HEADER MEMBRANE PROTEIN 11-DEC-21 7W9W TITLE 2.02 ANGSTROM CRYO-EM STRUCTURE OF THE PUMP-LIKE CHANNELRHODOPSIN TITLE 2 CHRMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHRMINE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOMONAS LENS; SOURCE 3 ORGANISM_TAXID: 354590; SOURCE 4 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS CHANNELRHODOPSIN, ION CHANNEL, PHOTORECEPTOR, CRYO-EM, MEMBRANE KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR K.E.KISHI,Y.KIM,M.FUKUDA,K.YAMASHITA,K.DEISSEROTH,H.E.KATO REVDAT 3 09-MAR-22 7W9W 1 JRNL REVDAT 2 16-FEB-22 7W9W 1 JRNL REVDAT 1 02-FEB-22 7W9W 0 JRNL AUTH K.E.KISHI,Y.S.KIM,M.FUKUDA,M.INOUE,T.KUSAKIZAKO,P.Y.WANG, JRNL AUTH 2 C.RAMAKRISHNAN,E.F.X.BYRNE,E.THADHANI,J.M.PAGGI,T.E.MATSUI, JRNL AUTH 3 K.YAMASHITA,T.NAGATA,M.KONNO,S.QUIRIN,M.LO,T.BENSTER, JRNL AUTH 4 T.UEMURA,K.LIU,M.SHIBATA,N.NOMURA,S.IWATA,O.NUREKI,R.O.DROR, JRNL AUTH 5 K.INOUE,K.DEISSEROTH,H.E.KATO JRNL TITL STRUCTURAL BASIS FOR CHANNEL CONDUCTION IN THE PUMP-LIKE JRNL TITL 2 CHANNELRHODOPSIN CHRMINE. JRNL REF CELL V. 185 672 2022 JRNL REFN ISSN 1097-4172 JRNL PMID 35114111 JRNL DOI 10.1016/J.CELL.2022.01.007 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 2.020 REMARK 3 NUMBER OF PARTICLES : 185895 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 7W9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1300026267. 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 : CHRMINE 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 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) : 5153.30 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 180.75898 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 48.43423 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 48.43422 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 180.75898 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 GLY A -1 REMARK 465 PRO A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 HIS A 3 REMARK 465 ALA A 4 REMARK 465 PRO A 5 REMARK 465 GLY A 6 REMARK 465 THR A 7 REMARK 465 ASP A 8 REMARK 465 GLN A 9 REMARK 465 GLU A 280 REMARK 465 GLN A 281 REMARK 465 LEU A 282 REMARK 465 GLY A 283 REMARK 465 HIS A 284 REMARK 465 ASP A 285 REMARK 465 GLU A 286 REMARK 465 ASP A 287 REMARK 465 GLU A 288 REMARK 465 PHE A 289 REMARK 465 GLN A 290 REMARK 465 LYS A 291 REMARK 465 LEU A 292 REMARK 465 GLU A 293 REMARK 465 LEU A 294 REMARK 465 ASP A 295 REMARK 465 MET A 296 REMARK 465 ARG A 297 REMARK 465 LEU A 298 REMARK 465 SER A 299 REMARK 465 SER A 300 REMARK 465 ASN A 301 REMARK 465 GLY A 302 REMARK 465 GLU A 303 REMARK 465 ARG A 304 REMARK 465 LEU A 305 REMARK 465 GLU A 306 REMARK 465 VAL A 307 REMARK 465 LEU A 308 REMARK 465 PHE A 309 REMARK 465 GLN A 310 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 TYR A 116 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 