HEADER RIBOSOME 24-SEP-25 9SR9 TITLE P. ABYSSI HIBERNATION FACTOR HIB BOUND TO ATP (HIB-PTC CONFORMATION) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEHYDROGENASE; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI GE5; SOURCE 3 ORGANISM_TAXID: 272844; SOURCE 4 GENE: PAB0961; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 70S, RIBOSOME, HIBERNATION, PYROCOCCUS ABYSSI EXPDTA ELECTRON MICROSCOPY AUTHOR C.M.MADRU,G.B.BOURGEOIS,Y.M.MECHULAM,E.S.SCHMITT REVDAT 1 12-AUG-26 9SR9 0 JRNL AUTH C.MADRU,G.BOURGEOIS,R.DULERMO,R.CAPEYROU,G.JONCOUR, JRNL AUTH 2 K.FIGUIGUI,M.DUCHATEAU,J.CHAMOT-ROOKE,C.DUBOC,S.L'HARIDON, JRNL AUTH 3 L.MC TEER,M.KWAPISZ,B.CLOUET-D'ORVAL,M.BOUVIER,Y.MECHULAM, JRNL AUTH 4 G.BORREL,E.SCHMITT,D.FLAMENT JRNL TITL A FAMILY OF RIBOSOME HIBERNATION FACTORS WIDESPREAD IN JRNL TITL 2 ARCHAEA. JRNL REF NAT COMMUN V. 17 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 42045235 JRNL DOI 10.1038/S41467-026-72341-8 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX 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) : 2.500 REMARK 3 NUMBER OF PARTICLES : 20409 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 9SR9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1292150927. 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 : P. ABYSSI HIBERNATION FACTOR REMARK 245 HIB BOUND TO ATP (HIB-PTC REMARK 245 CONFORMATION) 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) : 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) : 4000.00 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: H 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 H 1 REMARK 465 LEU H 388 REMARK 465 GLU H 389 REMARK 465 LEU H 390 REMARK 465 TRP H 391 REMARK 465 ARG H 392 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 O VAL H 123 NH1 ARG H 228 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN H 105 -167.19 -162.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-55134 RELATED DB: EMDB REMARK 900 P. ABYSSI HIBERNATION FACTOR HIB BOUND TO ATP (HIB-PTC CONFORMATION) DBREF 9SR9 H 1 392 UNP Q9UYR4 Q9UYR4_PYRAB 1 392 SEQRES 1 H 392 MET VAL GLY ILE GLN VAL GLN GLU VAL MET THR ASP ARG SEQRES 2 H 392 TYR ALA LYS ILE ASP ILE ASN ALA PRO LEU SER GLU ALA SEQRES 3 H 392 ILE GLY ILE ILE GLU LYS GLU ASP PRO ASP LEU ILE LEU SEQRES 4 H 392 VAL PHE ASP ASP ASN VAL TYR LYS GLY VAL LEU THR GLN SEQRES 5 H 392 ASP LEU ILE ILE ARG SER HIS LEU LYS TRP ASP PRO THR SEQRES 6 H 392 LYS ALA LYS VAL ARG ASP VAL TYR LYS PRO ALA PRO VAL SEQRES 7 H 392 VAL LYS PRO THR ASP ASP LEU SER HIS ALA ALA LYS LEU SEQRES 8 H 392 LEU LEU GLU THR ASP LEU ARG SER LEU PRO VAL GLY GLU SEQRES 9 H 392 ASN LYS ALA GLU ILE LEU GLY VAL ILE SER ASP MET ALA SEQRES 10 H 392 LEU LEU GLU ARG VAL VAL ALA GLU GLU PHE GLY LYS ARG SEQRES 11 H 392 LYS VAL GLU GLU PHE MET THR LYS ASP VAL ILE THR LEU SEQRES 12 H 392 GLY PRO ASP ASP THR VAL ALA LYS ALA LEU ALA THR MET SEQRES 13 H 392 ARG ASP HIS GLY ILE SER ARG ILE PRO VAL VAL ASP GLU SEQRES 14 H 392 GLU GLY LYS LEU GLU GLY LEU VAL THR LEU HIS ASP LEU SEQRES 15 H 392 ILE ILE ARG PHE ILE LYS PRO ARG PHE LYS ALA GLN TYR SEQRES 16 H 392 GLY GLU LEU ALA GLY GLU LYS ILE PRO PRO