HEADER DNA BINDING PROTEIN 11-APR-25 9QV5 TITLE ASGARD ARCHAEAL HHOB NUCLEOSOME IN THE CLOSED CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARCHAEAL HISTONE A; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (120-MER) PART OF A FULL 147 BP WIDOM601 DNA; COMPND 7 CHAIN: X; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (120-MER) PART OF A FULL 147 BP WIDOM601 DNA; COMPND 11 CHAIN: Y; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDATUS HEIMDALLARCHAEOTA ARCHAEON LC_3; SOURCE 3 ORGANISM_TAXID: 1841598; SOURCE 4 STRAIN: LC_3; SOURCE 5 GENE: HEIMC3_17480; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: MACROLABS LIC-1B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 OTHER_DETAILS: PCR; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630 KEYWDS ARCHAEA, ASGARD, CHROMATIN, NUCLEOSOME, DNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.M.RANAWAT,S.O.DODONOVA REVDAT 4 03-DEC-25 9QV5 1 JRNL REVDAT 3 12-NOV-25 9QV5 1 JRNL REVDAT 2 05-NOV-25 9QV5 1 JRNL REVDAT 1 29-OCT-25 9QV5 0 JRNL AUTH H.M.RANAWAT,M.K.CAJILI,N.LOPEZ-BARBOSA,T.QUAIL,R.T.DAME, JRNL AUTH 2 S.O.DODONOVA JRNL TITL CRYO-EM REVEALS OPEN AND CLOSED ASGARD CHROMATIN ASSEMBLIES. JRNL REF MOL.CELL V. 85 4152 2025 JRNL REFN ISSN 1097-2765 JRNL PMID 41161312 JRNL DOI 10.1016/J.MOLCEL.2025.10.001 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, UCSF CHIMERAX, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, PHENIX, COOT, REMARK 3 UCSF CHIMERAX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1AOI REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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 : 117260 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: IN CRYOSPARC REMARK 4 REMARK 4 9QV5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-APR-25. REMARK 100 THE DEPOSITION ID IS D_1292146293. 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 : CLOSED COMPLEX OF HHOB ASGARD REMARK 245 ARCHAEAL HISTONE HHOB AND DNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.19 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : AT 20* C REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : IN PRESENCE OF 1MM MG 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 : TFS FALCON 4I (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1750.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5940.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 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: DECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, X, Y 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 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 MET G 1 CB CG SD CE REMARK 470 ALA G 2 CB REMARK 470 ASN G 4 CB CG OD1 ND2 REMARK 470 PHE G 5 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 ALA G 6 CB REMARK 470 ASN G 7 CB CG OD1 ND2 REMARK 470 ALA G 8 CB REMARK 470 ARG G 9 CB CG CD NE CZ NH1 NH2 REMARK 470 VAL G 