HEADER MEMBRANE PROTEIN 09-DEC-25 21DF TITLE MTSZR METHANOGENIC SCHIZORHODOPSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCULLEUS TAIWANENSIS; SOURCE 3 ORGANISM_TAXID: 1550565; SOURCE 4 GENE: ABH15_09795; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SCHIZORHODOPSIN, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR I.EBISU,T.TANAKA,S.MURAKOSHI,W.SHIHOYA,O.NUREKI REVDAT 1 11-NOV-26 21DF 0 JRNL AUTH I.EBISU,T.TANAKA,Y.KAWASAKI,S.MURAKOSHI,K.SHIBATA,Y.KATO, JRNL AUTH 2 M.KONNO,W.SHIHOYA,K.INOUE,O.NUREKI JRNL TITL MTSZR METHANOGENIC SCHIZORHODOPSIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, 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) : 2.380 REMARK 3 NUMBER OF PARTICLES : 869225 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 21DF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1300066707. 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 : MTSZR 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 : 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) : 1500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : DARK FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 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 = C3). 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 -0.500000 -0.866025 0.000000 314.20830 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 84.19215 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 84.19161 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 314.20844 REMARK 350 BIOMT3 3 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 ALA A 2 REMARK 465 GLY A 3 REMARK 465 PHE A 212 REMARK 465 ARG A 213 REMARK 465 GLN A 214 REMARK 465 PRO A 215 REMARK 465 ILE A 216 REMARK 465 GLY A 217 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 PRO A 31 45.44 -78.74 REMARK 500 TYR A 33 32.57 -95.99 REMARK 500 ALA A 149 -97.49 53.30 REMARK 500 ILE A 209 -51.05 -120.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PC1 A 302 REMARK 610 PC1 A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-67584 RELATED DB: EMDB REMARK 900 MTSZR METHANOGENIC SCHIZORHODOPSIN DBREF1 21DF A 1 217 UNP A0A498H310_9EURY DBREF2 21DF A A0A498H310 1 217 SEQRES 1 A 217 MET ALA GLY GLU GLU MET LEU VAL PHE TRP ALA GLY ALA SEQRES 2 A 217 VAL ILE PHE GLY LEU ALA THR LEU LEU PHE VAL VAL LEU SEQRES 3 A 217 LYS LEU ARG ARG PRO GLU TYR GLY ILE PHE TYR GLY SER SEQRES 4 A 217 ASP ILE PHE VAL CYS PHE ILE THR THR ILE SER TYR VAL SEQRES 5 A 217 THR MET ALA LEU ALA LEU GLY THR SER VAL ALA ALA ASP SEQRES 6 A 217 GLY GLN PRO ILE TYR TRP THR ARG TRP LEU TYR TYR ILE SEQRES 7 A 217 ALA SER CYS SER ILE LEU THR LEU ASP VAL ALA TYR LEU SEQRES 8 A 217 ALA GLY ARG PRO THR VAL THR LYS PHE GLU VAL ALA LEU SEQRES 9 A 217 PHE THR GLY LEU VAL MET PHE CYS GLY PHE LEU ALA SER SEQRES 10 A 217 PHE LEU THR GLY PRO GLU ARG TRP TRP PHE PHE ALA