HEADER PROTON TRANSPORT 15-JAN-23 8I2Z TITLE CRYO-EM STRUCTURE OF THE ZEAXANTHIN-BOUND KIN4B8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: XANTHORHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: KIN4B8; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCULTURED BDELLOVIBRIONALES BACTERIUM; SOURCE 3 ORGANISM_TAXID: 395355; SOURCE 4 GENE: TMP_000014; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RHODOPSIN, CRYO-EM, ANNTENA, PROTON TRANSPORT EXPDTA ELECTRON MICROSCOPY AUTHOR S.MURAKOSHI,A.CHAZAN,W.SHIHOYA,O.BEJA,O.NUREKI REVDAT 2 19-APR-23 8I2Z 1 AUTHOR REVDAT 1 29-MAR-23 8I2Z 0 JRNL AUTH A.CHAZAN,I.DAS,T.FUJIWARA,S.MURAKOSHI,A.ROZENBERG, JRNL AUTH 2 A.MOLINA-MARQUEZ,F.K.SANO,T.TANAKA,P.GOMEZ-VILLEGAS,S.LAROM, JRNL AUTH 3 A.PUSHKAREV,P.MALAKAR,M.HASEGAWA,Y.TSUKAMOTO,T.ISHIZUKA, JRNL AUTH 4 M.KONNO,T.NAGATA,Y.MIZUNO,K.KATAYAMA,R.ABE-YOSHIZUMI, JRNL AUTH 5 S.RUHMAN,K.INOUE,H.KANDORI,R.LEON,W.SHIHOYA,S.YOSHIZAWA, JRNL AUTH 6 M.SHEVES,O.NUREKI,O.BEJA JRNL TITL PHOTOTROPHY BY ANTENNA-CONTAINING RHODOPSIN PUMPS IN AQUATIC JRNL TITL 2 ENVIRONMENTS. JRNL REF NATURE V. 615 535 2023 JRNL REFN ESSN 1476-4687 JRNL PMID 36859551 JRNL DOI 10.1038/S41586-023-05774-6 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, CRYOSPARC, CRYOSPARC 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) : 2.300 REMARK 3 NUMBER OF PARTICLES : 433754 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 8I2Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300033933. 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 : KIN4B8 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : VITRIFICATION CARRIED OUT IN REMARK 245 ETHANE ATMOSPHERE. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 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 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 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) : 5014.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C5). 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 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 0.309017 -0.951057 0.000000 245.32069 REMARK 350 BIOMT2 2 0.951057 0.309017 0.000000 -38.85498 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.809017 -0.587785 0.000000 358.08224 REMARK 350 BIOMT2 3 0.587785 -0.809017 0.000000 182.45202 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.809017 0.587785 0.000000 182.45201 REMARK 350 BIOMT2 4 -0.587785 -0.809017 0.000000 358.08224 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.309017 0.951057 0.000000 -38.85498 REMARK 350 BIOMT2 5 -0.951057 0.309017 0.000000 245.32069 REMARK 350 BIOMT3 5 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 1 REMARK 465 SER A 2 REMARK 465 HIS A 257 