HEADER DNA BINDING PROTEIN 26-JUN-23 8PKI TITLE CRYO-EM STRUCTURE OF NR5A2-NUCLEOSOME COMPLEX SHL+5.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3.3; COMPND 3 CHAIN: A, E; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HISTONE H4; COMPND 7 CHAIN: B, F; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HISTONE H2A; COMPND 11 CHAIN: C, G; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: HISTONE H2B TYPE 1-C/E/G; COMPND 15 CHAIN: D, H; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: DNA; COMPND 19 CHAIN: I; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 6; COMPND 22 MOLECULE: DNA; COMPND 23 CHAIN: J; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 7; COMPND 26 MOLECULE: NUCLEAR RECEPTOR SUBFAMILY 5 GROUP A MEMBER 2; COMPND 27 CHAIN: K; COMPND 28 SYNONYM: ALPHA-1-FETOPROTEIN TRANSCRIPTION FACTOR,B1-BINDING FACTOR, COMPND 29 HB1F,CYP7A PROMOTER-BINDING FACTOR,HEPATOCYTIC TRANSCRIPTION FACTOR, COMPND 30 LIVER RECEPTOR HOMOLOG 1,LRH-1; COMPND 31 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: H3-3A, H3.3A, H3F3A, H3-3B, H3.3B, H3F3B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 GENE: H4C1, HIST1H4A, H4C2, H4-53, HIST1H4B, H4C3, H4-12, HIST1H4C, SOURCE 13 H4C4, HIST1H4D, H4C6, HIST1H4F, H4C8, HIST1H4H, H4C9, HIST1H4I, SOURCE 14 H4C11, HIST1H4J, H4C12, HIST1H4K, HIST1H4M, H4C14, HIST2H4, SOURCE 15 HIST2H4A, H4C16, H4F16, HIST4H4; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 MOL_ID: 3; SOURCE 19 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 20 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 21 ORGANISM_TAXID: 10090; SOURCE 22 GENE: HIST1H2AD; SOURCE 23 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 24 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 25 MOL_ID: 4; SOURCE 26 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 27 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 28 ORGANISM_TAXID: 10090; SOURCE 29 GENE: H2BC4, HIST1H2BC, H2BC6, HIST1H2BE, H2BC8, HIST1H2BG; SOURCE 30 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 31 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 32 MOL_ID: 5; SOURCE 33 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 34 ORGANISM_TAXID: 32630; SOURCE 35 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 36 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 37 MOL_ID: 6; SOURCE 38 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 39 ORGANISM_TAXID: 32630; SOURCE 40 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 41 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 42 MOL_ID: 7; SOURCE 43 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 44 ORGANISM_COMMON: HUMAN; SOURCE 45 ORGANISM_TAXID: 9606; SOURCE 46 GENE: NR5A2, B1F, CPF, FTF; SOURCE 47 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 48 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOSOME, NUCLEAR RECEPTOR, NR5A2, DNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR W.KOBAYASHI,A.SAPPLER,D.BOLLSCHWEILER,M.KUMMECKE,J.BASQUIN, AUTHOR 2 E.ARSLANTAS,S.RUANGROENGKULRITH,R.HORNBERGER,K.DUDERSTADT, AUTHOR 3 K.TACHIBANA REVDAT 3 29-MAY-24 8PKI 1 JRNL REVDAT 2 06-MAR-24 8PKI 1 JRNL REVDAT 1 28-FEB-24 8PKI 0 JRNL AUTH W.KOBAYASHI,A.H.SAPPLER,D.BOLLSCHWEILER,M.KUMMECKE, JRNL AUTH 2 J.BASQUIN,E.N.ARSLANTAS,S.RUANGROENGKULRITH,R.HORNBERGER, JRNL AUTH 3 K.DUDERSTADT,K.TACHIBANA JRNL TITL NUCLEOSOME-BOUND NR5A2 STRUCTURE REVEALS PIONEER FACTOR JRNL TITL 2 MECHANISM BY DNA MINOR GROOVE ANCHOR COMPETITION. JRNL REF NAT.STRUCT.MOL.BIOL. V. 31 757 2024 JRNL REFN ESSN 1545-9985 JRNL PMID 38409506 JRNL DOI 10.1038/S41594-024-01239-0 REMARK 2 REMARK 2 RESOLUTION. 