PHE SER MET SEQRES 17 H 392 LYS LEU ARG GLU ALA MET ILE LYS GLY VAL ILE THR ILE SEQRES 18 H 392 MET PRO GLU ALA THR ILE ARG GLU ALA VAL SER THR MET SEQRES 19 H 392 LYS ASP ASN ASN ILE ASP GLY LEU VAL VAL VAL ASP GLU SEQRES 20 H 392 ASN ASN LYS VAL VAL GLY ILE LEU THR VAL LYS ASP LEU SEQRES 21 H 392 LEU LEU PRO ILE SER ARG MET VAL GLU LYS GLU ALA ARG SEQRES 22 H 392 PHE TYR LEU GLN LEU GLY GLY ASP ALA SER ALA LEU SER SEQRES 23 H 392 GLU PHE THR ARG GLU ARG ILE ILE ASN ASP ILE LYS ARG SEQRES 24 H 392 PHE VAL ASP GLY TYR ALA ASP LEU LEU GLY ASN GLU GLY SEQRES 25 H 392 ILE ILE TYR LEU TYR ILE ARG ARG PHE ASN GLU LYS PHE SEQRES 26 H 392 ARG GLY VAL HIS LEU TYR GLN ALA ARG MET ARG VAL VAL SEQRES 27 H 392 THR ASP ARG GLY VAL PHE ILE ALA ARG GLY GLU THR TRP SEQRES 28 H 392 GLY ALA ILE GLN ALA VAL HIS ASP ALA ILE ARG ALA ILE SEQRES 29 H 392 GLU ARG GLN LEU LEU GLN LYS ALA GLU LEU GLU ARG ASP SEQRES 30 H 392 ILE ARG TYR ALA LYS ARG PHE ILE GLU LYS LEU GLU LEU SEQRES 31 H 392 TRP ARG HET ATP H 401 31 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 2 ATP C10 H16 N5 O13 P3 HELIX 1 AA1 PRO H 22 GLU H 33 1 12 HELIX 2 AA2 THR H 51 TRP H 62 1 12 HELIX 3 AA3 LYS H 68 TYR H 73 1 6 HELIX 4 AA4 ASP H 84 ASP H 96 1 13 HELIX 5 AA5 ASP H 115 ALA H 124 1 10 HELIX 6 AA6 GLU H 125 ARG H 130 5 6 HELIX 7 AA7 LYS H 131 MET H 136 1 6 HELIX 8 AA8 THR H 148 GLY H 160 1 13 HELIX 9 AA9 LEU H 179 ILE H 187 1 9 HELIX 10 AB1 LYS H 209 ALA H 213 5 5 HELIX 11 AB2 THR H 226 ASN H 238 1 13 HELIX 12 AB3 VAL H 257 MET H 267 1 11 HELIX 13 AB4 ALA H 282 LEU H 285 5 4 HELIX 14 AB5 SER H 286 GLY H 309 1 24 HELIX 15 AB6 GLY H 352 ASP H 377 1 26 SHEET 1 AA1 3 ALA H 15 ASP H 18 0 SHEET 2 AA1 3 ILE H 38 PHE H 41 1 O LEU H 39 N ALA H 15 SHEET 3 AA1 3 TYR H 46 LEU H 50 -1 O LEU H 50 N ILE H 38 SHEET 1 AA2 2 SER H 99 VAL H 102 0 SHEET 2 AA2 2 GLY H 111 SER H 114 -1 O GLY H 111 N VAL H 102 SHEET 1 AA3 2 ARG H 163 VAL H 167 0 SHEET 2 AA3 2 LEU H 173 THR H 178 -1 O GLU H 174 N VAL H 166 SHEET 1 AA4 3 THR H 220 ILE H 221 0 SHEET 2 AA4 3 GLY H 241 VAL H 245 1 O VAL H 245 N ILE H 221 SHEET 3 AA4 3 VAL H 251 THR H 256 -1 O LEU H 255 N LEU H 242 SHEET 1 AA5 4 PHE H 274 GLY H 280 0 SHEET 2 AA5 4 GLY H 312 PHE H 325 1 O LEU H 316 N GLY H 279 SHEET 3 AA5 4 VAL H 328 THR H 339 -1 O ARG H 336 N TYR H 315 SHEET 4 AA5 4 GLY H 342 TRP H 351 -1 O GLY H 348 N ALA H 333 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 CONECT 3076 3077 3078 3079 3083 CONECT 3077 3076 CONECT 3078 3076 CONECT 3079 3076 CONECT 3080 3081 3082 3083 3087 CONECT 3081 3080 CONECT 3082 3080 CONECT 3083 3076 3080 CONECT 3084 3085 3086 3087 3088 CONECT 3085 3084 CONECT 3086 3084 CONECT 3087 3080 3084 CONECT 3088 3084 3089 CONECT 3089 3088 3090 CONECT 3090 3089 3091 3092 CONECT 3091 3090 3096 CONECT 3092 3090 3093 3094 CONECT 3093 3092 CONECT 3094 3092 3095 3096 CONECT 3095 3094 CONECT 3096 3091 3094 3097 CONECT 3097 3096 3098 3106 CONECT 3098 3097 3099 CONECT 3099 3098 3100 CONECT 3100 3099 3101 3106 CONECT 3101 3100 3102 3103 CONECT 3102 3101 CONECT 3103 3101 3104 CONECT 3104 3103 3105 CONECT 3105 3104 3106 CONECT 3106 3097 3100 3105 MASTER 143 0 1 15 14 0 0 6 3105 1 31 31 END