REMARK 465 HIS A 258 REMARK 465 HIS A 259 REMARK 465 HIS A 260 REMARK 465 HIS A 261 REMARK 465 HIS A 262 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-35143 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE ZEAXANTHIN-BOUND KIN4B8 DBREF1 8I2Z A 1 256 UNP A0A977XLG0_9PROT DBREF2 8I2Z A A0A977XLG0 1 256 SEQADV 8I2Z HIS A 257 UNP A0A977XLG EXPRESSION TAG SEQADV 8I2Z HIS A 258 UNP A0A977XLG EXPRESSION TAG SEQADV 8I2Z HIS A 259 UNP A0A977XLG EXPRESSION TAG SEQADV 8I2Z HIS A 260 UNP A0A977XLG EXPRESSION TAG SEQADV 8I2Z HIS A 261 UNP A0A977XLG EXPRESSION TAG SEQADV 8I2Z HIS A 262 UNP A0A977XLG EXPRESSION TAG SEQRES 1 A 262 MET SER ALA THR THR LEU THR LEU GLN GLN PHE SER THR SEQRES 2 A 262 VAL TYR ASN MET LEU SER PHE ALA VAL ALA SER MET LEU SEQRES 3 A 262 GLY ALA PHE ALA PHE PHE VAL MET GLY ARG LYS ILE VAL SEQRES 4 A 262 GLY PRO LYS TYR ARG LEU ALA LEU VAL VAL SER SER LEU SEQRES 5 A 262 VAL VAL LEU ILE ALA GLY TYR HIS TYR TRP ARG ILE MET SEQRES 6 A 262 GLY SER TRP THR ALA ALA TYR ALA LEU LYS ASP GLY MET SEQRES 7 A 262 TYR VAL PRO THR GLY GLU PRO PHE ASN ASP ALA TYR ARG SEQRES 8 A 262 TYR VAL ASP TRP LEU LEU THR VAL PRO LEU LEU LEU THR SEQRES 9 A 262 GLU LEU VAL LEU VAL MET LYS LEU LYS LYS GLU SER GLY SEQRES 10 A 262 SER VAL LEU ALA LYS LEU ILE LEU ALA ALA ILE ALA MET SEQRES 11 A 262 ILE ALA LEU GLY TYR PRO GLY GLU ILE SER ASN PRO GLU SEQRES 12 A 262 SER GLN ALA GLY ALA ARG LEU MET TRP GLY VAL LEU SER SEQRES 13 A 262 THR VAL PRO PHE LEU TYR ILE LEU TYR VAL LEU TRP VAL SEQRES 14 A 262 ARG LEU GLY ASP ALA ILE GLY GLU HIS PRO ALA LYS VAL SEQRES 15 A 262 GLN VAL LEU LEU LYS ASN THR ARG TYR LEU ILE LEU LEU SEQRES 16 A 262 THR TRP GLY PHE TYR PRO ILE VAL TYR ALA MET GLY SER SEQRES 17 A 262 TYR GLY TRP LEU GLY GLY ALA GLY SER VAL VAL ALA VAL SEQRES 18 A 262 GLN VAL GLY TYR SER ILE ALA ASP VAL THR ALA LYS ALA SEQRES 19 A 262 LEU TYR GLY VAL MET ILE PHE ALA ILE ALA TYR ALA LYS SEQRES 20 A 262 SER GLU ALA ASP GLY SER LEU PRO ALA HIS HIS HIS HIS SEQRES 21 A 262 HIS HIS HET RET A 301 20 HET K3I A 302 42 HETNAM RET RETINAL HETNAM K3I ZEAXANTHIN HETSYN K3I ZEAXANTHIN FORMUL 2 RET C20 H28 O FORMUL 3 K3I C40 H56 O2 FORMUL 4 HOH *33(H2 O) HELIX 1 AA1 THR A 7 ARG A 36 1 30 HELIX 2 AA2 LYS A 37 VAL A 39 5 3 HELIX 3 AA3 TYR A 43 ALA A 71 1 29 HELIX 4 AA4 ASP A 88 LYS A 111 1 24 HELIX 5 AA5 GLU A 115 ILE A 139 1 25 HELIX 6 AA6 GLN A 145 VAL A 169 1 25 HELIX 7 AA7 ARG A 170 GLY A 176 1 7 HELIX 8 AA8 PRO A 179 GLY A 198 1 20 HELIX 9 AA9 GLY A 198 TYR A 209 1 12 HELIX 10 AB1 GLY A 214 ASP A 251 1 38 SHEET 1 AA1 2 TYR A 72 LYS A 75 0 SHEET 2 AA1 2 MET A 78 PRO A 81 -1 O MET A 78 N LYS A 75 LINK NZ LYS A 233 C15 RET A 301 1555 1555 1.35 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