2.58 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) : 2.580 REMARK 3 NUMBER OF PARTICLES : 653440 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 8PKI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131474. 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 : CRYO-EM STRUCTURE OF THE REMARK 245 NUCLEOSOME CONTAINING NR5A2 REMARK 245 MOTIF AT SHL+5.5 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 6540.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN 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: 11-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 11-MERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER 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 ARG A 40 REMARK 465 TYR A 41 REMARK 465 ARG A 42 REMARK 465 ALA A 135 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 ALA C 10 REMARK 465 ARG C 11 REMARK 465 ALA C 12 REMARK 465 LYS C 119 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 MET D 0 REMARK 465 PRO D 1 REMARK 465 GLU D 2 REMARK 465 PRO D 3 REMARK 465 ALA D 4 REMARK 465 LYS D 5 REMARK 465 SER D 6 REMARK 465 ALA D 7 REMARK 465 PRO D 8 REMARK 465 ALA D 9 REMARK 465 PRO D 10 REMARK 465 LYS D 11 REMARK 465 LYS D 12 REMARK 465 GLY D 13 REMARK 465 SER D 14 REMARK 465 LYS D 15 REMARK 465 LYS D 16 REMARK 465 ALA D 17 REMARK 465 VAL D 18 REMARK 465 THR D 19 REMARK 465 LYS D 20 REMARK 465 ALA D 21 REMARK 465 GLN D 22 REMARK 465 LYS D 23 REMARK 465 LYS D 24 REMARK 465 ASP D 25 REMARK 465 GLY D 26 REMARK 465 LYS D 27 REMARK 465 LYS D 28 REMARK 465 ARG D 29 REMARK 465 LYS D 30 REMARK 465 ARG D 31 REMARK 465 SER D 32 REMARK 465 ARG D 33 REMARK 465 LYS D 34 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 SER 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 MET F -1 REMARK 465 SER F 0 REMARK 465 GLY F 1 REMARK 465 ARG F 2 REMARK 465 GLY F 3 REMARK 465 LYS F 4 REMARK 465 GLY F 5 REMARK 465 GLY F 6 REMARK 465 LYS F 7 REMARK 465 GLY F 8 REMARK 465 LEU F 9 REMARK 465 GLY F 10 REMARK 465 LYS F 11 REMARK 465 GLY F 12 REMARK 465 GLY F 13 REMARK 465 ALA F 14 REMARK 465 LYS F 15 REMARK 465 ARG F 16 REMARK 465 HIS F 17 REMARK 465 ARG F 18 REMARK 465 LYS F 19 REMARK 465 VAL F 20 REMARK 465 LEU F 21 REMARK 465 ARG F 22 REMARK 465 GLY F 101 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 ALA G 10 REMARK 465 ARG G 11 REMARK 465 ALA G 12 REMARK 465 LYS G 13 REMARK 465 GLN G 112 REMARK 465 ALA G 113 REMARK 465 VAL G 114 REMARK 465 LEU G 115 REMARK 465 LEU G 116 REMARK 465 PRO G 117 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 MET H 0 REMARK 465 PRO H 1 REMARK 465 GLU H 2 REMARK 465 PRO H 3 REMARK 465 ALA H 4 REMARK 465 LYS H 5 REMARK 465 SER H 6 REMARK 465 ALA H 7 REMARK 465 PRO H 8 REMARK 465 ALA H 