HEADER MEMBRANE PROTEIN 21-AUG-25 9WFA TITLE CRYO-EM STRUCTURE OF PSXR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSXR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLOEOBACTER VIOLACEUS; SOURCE 3 ORGANISM_TAXID: 33072; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RHODOPSIN, INWARD PROTON PUMP, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.MURAKOSHI,M.C.MARIN,T.TANAKA,W.SHIHOYA,O.BEJA,O.NUREKI REVDAT 1 18-MAR-26 9WFA 0 JRNL AUTH M.D.C.MARIN,S.MURAKOSHI,A.ROZENBERG,T.TANAKA,M.KONNO, JRNL AUTH 2 W.SHIHOYA,O.NUREKI,O.BEJA,K.INOUE JRNL TITL LIGHT-HARVESTING BY ANTENNA-CONTAINING XANTHORHODOPSIN FROM JRNL TITL 2 AN ANTARCTIC PSEUDANABAENACEAE CYANOBACTERIUM. JRNL REF COMMUN BIOL V. 9 28 2025 JRNL REFN ESSN 2399-3642 JRNL PMID 41318824 JRNL DOI 10.1038/S42003-025-09294-Z REMARK 2 REMARK 2 RESOLUTION. 2.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, EPU, 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) : 2.640 REMARK 3 NUMBER OF PARTICLES : 327293 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 9WFA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1300062777. 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 : CYANOBACTERIAL XANTHORHODOPSIN REMARK 245 RECONSTITUTED IN MSP2N2 REMARK 245 NANODISCS WITH SOYPC 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 : 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 : 5949 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) : 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) : 4800.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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: PENTAMERIC 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 0.309000 0.951100 0.000000 -31.08410 REMARK 350 BIOMT2 2 -0.951100 0.309000 0.000000 196.25640 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.809000 0.587800 0.000000 145.96130 REMARK 350 BIOMT2 3 -0.587800 -0.809000 0.000000 286.46590 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.809000 -0.587800 0.000000 286.46570 REMARK 350 BIOMT2 4 0.587800 -0.809000 0.000000 145.96220 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.309000 -0.951100 0.000000 196.25720 REMARK 350 BIOMT2 5 0.951100 0.309000 0.000000 -31.08370 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 ILE A 3 REMARK 465 SER A 4 REMARK 465 LEU A 5 REMARK 465 ILE A 6 REMARK 465 THR A 7 REMARK 465 ASP A 8 REMARK 465 PHE A 9 REMARK 465 ALA A 10 REMARK 465 LEU A 11 REMARK 465 LEU A 12 REMARK 465 ALA A 13 REMARK 465 GLN A 14 REMARK 465 SER A 15 REMARK 465 ASN A 16 REMARK 465 LEU A 17 REMARK 465 PRO A 18 REMARK 465 GLU A 19 REMARK 465 THR A 20 REMARK 465 VAL A 21 REMARK 465 SER A 22 REMARK 465 LYS A 23 REMARK 465 VAL A 24 REMARK 465 ASP A 25 REMARK 465 GLY A 271 REMARK 465 GLU A 272 REMARK 465 GLN A 273 REMARK 465 PRO A 274 REMARK 465 THR A 275 REMARK 465 LYS A 276 REMARK 465 GLU A 277 REMARK 465 SER A 278 REMARK 465 PRO A 279 REMARK 465 MET A 280 REMARK 465 THR A 281 REMARK 465 MET A 282 REMARK 465 ILE A 283 REMARK 465 SER A 284 REMARK 465 SER A 285 REMARK 465 HIS A 286 REMARK 465 HIS A 287 REMARK 465 HIS A 288 REMARK 465 HIS A 289 REMARK 465 HIS A 290 REMARK 465 HIS A 291 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 ILE A 188 -55.43 -125.