR E 552 SHEET 4 AA6 4 VAL E 752 CYS E 763 -1 O ARG E 758 N TRP E 683 SHEET 1 AA7 5 VAL E 558 SER E 560 0 SHEET 2 AA7 5 ARG E 870 ASP E 875 -1 O LEU E 874 N GLU E 559 SHEET 3 AA7 5 GLY E 878 PRO E 884 -1 O TRP E 880 N LEU E 872 SHEET 4 AA7 5 PRO E 634 VAL E 641 -1 N TYR E 637 O CYS E 881 SHEET 5 AA7 5 PHE E 944 TYR E 950 -1 O GLU E 945 N ASP E 640 SHEET 1 AA8 4 GLY E 564 ARG E 567 0 SHEET 2 AA8 4 ALA E 952 LEU E 955 -1 O LEU E 955 N GLY E 564 SHEET 3 AA8 4 TYR E 969 PHE E 972 -1 O ALA E 970 N ILE E 954 SHEET 4 AA8 4 LEU E 978 LYS E 982 -1 O GLU E 980 N VAL E 971 SHEET 1 AA9 2 ASN E 572 LYS E 575 0 SHEET 2 AA9 2 ILE E 629 GLU E 632 -1 O GLU E 632 N ASN E 572 SHEET 1 AB1 2 THR E 708 PRO E 710 0 SHEET 2 AB1 2 VAL E 720 THR E 722 -1 O LEU E 721 N PHE E 709 SHEET 1 AB2 2 THR E 890 THR E 894 0 SHEET 2 AB2 2 LYS E 900 SER E 904 -1 O LEU E 903 N TYR E 891 SHEET 1 AB3 2 ASN E 920 ASP E 928 0 SHEET 2 AB3 2 ILE E 933 GLU E 939 -1 O GLU E 939 N ASN E 920 SHEET 1 AB4 4 GLU E 991 LEU E 992 0 SHEET 2 AB4 4 GLU E1048 SER E1051 -1 O ASN E1049 N GLU E 991 SHEET 3 AB4 4 GLN E1088 ILE E1093 -1 O TYR E1091 N GLU E1048 SHEET 4 AB4 4 ALA E1106 PRO E1108 -1 O ILE E1107 N ILE E1092 LINK SG CYS E 665 FE1 SF4 E1401 1555 1555 2.40 LINK SG CYS E 668 FE4 SF4 E1401 1555 1555 1.96 LINK SG CYS E 677 FE2 SF4 E1401 1555 1555 2.41 CISPEP 1 GLY E 948 PRO E 949 0 6.77 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