9 REMARK 465 PRO H 10 REMARK 465 LYS H 11 REMARK 465 LYS H 12 REMARK 465 GLY H 13 REMARK 465 SER H 14 REMARK 465 LYS H 15 REMARK 465 LYS H 16 REMARK 465 ALA H 17 REMARK 465 VAL H 18 REMARK 465 THR H 19 REMARK 465 LYS H 20 REMARK 465 ALA H 21 REMARK 465 GLN H 22 REMARK 465 LYS H 23 REMARK 465 LYS H 24 REMARK 465 ASP H 25 REMARK 465 GLY H 26 REMARK 465 LYS H 27 REMARK 465 LYS H 28 REMARK 465 ARG H 29 REMARK 465 LYS H 30 REMARK 465 ARG H 31 REMARK 465 SER H 32 REMARK 465 ARG H 33 REMARK 465 LYS H 34 REMARK 465 LYS H 125 REMARK 465 DA I -3 REMARK 465 DT I -2 REMARK 465 DC I -1 REMARK 465 DC I 0 REMARK 465 DA I 138 REMARK 465 DC I 139 REMARK 465 DA I 140 REMARK 465 DT I 141 REMARK 465 DC I 142 REMARK 465 DC I 143 REMARK 465 DT I 144 REMARK 465 DG I 145 REMARK 465 DT I 146 REMARK 465 DG I 147 REMARK 465 DA I 148 REMARK 465 DT I 149 REMARK 465 DA J -76 REMARK 465 DT J -75 REMARK 465 DC J -74 REMARK 465 DA J -73 REMARK 465 DC J -72 REMARK 465 DA J -71 REMARK 465 DG J -70 REMARK 465 DG J -69 REMARK 465 DA J -68 REMARK 465 DT J -67 REMARK 465 DG J -66 REMARK 465 DG J 73 REMARK 465 DG J 74 REMARK 465 DA J 75 REMARK 465 DT J 76 REMARK 465 ILE K 123 REMARK 465 GLU K 124 REMARK 465 ASN K 125 REMARK 465 GLN K 126 REMARK 465 ASN K 127 REMARK 465 CYS K 128 REMARK 465 GLN K 129 REMARK 465 ILE K 130 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 ARG A 134 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 118 CG CD CE NZ REMARK 470 LYS D 125 CG CD CE NZ REMARK 470 ASP F 23 CG OD1 OD2 REMARK 470 LYS G 74 CG CD CE NZ REMARK 470 ASN G 110 CG OD1 ND2 REMARK 470 GLU H 35 CG CD OE1 OE2 REMARK 470 SER H 124 CB OG REMARK 470 DT I 1 P OP1 OP2 REMARK 470 LEU K 85 CG CD1 CD2 REMARK 470 VAL K 88 CG1 CG2 REMARK 470 ASP K 91 CG OD1 OD2 REMARK 470 LYS K 92 CG CD CE NZ REMARK 470 VAL K 93 CG1 CG2 REMARK 470 THR K 113 OG1 CG2 REMARK 470 ASN K 116 CG OD1 ND2 REMARK 470 ASN K 117 CG OD1 ND2 REMARK 470 LYS K 118 CG CD CE NZ REMARK 470 ARG K 119 CG CD NE CZ NH1 NH2 REMARK 470 TYR K 120 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 THR K 121 OG1 CG2 REMARK 470 ASP K 131 CG OD1 OD2 REMARK 470 LYS K 132 CG CD CE NZ REMARK 470 THR K 133 OG1 CG2 REMARK 470 GLN K 134 CG CD OE1 NE2 REMARK 470 ARG K 135 CG CD NE CZ NH1 NH2 REMARK 470 LYS K 136 CG CD CE NZ REMARK 470 ARG K 137 CG CD NE CZ NH1 NH2 REMARK 470 ARG K 142 CG CD NE CZ NH1 NH2 REMARK 470 MET K 161 CG SD CE REMARK 470 LYS K 167 CG CD CE NZ REMARK 470 MET K 171 CG SD CE REMARK 470 LYS K 173 CG CD CE NZ REMARK 470 ARG K 174 CG CD NE CZ NH1 NH2 REMARK 470 ASP K 175 CG OD1 OD2 REMARK 470 ARG K 176 CG CD NE CZ NH1 NH2 REMARK 470 LEU K 178 CG CD1 CD2 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 J -36 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA J 16 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT J 67 O4' - C1' - N1 ANGL. DEV. = 1.8 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 THR A 58 19.88 52.85 REMARK 500 ASP D 51 76.38 -100.72 REMARK 500 LYS G 36 52.64 -94.40 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS K 86 SG REMARK 620 2 CYS K 89 SG 108.8 REMARK 620 3 CYS K 103 SG 114.1 106.7 REMARK 620 4 CYS K 106 SG 110.2 108.9 108.1 