10 CB CG1 CG2 REMARK 470 GLU G 11 CB CG CD OE1 OE2 REMARK 470 LYS G 12 CB CG CD CE NZ REMARK 470 LEU G 13 CB CG CD1 CD2 REMARK 470 ILE G 14 CB CG1 CG2 CD1 REMARK 470 ARG G 15 CB CG CD NE CZ NH1 NH2 REMARK 470 GLN G 16 CB CG CD OE1 NE2 REMARK 470 ALA G 17 CB REMARK 470 ALA G 19 CB REMARK 470 GLN G 20 CB CG CD OE1 NE2 REMARK 470 ARG G 21 CB CG CD NE CZ NH1 NH2 REMARK 470 VAL G 22 CB CG1 CG2 REMARK 470 SER G 23 CB OG REMARK 470 ALA G 24 CB REMARK 470 ASP G 25 CB CG OD1 OD2 REMARK 470 ALA G 26 CB REMARK 470 VAL G 27 CB CG1 CG2 REMARK 470 ASP G 28 CB CG OD1 OD2 REMARK 470 LYS G 29 CB CG CD CE NZ REMARK 470 MET G 30 CB CG SD CE REMARK 470 ASN G 31 CB CG OD1 ND2 REMARK 470 GLU G 32 CB CG CD OE1 OE2 REMARK 470 ILE G 33 CB CG1 CG2 CD1 REMARK 470 LEU G 34 CB CG CD1 CD2 REMARK 470 THR G 35 CB OG1 CG2 REMARK 470 ASP G 36 CB CG OD1 OD2 REMARK 470 TRP G 37 CB CG CD1 CD2 NE1 CE2 CE3 REMARK 470 TRP G 37 CZ2 CZ3 CH2 REMARK 470 LYS G 39 CB CG CD CE NZ REMARK 470 ASN G 40 CB CG OD1 ND2 REMARK 470 ILE G 41 CB CG1 CG2 CD1 REMARK 470 ALA G 42 CB REMARK 470 LYS G 43 CB CG CD CE NZ REMARK 470 TYR G 44 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR G 44 OH REMARK 470 ALA G 45 CB REMARK 470 VAL G 46 CB CG1 CG2 REMARK 470 GLU G 47 CB CG CD OE1 OE2 REMARK 470 ILE G 48 CB CG1 CG2 CD1 REMARK 470 ALA G 49 CB REMARK 470 ARG G 50 CB CG CD NE CZ NH1 NH2 REMARK 470 HIS G 51 CB CG ND1 CD2 CE1 NE2 REMARK 470 SER G 52 CB OG REMARK 470 ARG G 54 CB CG CD NE CZ NH1 NH2 REMARK 470 LYS G 55 CB CG CD CE NZ REMARK 470 THR G 56 CB OG1 CG2 REMARK 470 VAL G 57 CB CG1 CG2 REMARK 470 LYS G 58 CB CG CD CE NZ REMARK 470 GLU G 59 CB CG CD OE1 OE2 REMARK 470 ASN G 60 CB CG OD1 ND2 REMARK 470 ASP G 61 CB CG OD1 OD2 REMARK 470 ILE G 62 CB CG1 CG2 CD1 REMARK 470 LYS G 63 CB CG CD CE NZ REMARK 470 LEU G 64 CB CG CD1 CD2 REMARK 470 ALA G 65 CB REMARK 470 ALA G 66 CB REMARK 470 GLN G 67 CB CG CD OE1 NE2 REMARK 470 LYS G 68 CB CG CD CE NZ REMARK 470 MET H 1 CB CG SD CE REMARK 470 ALA H 2 CB REMARK 470 ASN H 4 CB CG OD1 ND2 REMARK 470 PHE H 5 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 ALA H 6 CB REMARK 470 ASN H 7 CB CG OD1 ND2 REMARK 470 ALA H 8 CB REMARK 470 ARG H 9 CB CG CD NE CZ NH1 NH2 REMARK 470 VAL H 10 CB CG1 CG2 REMARK 470 GLU H 11 CB CG CD OE1 OE2 REMARK 470 LYS H 12 CB CG CD CE NZ REMARK 470 LEU H 13 CB CG CD1 CD2 REMARK 470 ILE H 14 CB CG1 CG2 CD1 REMARK 470 ARG H 15 CB CG CD NE CZ NH1 NH2 REMARK 470 GLN H 16 CB CG CD OE1 NE2 REMARK 470 ALA H 17 CB REMARK 470 ALA H 19 CB REMARK 470 GLN H 20 CB CG CD OE1 NE2 REMARK 470 ARG H 21 CB CG CD NE CZ NH1 NH2 REMARK 470 VAL H 22 CB CG1 CG2 REMARK 470 SER H 23 CB OG REMARK 470 ALA H 24 CB REMARK 470 ASP H 25 CB CG OD1 OD2 REMARK 470 ALA H 26 CB REMARK 470 VAL H 27 CB CG1 CG2 REMARK 470 ASP H 28 CB CG OD1 OD2 REMARK 470 LYS H 29 CB CG CD CE NZ REMARK 470 MET H 30 CB CG SD CE REMARK 470 ASN H 31 CB CG OD1 ND2 REMARK 470 GLU H 32 CB CG CD OE1 OE2 