PHE SEQRES 11 A 217 SER SER ALA ALA TYR ALA GLY LEU LEU TYR THR LEU PHE SEQRES 12 A 217 ALA GLY THR GLY ARG ALA GLU PRO GLY MET LYS PRO VAL SEQRES 13 A 217 MET TRP PHE ILE LEU LEU PHE TRP THR LEU PHE PRO VAL SEQRES 14 A 217 VAL TRP VAL LEU ALA PRO THR GLY LEU GLY ILE ILE THR SEQRES 15 A 217 THR PRO ALA GLY ALA VAL LEU TYR ALA ILE LEU ASP ILE SEQRES 16 A 217 ILE THR LYS ILE VAL PHE GLY LEU TRP ILE THR MET ARG SEQRES 17 A 217 ILE LEU PRO PHE ARG GLN PRO ILE GLY HET RET A 301 20 HET PC1 A 302 41 HET PC1 A 303 15 HETNAM RET RETINAL HETNAM PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE HETSYN PC1 3-SN-PHOSPHATIDYLCHOLINE FORMUL 2 RET C20 H28 O FORMUL 3 PC1 2(C44 H88 N O8 P) FORMUL 5 HOH *23(H2 O) HELIX 1 AA1 GLU A 4 ARG A 30 1 27 HELIX 2 AA2 TYR A 33 LEU A 56 1 24 HELIX 3 AA3 TRP A 71 GLY A 93 1 23 HELIX 4 AA4 PRO A 95 LEU A 119 1 25 HELIX 5 AA5 GLU A 123 ALA A 144 1 22 HELIX 6 AA6 GLY A 152 ALA A 174 1 23 HELIX 7 AA7 THR A 182 ILE A 209 1 28 SHEET 1 AA1 2 SER A 61 VAL A 62 0 SHEET 2 AA1 2 PRO A 68 ILE A 69 -1 O ILE A 69 N SER A 61 LINK NZ LYS A 198 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 1532 1657 CONECT 1643 1644 1648 1658 1659 CONECT 1644 1643 1645 CONECT 1645 1644 1646 CONECT 1646 1645 1647 CONECT 1647 1646 1648 1660 CONECT 1648 1643 1647 1649 CONECT 1649 1648 1650 CONECT 1650 1649 1651 CONECT 1651 1650 1652 1661 CONECT 1652 1651 1653 CONECT 1653 1652 1654 CONECT 1654 1653 1655 CONECT 1655 1654 1656 1662 CONECT 1656 1655 1657 CONECT 1657 1532 1656 CONECT 1658 1643 CONECT 1659 1643 CONECT 1660 1647 CONECT 1661 1651 CONECT 1662 1655 CONECT 1663 1664 CONECT 1664 1663 1665 1666 1667 CONECT 1665 1664 CONECT 1666 1664 CONECT 1667 1664 1668 CONECT 1668 1667 1669 CONECT 1669 1668 1670 1689 CONECT 1670 1669 1671 CONECT 1671 1670 1672 1673 CONECT 1672 1671 CONECT 1673 1671 1674 CONECT 1674 1673 1675 CONECT 1675 1674 1676 CONECT 1676 1675 1677 CONECT 1677 1676 1678 CONECT 1678 1677 1679 CONECT 1679 1678 1680 CONECT 1680 1679 1681 CONECT 1681 1680 1682 CONECT 1682 1681 1683 CONECT 1683 1682 1684 CONECT 1684 1683 1685 CONECT 1685 1684 1686 CONECT 1686 1685 1687 CONECT 1687 1686 1688 CONECT 1688 1687 CONECT 1689 1669 1690 CONECT 1690 1689 1691 CONECT 1691 1690 1692 1693 CONECT 1692 1691 CONECT 1693 1691 1694 CONECT 1694 1693 1695 CONECT 1695 1694 1696 CONECT 1696 1695 1697 CONECT 1697 1696 1698 CONECT 1698 1697 1699 CONECT 1699 1698 1700 CONECT 1700 1699 1701 CONECT 1701 1700 1702 CONECT 1702 1701 1703 CONECT 1703 1702 CONECT 1704 1705 CONECT 1705 1704 1706 CONECT 1706 1705 1707 CONECT 1707 1706 1708 CONECT 1708 1707 1709 CONECT 1709 1708 1710 CONECT 1710 1709 1711 CONECT 1711 1710 1712 CONECT 1712 1711 1713 CONECT 1713 1712 1714 CONECT 1714 1713 1715 CONECT 1715 1714 1716 CONECT 1716 1715 1717 CONECT 1717 1716 1718 CONECT 1718 1717 MASTER 149 0 3 7 2 0 0 6 1740 1 77 17 END