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17740 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF NR5A2-NUCLEOSOME COMPLEX SHL+5.5 DBREF 8PKI A 0 135 UNP P84244 H33_MOUSE 1 136 DBREF 8PKI B 0 102 UNP P62806 H4_MOUSE 1 103 DBREF 8PKI C 0 129 UNP B2RVF0 B2RVF0_MOUSE 1 130 DBREF 8PKI D 0 125 UNP Q6ZWY9 H2B1C_MOUSE 1 126 DBREF 8PKI E 0 135 UNP P84244 H33_MOUSE 1 136 DBREF 8PKI F -1 101 UNP P62806 H4_MOUSE 1 103 DBREF 8PKI G 0 129 UNP B2RVF0 B2RVF0_MOUSE 1 130 DBREF 8PKI H 0 125 UNP Q6ZWY9 H2B1C_MOUSE 1 126 DBREF 8PKI I -3 149 PDB 8PKI 8PKI -3 149 DBREF 8PKI J -76 76 PDB 8PKI 8PKI -76 76 DBREF 8PKI K 85 178 UNP O00482 NR5A2_HUMAN 39 132 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 SER 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 ALA ALA ILE GLY 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 ALA 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 SER 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 ILE 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 ALA VAL LEU LEU SEQRES 10 C 130 PRO LYS LYS THR GLU SER HIS HIS LYS ALA LYS GLY 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 ALA GLN LYS LYS ASP SEQRES 3 D 126 GLY LYS LYS ARG LYS ARG SER ARG LYS GLU SER TYR SER SEQRES 4 D 126 VAL TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP SEQRES 5 D 126 THR GLY ILE SER SER LYS ALA MET GLY ILE MET ASN SER SEQRES 6 D 126 PHE VAL ASN ASP ILE 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 SER 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 SER 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 ALA ALA ILE GLY 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 ALA 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 SER 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 ILE 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 ALA VAL LEU LEU SEQRES 10 G 130 PRO LYS LYS THR GLU SER HIS HIS LYS ALA LYS GLY 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 ALA GLN LYS LYS ASP SEQRES 3 H 126 GLY LYS LYS ARG LYS ARG SER ARG LYS GLU SER TYR SER SEQRES 4 H 126 VAL TYR VAL TYR LYS VAL LEU LYS GLN VAL HIS PRO ASP SEQRES 5 H 126 THR GLY ILE SER SER LYS ALA MET GLY ILE MET ASN SER SEQRES 6 H 126 PHE VAL ASN ASP ILE 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 SER LYS SEQRES 1 I 153 DA DT DC DC DT DG DG DA DG DA DA DT DC SEQRES 2 I 153 DC DC DG DG DT DG DC DC DG DA DG DG DC SEQRES 3 I 153 DC DG DC DT DC DA DA DT DT DG DG DT DC SEQRES 4 I 153 DG DT DA DG DA DC DA DG DC DT DC DT DA SEQRES 5 I 153 DG DC DA DC DC DG DC DT DT DA DA DA DC SEQRES 6 I 153 DG DC DA DC DG DT DA DC DG DC DG DC DT SEQRES 7 I 153 DG DT DC DC DC DC DC DG DC DG DT DT DT SEQRES 8 I 153 DT DA DA DC DC DG DC DC DA DA DG DG DG SEQRES 9 I 153 DG DA DT DT DA DC DT DC DC DC DT DA DG SEQRES 10 I 153 DT DC DT DC DC DA DG DG DC DA DC DG DT SEQRES 11 I 153 DT DC DA DA DG DG DC DC DA DA DT DA DC SEQRES 12 I 153 DA DT DC DC DT DG DT DG DA DT SEQRES 1 J 153 DA DT DC DA DC DA DG DG DA DT DG DT DA SEQRES 2 J 153 DT DT DG DG DC DC DT DT DG DA DA DC DG SEQRES 3 J 153 DT DG DC DC DT DG DG DA DG DA DC DT DA SEQRES 4 J 153 DG DG DG DA DG DT DA DA DT DC DC DC DC SEQRES 5 J 153 DT DT DG DG DC DG DG DT DT DA DA DA DA