REMARK 470 ILE H 33 CB CG1 CG2 CD1 REMARK 470 LEU H 34 CB CG CD1 CD2 REMARK 470 THR H 35 CB OG1 CG2 REMARK 470 ASP H 36 CB CG OD1 OD2 REMARK 470 TRP H 37 CB CG CD1 CD2 NE1 CE2 CE3 REMARK 470 TRP H 37 CZ2 CZ3 CH2 REMARK 470 LYS H 39 CB CG CD CE NZ REMARK 470 ASN H 40 CB CG OD1 ND2 REMARK 470 ILE H 41 CB CG1 CG2 CD1 REMARK 470 ALA H 42 CB REMARK 470 LYS H 43 CB CG CD CE NZ REMARK 470 TYR H 44 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR H 44 OH REMARK 470 ALA H 45 CB REMARK 470 VAL H 46 CB CG1 CG2 REMARK 470 GLU H 47 CB CG CD OE1 OE2 REMARK 470 ILE H 48 CB CG1 CG2 CD1 REMARK 470 ALA H 49 CB REMARK 470 ARG H 50 CB CG CD NE CZ NH1 NH2 REMARK 470 HIS H 51 CB CG ND1 CD2 CE1 NE2 REMARK 470 SER H 52 CB OG REMARK 470 ARG H 54 CB CG CD NE CZ NH1 NH2 REMARK 470 LYS H 55 CB CG CD CE NZ REMARK 470 THR H 56 CB OG1 CG2 REMARK 470 VAL H 57 CB CG1 CG2 REMARK 470 LYS H 58 CB CG CD CE NZ REMARK 470 GLU H 59 CB CG CD OE1 OE2 REMARK 470 ASN H 60 CB CG OD1 ND2 REMARK 470 ASP H 61 CB CG OD1 OD2 REMARK 470 ILE H 62 CB CG1 CG2 CD1 REMARK 470 LYS H 63 CB CG CD CE NZ REMARK 470 LEU H 64 CB CG CD1 CD2 REMARK 470 ALA H 65 CB REMARK 470 ALA H 66 CB REMARK 470 GLN H 67 CB CG CD OE1 NE2 REMARK 470 LYS H 68 CB CG CD CE NZ 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 X 6 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA X 7 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA X 16 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA X 17 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT X 22 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG X 37 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG X 60 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT X 62 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG X 63 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT X 64 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC X 67 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT X 91 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC X 96 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC X 97 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT X 102 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA X 107 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG X 109 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG X 115 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT X 116 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA X 118 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG X 119 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC Y 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT Y 3 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA Y 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC Y 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT Y 14 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG Y 16 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA Y 19 