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-65924 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF PSXR DBREF 9WFA A 1 291 PDB 9WFA 9WFA 1 291 SEQRES 1 A 291 MET SER ILE SER LEU ILE THR ASP PHE ALA LEU LEU ALA SEQRES 2 A 291 GLN SER ASN LEU PRO GLU THR VAL SER LYS VAL ASP PHE SEQRES 3 A 291 LEU SER SER GLY GLN TYR ASN LEU VAL TYR ASN ALA PHE SEQRES 4 A 291 SER PHE ALA ILE ALA THR MET LEU ALA ALA ALA LEU PHE SEQRES 5 A 291 PHE PHE ASN VAL ARG GLY GLN VAL GLY GLN LYS TYR GLN SEQRES 6 A 291 LEU ALA LEU ILE VAL SER ALA LEU VAL VAL SER ILE ALA SEQRES 7 A 291 GLY TYR HIS TYR TYR ARG ILE PHE GLY SER TRP GLU ALA SEQRES 8 A 291 ALA TYR SER LEU GLN ASN GLY ASN TYR VAL LEU THR GLY SEQRES 9 A 291 ALA PRO PHE ASN ASP ALA TYR ARG TYR VAL ASP TRP LEU SEQRES 10 A 291 LEU THR VAL PRO LEU LEU LEU VAL GLU THR VAL ALA VAL SEQRES 11 A 291 LEU ALA LEU PRO GLY MET GLU ALA ARG PRO LEU LEU ILE SEQRES 12 A 291 LYS LEU VAL VAL ALA ALA ILE LEU MET ILE ALA THR GLY SEQRES 13 A 291 TYR PRO GLY GLU ILE SER THR ASP LEU ASN THR ARG ILE SEQRES 14 A 291 VAL TRP GLY ALA VAL SER THR VAL PRO PHE ILE TYR ILE SEQRES 15 A 291 LEU TYR ILE LEU TRP ILE GLU LEU SER LYS SER LEU LEU SEQRES 16 A 291 ARG GLN PRO GLU GLY VAL GLN THR LEU VAL LYS ASN MET SEQRES 17 A 291 ARG LEU LEU LEU LEU PHE SER TRP GLY VAL TYR PRO ILE SEQRES 18 A 291 ALA TYR LEU LEU PRO MET LEU GLY ILE SER GLY ALA THR SEQRES 19 A 291 ALA ASP VAL GLY VAL GLN ILE GLY TYR THR ILE ALA ASP SEQRES 20 A 291 VAL LEU ALA LYS PRO ILE PHE GLY LEU LEU VAL PHE ALA SEQRES 21 A 291 ILE ALA LEU GLU LYS THR ARG VAL ASP ALA GLY GLU GLN SEQRES 22 A 291 PRO THR LYS GLU SER PRO MET THR MET ILE SER SER HIS SEQRES 23 A 291 HIS HIS HIS HIS HIS HET RET A 301 20 HET LUT A 302 42 HETNAM RET RETINAL HETNAM LUT (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA- HETNAM 2 LUT CAROTENE-3,3'-DIOL HETSYN LUT (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL; LUTEIN FORMUL 2 RET C20 H28 O FORMUL 3 LUT C40 H56 O2 FORMUL 4 HOH *25(H2 O) HELIX 1 AA1 SER A 28 ARG A 57 1 30 HELIX 2 AA2 GLY A 58 VAL A 60 5 3 HELIX 3 AA3 GLY A 61 LYS A 63 5 3 HELIX 4 AA4 TYR A 64 ALA A 92 1 29 HELIX 5 AA5 ASN A 108 ALA A 110 5 3 HELIX 6 AA6 TYR A 111 VAL A 130 1 20 HELIX 7 AA7 PRO A 134 ILE A 161 1 28 HELIX 8 AA8 ASP A 164 ILE A 188 1 25 HELIX 9 AA9 ILE A 188 LEU A 195 1 8 HELIX 10 AB1 PRO A 198 LEU A 225 1 28 HELIX 11 AB2 PRO A 226 GLY A 229 5 4 HELIX 12 AB3 GLY A 232 LYS A 251 1 20 HELIX 13 AB4 LYS A 251 ALA A 270 1 20 SHEET 1 AA1 2 TYR A 93 GLN A 96 0 SHEET 2 AA1 2 ASN A 99 LEU A 102 -1 O ASN A 99 N GLN A 96 LINK NZ LYS A 251 C15 RET A 301 1555 1555 1.34 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 1762 1924 CONECT 1910 1911 1915 1925 1926 CONECT 1911 1910 1912 CONECT 1912 1911 1913 CONECT 1913 1912 1914 CONECT 1914 1913 1915 1927 CONECT 1915 1910 1914 1916 CONECT 1916 1915 1917 CONECT 1917 1916 1918 CONECT 1918 1917 1919 1928 CONECT 1919 1918 1920 CONECT 1920 1919 1921 CONECT 1921 1920 1922 CONECT 1922 1921 1923 1929 CONECT 1923 1922 1924 CONECT 1924 1762 1923 CONECT 1925 1910 CONECT 1926 1910 CONECT 1927 1914 CONECT 1928 1918 CONECT 1929 1922 CONECT 1930 1931 1935 1945 1946 CONECT 1931 1930 1932 CONECT 1932 1931 1933 1950 CONECT 1933 1932 1934 CONECT 1934 1933 1935 1947 CONECT 1935 1930 1934 1936 CONECT 1936 1935 1937 CONECT 1937 1936 1938 CONECT 1938 1937 1939 1948 CONECT 1939 1938 1940 CONECT 1940 1939 1941 CONECT 1941 1940 1942 CONECT 1942 1941 1943 1949 CONECT 1943 1942 1944 CONECT 1944 1943 1965 CONECT 1945 1930 CONECT 1946 1930 CONECT 1947 1934 CONECT 1948 1938 CONECT 1949 1942 CONECT 1950 1932 CONECT 1951 1952 1956 1966 1967 CONECT 1952 1951 1953 CONECT 1953 1952 1954 1971 CONECT 1954 1953 1955 CONECT 1955 1954 1956 1968 CONECT 1956 1951 1955 1957 CONECT 1957 1956 1958 CONECT 1958 1957 1959 CONECT 1959 1958 1960 1969 CONECT 1960 1959 1961 CONECT 1961 1960 1962 CONECT 1962 1961 1963 CONECT 1963 1962 1964 1970 CONECT 1964 1963 1965 CONECT 1965 1944 1964 CONECT 1966 1951 CONECT 1967 1951 CONECT 1968 1955 CONECT 1969 1959 CONECT 1970 1963 CONECT 1971 1953 MASTER 183 0 2 13 2 0 0 6 1995 1 63 23 END