SEQRES 6 J 153 DC DG DC DG DG DG DG DG DA DC DA DG DC SEQRES 7 J 153 DG DC DG DT DA DC DG DT DG DC DG DT DT SEQRES 8 J 153 DT DA DA DG DC DG DG DT DG DC DT DA DG SEQRES 9 J 153 DA DG DC DT DG DT DC DT DA DC DG DA DC SEQRES 10 J 153 DC DA DA DT DT DG DA DG DC DG DG DC DC SEQRES 11 J 153 DT DC DG DG DC DA DC DC DG DG DG DA DT SEQRES 12 J 153 DT DC DT DC DC DA DG DG DA DT SEQRES 1 K 94 LEU CYS PRO VAL CYS GLY ASP LYS VAL SER GLY TYR HIS SEQRES 2 K 94 TYR GLY LEU LEU THR CYS GLU SER CYS LYS GLY PHE PHE SEQRES 3 K 94 LYS ARG THR VAL GLN ASN ASN LYS ARG TYR THR CYS ILE SEQRES 4 K 94 GLU ASN GLN ASN CYS GLN ILE ASP LYS THR GLN ARG LYS SEQRES 5 K 94 ARG CYS PRO TYR CYS ARG PHE GLN LYS CYS LEU SER VAL SEQRES 6 K 94 GLY MET LYS LEU GLU ALA VAL ARG ALA ASP ARG MET ARG SEQRES 7 K 94 GLY GLY ARG ASN LYS PHE GLY PRO MET TYR LYS ARG ASP SEQRES 8 K 94 ARG ALA LEU HET ZN K 201 1 HETNAM ZN ZINC ION FORMUL 12 ZN ZN 2+ HELIX 1 AA1 GLY A 44 SER A 57 1 14 HELIX 2 AA2 ARG A 63 LYS A 79 1 17 HELIX 3 AA3 GLN A 85 ALA A 114 1 30 HELIX 4 AA4 MET A 120 GLY A 132 1 13 HELIX 5 AA5 ASN B 25 ILE B 29 5 5 HELIX 6 AA6 THR B 30 GLY B 41 1 12 HELIX 7 AA7 LEU B 49 HIS B 75 1 27 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 ASN C 73 1 28 HELIX 12 AB3 ILE C 79 ASN C 89 1 11 HELIX 13 AB4 ASP C 90 LEU C 97 1 8 HELIX 14 AB5 TYR D 37 HIS D 49 1 13 HELIX 15 AB6 SER D 55 ASN D 84 1 30 HELIX 16 AB7 THR D 90 LEU D 102 1 13 HELIX 17 AB8 PRO D 103 SER D 124 1 22 HELIX 18 AB9 GLY E 44 GLN E 55 1 12 HELIX 19 AC1 ARG E 63 ASP E 77 1 15 HELIX 20 AC2 GLN E 85 ALA E 114 1 30 HELIX 21 AC3 MET E 120 ARG E 131 1 12 HELIX 22 AC4 ASP F 23 ILE F 28 5 6 HELIX 23 AC5 THR F 29 GLY F 40 1 12 HELIX 24 AC6 LEU F 48 ALA F 75 1 28 HELIX 25 AC7 THR F 81 GLN F 92 1 12 HELIX 26 AC8 THR G 16 GLY G 22 1 7 HELIX 27 AC9 PRO G 26 LYS G 36 1 11 HELIX 28 AD1 GLY G 46 ASN G 73 1 28 HELIX 29 AD2 ILE G 79 ASN G 89 1 11 HELIX 30 AD3 ASP G 90 LEU G 97 1 8 HELIX 31 AD4 TYR H 37 HIS H 49 1 13 HELIX 32 AD5 SER H 55 ASN H 84 1 30 HELIX 33 AD6 THR H 90 LEU H 102 1 13 HELIX 34 AD7 PRO H 103 SER H 124 1 22 HELIX 35 AD8 CYS K 103 ASN K 117 1 15 HELIX 36 AD9 LYS K 132 ARG K 137 5 6 HELIX 37 AE1 CYS K 138 VAL K 149 1 12 HELIX 38 AE2 PHE K 168 LEU K 178 1 11 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 88 ILE D 89 1 O ILE D 89 N ARG C 42 SHEET 1 AA5 2 ARG C 77 ILE C 78 0 SHEET 2 AA5 2 GLY D 53 ILE D 54 1 O GLY D 53 N ILE C 78 SHEET 1 AA6 2 VAL C 100 ILE C 102 0 SHEET 2 AA6 2 THR F 95 TYR F 97 1 O THR F 95 N THR C 101 SHEET 1 AA7 2 ARG E 83 PHE E 84 0 SHEET 2 AA7 2 THR F 79 VAL F 80 1 O VAL F 80 N ARG E 83 SHEET 1 AA8 2 THR E 118 ILE E 119 0 SHEET 2 AA8 2 ARG F 44 ILE F 45 1 O ARG F 44 N ILE E 119 SHEET 1 AA9 2 ARG G 42 VAL G 43 0 SHEET 2 AA9 2 THR H 88 ILE H 89 1 O ILE H 89 N ARG G 42 SHEET 1 AB1 2 ARG G 77 ILE G 78 0 SHEET 2 AB1 2 GLY H 53 ILE H 54 1 O GLY H 53 N ILE G 78 SHEET 1 AB2 2 GLY K 95 HIS K 97 0 SHEET 2 AB2 2 LEU K 100 THR K 102 -1 O LEU K 100 N HIS K 97 LINK SG CYS K 86 ZN ZN K 201 1555 1555 2.33 LINK SG CYS K 89 ZN ZN K 201 1555 1555 2.33 LINK SG CYS K 103 ZN ZN K 201 1555 1555 2.33 LINK SG CYS K 106 ZN ZN K 201 1555 1555 2.33 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