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG Y 24 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA Y 26 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG Y 27 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT Y 28 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA Y 29 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT Y 36 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA Y 45 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA Y 46 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC Y 49 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG Y 50 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG Y 56 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA Y 66 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG Y 81 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG Y 83 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT Y 91 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA Y 96 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA Y 103 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG Y 106 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA H 2 49.45 -105.85 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 A 9 0.13 SIDE CHAIN REMARK 500 ARG A 15 0.14 SIDE CHAIN REMARK 500 ARG A 50 0.11 SIDE CHAIN REMARK 500 ARG A 54 0.10 SIDE CHAIN REMARK 500 ARG B 9 0.13 SIDE CHAIN REMARK 500 ARG B 15 0.17 SIDE CHAIN REMARK 500 ARG B 50 0.10 SIDE CHAIN REMARK 500 ARG B 54 0.14 SIDE CHAIN REMARK 500 ARG C 9 0.19 SIDE CHAIN REMARK 500 ARG C 15 0.13 SIDE CHAIN REMARK 500 ARG C 50 0.10 SIDE CHAIN REMARK 500 ARG C 54 0.14 SIDE CHAIN REMARK 500 ARG D 9 0.14 SIDE CHAIN REMARK 500 ARG D 15 0.15 SIDE CHAIN REMARK 500 ARG D 50 0.09 SIDE CHAIN REMARK 500 ARG D 54 0.13 SIDE CHAIN REMARK 500 ARG E 9 0.15 SIDE CHAIN REMARK 500 ARG E 15 0.14 SIDE CHAIN REMARK 500 ARG E 50 0.10 SIDE CHAIN REMARK 500 ARG E 54 0.10 SIDE CHAIN REMARK 500 ARG F 9 0.16 SIDE CHAIN REMARK 500 ARG F 15 0.14 SIDE CHAIN REMARK 500 ARG F 50 0.10 SIDE CHAIN REMARK 500 ARG F 54 0.30 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-53386 RELATED DB: EMDB REMARK 900 ASGARD ARCHAEAL HHOB NUCLEOSOME IN THE CLOSED CONFORMATION REMARK 900 RELATED ID: 9QV5 RELATED DB: PDB REMARK 900 RELATED ID: 9QV6 RELATED DB: PDB REMARK 900 RELATED ID: 9QV7 RELATED DB: PDB REMARK 900 RELATED ID: EMD-53387 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-53388 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-53389 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-53390 RELATED DB: EMDB DBREF1 9QV5 A 1 68 UNP A0A1Q9NRY6_9ARCH DBREF2 9QV5 A A0A1Q9NRY6 1 68 DBREF1 9QV5 B 1 68 UNP A0A1Q9NRY6_9ARCH DBREF2 9QV5 B A0A1Q9NRY6 1 68 DBREF1 9QV5 C 1 68 UNP A0A1Q9NRY6_9ARCH DBREF2 9QV5 C A0A1Q9NRY6 1 68 DBREF1 9QV5 D 1 68 UNP A0A1Q9NRY6_9ARCH DBREF2 9QV5 D A0A1Q9NRY6 1 68 DBREF1 9QV5 E 1 68 UNP A0A1Q9NRY6_9ARCH DBREF2 9QV5 E A0A1Q9NRY6 1 68 DBREF1 9QV5 F 1 68 UNP A0A1Q9NRY6_9ARCH DBREF2 9QV5 F A0A1Q9NRY6 1 68 DBREF1 9QV5 G 1 68 UNP A0A1Q9NRY6_9ARCH DBREF2 9QV5 G A0A1Q9NRY6 1 68 DBREF1 9QV5 H 1 68 UNP A0A1Q9NRY6_9ARCH DBREF2 9QV5 H A0A1Q9NRY6 1 68 DBREF 9QV5 X 1 120 PDB 9QV5 9QV5 1 120 DBREF 9QV5 Y 1 120 PDB 9QV5 9QV5 1 120 SEQRES 1 A 68 MET ALA GLY ASN PHE ALA ASN ALA ARG VAL GLU LYS LEU SEQRES 2 A 68 ILE ARG GLN ALA GLY ALA GLN ARG VAL SER ALA ASP ALA SEQRES 3 A 68 VAL ASP LYS MET ASN GLU ILE LEU THR ASP TRP GLY LYS SEQRES 4 A 68 ASN ILE ALA LYS TYR ALA VAL GLU ILE ALA ARG HIS SER SEQRES 5 A 68 GLY ARG LYS THR VAL LYS GLU ASN ASP ILE LYS LEU ALA SEQRES 6 A 68 ALA GLN LYS SEQRES 1 B 68 MET ALA GLY ASN PHE ALA ASN ALA ARG VAL GLU LYS LEU SEQRES 2 B 68 ILE ARG GLN ALA GLY ALA GLN ARG VAL SER ALA ASP ALA SEQRES 3 B 68 VAL ASP LYS MET ASN GLU ILE LEU THR ASP TRP GLY LYS SEQRES 4 B 68 ASN ILE ALA LYS TYR ALA VAL GLU ILE ALA ARG HIS SER SEQRES 5 B 68 GLY ARG LYS THR VAL LYS GLU ASN ASP ILE LYS LEU ALA SEQRES 6 B 68 ALA GLN LYS SEQRES 1 C 68 MET ALA GLY ASN PHE ALA ASN ALA ARG VAL GLU LYS LEU SEQRES 2 C 68 ILE ARG GLN ALA GLY ALA GLN ARG VAL SER ALA ASP ALA SEQRES 3 C 68 VAL ASP LYS MET ASN GLU ILE LEU THR ASP TRP GLY LYS SEQRES 4 C 68 ASN ILE ALA LYS TYR ALA VAL GLU ILE ALA ARG HIS SER SEQRES 5 C 68 GLY ARG LYS THR VAL LYS GLU ASN ASP ILE LYS LEU ALA SEQRES 6 C 68 ALA GLN LYS SEQRES 1 D 68 MET ALA GLY ASN PHE ALA ASN ALA ARG VAL GLU LYS LEU SEQRES 2 D 68 ILE ARG GLN ALA GLY ALA GLN ARG VAL SER ALA ASP ALA SEQRES 3 D 68 VAL ASP LYS MET ASN GLU ILE LEU THR ASP TRP GLY LYS SEQRES 4 D 68 ASN ILE ALA LYS TYR ALA VAL GLU ILE ALA ARG HIS SER SEQRES 5 D 68 GLY ARG LYS THR VAL LYS GLU ASN ASP ILE LYS LEU ALA SEQRES 6 D 68 ALA GLN LYS SEQRES 1 E 68 MET ALA GLY ASN PHE ALA ASN ALA ARG VAL GLU LYS LEU SEQRES 2 E 68 ILE ARG GLN ALA GLY ALA GLN ARG VAL SER ALA ASP ALA SEQRES 3 E 68 VAL ASP LYS MET ASN GLU ILE LEU THR ASP TRP GLY LYS SEQRES 4 E 68 ASN ILE ALA LYS TYR ALA VAL GLU ILE ALA ARG HIS SER SEQRES 5 E 68 GLY ARG LYS THR VAL LYS GLU ASN ASP ILE LYS LEU ALA SEQRES 6 E 68 ALA GLN LYS SEQRES 1 F 68 MET ALA GLY ASN PHE ALA ASN ALA ARG VAL GLU LYS LEU SEQRES 2 F 68 ILE ARG GLN ALA GLY ALA GLN ARG VAL SER ALA ASP ALA SEQRES 3 F 68 VAL ASP LYS MET ASN GLU ILE LEU THR ASP TRP GLY LYS SEQRES 4 F 68 ASN ILE ALA LYS TYR ALA VAL GLU ILE ALA ARG HIS SER SEQRES 5 F 68 GLY ARG LYS THR VAL LYS GLU ASN ASP ILE LYS LEU ALA SEQRES 6 F 68 ALA GLN LYS SEQRES 1 G 68 MET ALA GLY ASN PHE ALA ASN ALA ARG VAL GLU LYS LEU SEQRES 2 G 68 ILE ARG GLN ALA GLY ALA GLN ARG VAL SER ALA ASP ALA SEQRES 3 G 68 VAL ASP LYS MET ASN GLU ILE LEU THR ASP TRP GLY LYS SEQRES 4 G 68 ASN ILE ALA LYS TYR ALA VAL GLU ILE ALA ARG HIS SER SEQRES 5 G 68 GLY ARG LYS THR VAL LYS GLU ASN ASP ILE LYS LEU ALA SEQRES 6 G 68 ALA GLN LYS SEQRES 1 H 68 MET ALA GLY ASN PHE ALA ASN ALA ARG VAL GLU LYS LEU SEQRES 2 H 68 ILE ARG GLN ALA GLY ALA GLN ARG VAL SER ALA ASP ALA SEQRES 3 H 68 VAL ASP LYS MET ASN GLU ILE LEU THR ASP TRP GLY LYS SEQRES 4 H 68 ASN ILE ALA LYS TYR ALA VAL GLU ILE ALA ARG HIS SER SEQRES 5 H 68 GLY ARG LYS THR VAL LYS GLU ASN ASP ILE LYS LEU ALA SEQRES 6 H 68 ALA GLN LYS SEQRES 1 X 120 DG DT DG DC DC DG DA DG DG DC DC DG DC SEQRES 2 X 120 DT DC DA DA DT DT DG DG DT DC DG DT DA SEQRES 3 X 120 DG DA DC DA DG DC DT DC DT DA DG DC DA SEQRES 4 X 120 DC DC DG DC DT DT DA DA DA DC DG DC DA SEQRES 5 X 120 DC DG DT DA DC DG DC DG DC DT DG DT DC SEQRES 6 X 120 DC DC DC DC DG DC DG DT DT DT DT DA DA SEQRES 7 X 120 DC DC DG DC DC DA DA DG DG DG DG DA DT SEQRES 8 X 120 DT DA DC DT DC DC DC DT DA DG DT DC DT SEQRES 9 X 120 DC DC DA DG DG DC DA DC DG DT DG DT DC SEQRES 10 X 120 DA DG DA SEQRES 1 Y 120 DT DC DT DG DA DC DA DC DG DT DG DC DC SEQRES 2 Y 120 DT DG DG DA DG DA DC DT DA DG DG DG DA SEQRES 3 Y 120 DG DT DA DA DT DC DC DC DC DT DT DG DG SEQRES 4 Y 120 DC DG DG DT DT DA DA DA DA DC DG DC DG SEQRES 5 Y 120 DG DG DG DG DA DC DA DG DC DG DC DG DT SEQRES 6 Y 120 DA DC DG DT DG DC DG DT DT DT DA DA DG SEQRES 7 Y 120 DC DG DG DT DG DC DT DA DG DA DG DC DT SEQRES 8 Y 120 DG DT DC DT DA DC DG DA DC DC DA DA DT SEQRES 9 Y 120 DT DG DA DG DC DG DG DC DC DT DC DG DG SEQRES 10 Y 120 DC DA DC HELIX 1 AA1 ALA A 6 ALA A 17 1 12 HELIX 2 AA2 SER A 23 SER A 52 1 30 HELIX 3 AA3 LYS A 58 GLN A 67 1 10 HELIX 4 AA4 ALA B 6 ALA B 17 1 12 HELIX 5 AA5 SER B 23 SER B 52 1 30 HELIX 6 AA6 LYS B 58 GLN B 67 1 10 HELIX 7 AA7 ALA C 6 ALA C 17 1 12 HELIX 8 AA8 SER C 23 GLY C 53 1 31 HELIX 9 AA9 LYS C 58 GLN C 67 1 10 HELIX 10 AB1 ALA D 6 ALA D 17 1 12 HELIX 11 AB2 SER D 23 SER D 52 1 30 HELIX 12 AB3 LYS D 58 GLN D 67 1 10 HELIX 13 AB4 ALA E 6 ALA E 17 1 12 HELIX 14 AB5 SER E 23 SER E 52 1 30 HELIX 15 AB6 LYS E 58 GLN E 67 1 10 HELIX 16 AB7 ALA F 6 ALA F 17 1 12 HELIX 17 AB8 SER F 23 SER F 52 1 30 HELIX 18 AB9 LYS F 58 GLN F 67 1 10 HELIX 19 AC1 ALA G 6 ALA G 17 1 12 HELIX 20 AC2 SER G 23 GLY G 53 1 31 HELIX 21 AC3 LYS G 58 LYS G 68 1 11 HELIX 22 AC4 ALA H 6 ALA H 17 1 12 HELIX 23 AC5 SER H 23 SER H 52 1 30 HELIX 24 AC6 LYS H 58 LYS H 68 1 11 SHEET 1 AA1 2 ARG A 21 VAL A 22 0 SHEET 2 AA1 2 THR B 56 VAL B 57 1 O VAL B 57 N ARG A 21 SHEET 1 AA2 2 THR A 56 VAL A 57 0 SHEET 2 AA2 2 ARG B 21 VAL B 22 1 O ARG B 21 N VAL A 57 SHEET 1 AA3 2 ARG C 21 VAL C 22 0 SHEET 2 AA3 2 THR D 56 VAL D 57 1 O VAL D 57 N ARG C 21 SHEET 1 AA4 2 THR C 56 VAL C 57 0 SHEET 2 AA4 2 ARG D 21 VAL D 22 1 O ARG D 21 N VAL C 57 SHEET 1 AA5 2 ARG E 21 VAL E 22 0 SHEET 2 AA5 2 THR F 56 VAL F 57 1 O VAL F 57 N ARG E 21 SHEET 1 AA6 2 THR E 56 VAL E 57 0 SHEET 2 AA6 2 ARG F 21 VAL F 22 1 O ARG F 21 N VAL E 57 SHEET 1 AA7 2 ARG G 21 VAL G 22 0 SHEET 2 AA7 2 THR H 56 VAL H 57 1 O VAL H 57 N ARG G 21 SHEET 1 AA8 2 THR G 56 VAL G 57 0 SHEET 2 AA8 2 ARG H 21 VAL H 22 1 O ARG H 21 N VAL G 57 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 MASTER 368 0 0 24 16 0 0 6 8628 10 0 68 END