TYR A 116 CB - CG - CD1 ANGL. DEV. = 3.7 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 TYR A 113 -9.25 79.00 REMARK 500 GLN A 201 -123.62 55.27 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 PLM A 405 REMARK 610 PLM A 407 REMARK 610 PLM A 408 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32377 RELATED DB: EMDB REMARK 900 2.02 ANGSTROM CRYO-EM STRUCTURE OF THE PUMP-LIKE CHANNELRHODOPSIN REMARK 900 CHRMINE DBREF 7W9W A -1 310 PDB 7W9W 7W9W -1 310 SEQRES 1 A 312 GLY PRO MET ALA HIS ALA PRO GLY THR ASP GLN MET PHE SEQRES 2 A 312 TYR VAL GLY THR MET ASP GLY TRP TYR LEU ASP THR LYS SEQRES 3 A 312 LEU ASN SER VAL ALA ILE GLY ALA HIS TRP SER CYS PHE SEQRES 4 A 312 ILE VAL LEU THR ILE THR THR PHE TYR LEU GLY TYR GLU SEQRES 5 A 312 SER TRP THR SER ARG GLY PRO SER LYS ARG THR SER PHE SEQRES 6 A 312 TYR ALA GLY TYR GLN GLU GLU GLN ASN LEU ALA LEU PHE SEQRES 7 A 312 VAL ASN PHE PHE ALA MET LEU SER TYR PHE GLY LYS ILE SEQRES 8 A 312 VAL ALA ASP THR LEU GLY HIS ASN PHE GLY ASP VAL GLY SEQRES 9 A 312 PRO PHE ILE ILE GLY PHE GLY ASN TYR ARG TYR ALA ASP SEQRES 10 A 312 TYR MET LEU THR CYS PRO MET LEU VAL TYR ASP LEU LEU SEQRES 11 A 312 TYR GLN LEU ARG ALA PRO TYR ARG VAL SER CYS SER ALA SEQRES 12 A 312 ILE ILE PHE ALA ILE LEU MET SER GLY VAL LEU ALA GLU SEQRES 13 A 312 PHE TYR ALA GLU GLY ASP PRO ARG LEU ARG ASN GLY ALA SEQRES 14 A 312 TYR ALA TRP TYR GLY PHE GLY CYS PHE TRP PHE ILE PHE SEQRES 15 A 312 ALA TYR SER ILE VAL MET SER ILE VAL ALA LYS GLN TYR SEQRES 16 A 312 SER ARG LEU ALA GLN LEU ALA GLN ASP THR GLY ALA GLU SEQRES 17 A 312 HIS SER LEU HIS VAL LEU LYS PHE ALA VAL PHE THR PHE SEQRES 18 A 312 SER MET LEU TRP ILE LEU PHE PRO LEU VAL TRP ALA ILE SEQRES 19 A 312 CYS PRO ARG GLY PHE GLY TRP ILE ASP ASP ASN TRP THR SEQRES 20 A 312 GLU VAL ALA HIS CYS VAL CYS ASP ILE VAL ALA LYS SER SEQRES 21 A 312 CYS TYR GLY PHE ALA LEU ALA ARG PHE ARG LYS THR TYR SEQRES 22 A 312 ASP GLU GLU LEU PHE ARG LEU LEU GLU GLN LEU GLY HIS SEQRES 23 A 312 ASP GLU ASP GLU PHE GLN LYS LEU GLU LEU ASP MET ARG SEQRES 24 A 312 LEU SER SER ASN GLY GLU ARG LEU GLU VAL LEU PHE GLN HET RET A 401 20 HET CLR A 402 28 HET CLR A 403 28 HET PLM A 404 18 HET PLM A 405 12 HET PLM A 406 18 HET PLM A 407 12 HET PLM A 408 12 HETNAM RET RETINAL HETNAM CLR CHOLESTEROL HETNAM PLM PALMITIC ACID FORMUL 2 RET C20 H28 O FORMUL 3 CLR 2(C27 H46 O) FORMUL 5 PLM 5(C16 H32 O2) FORMUL 10 HOH *48(H2 O) HELIX 1 AA1 THR A 15 TYR A 20 1 6 HELIX 2 AA2 ASN A 26 SER A 54 1 29 HELIX 3 AA3 PHE A 63 GLN A 68 1 6 HELIX 4 AA4 GLU A 69 GLN A 71 5 3 HELIX 5 AA5 ASN A 72 GLY A 95 1 24 HELIX 6 AA6 ASP A 115 LEU A 131 1 17 HELIX 7 AA7 TYR A 135 GLY A 159 1 25 HELIX 8 AA8 ASP A 160 LEU A 163 5 4 HELIX 9 AA9 ARG A 164 GLN A 201 1 38 HELIX 10 AB1 GLY A 204 TRP A 223 1 20 HELIX 11 AB2 ILE A 224 CYS A 233 1 10 HELIX 12 AB3 ASP A 241 LYS A 257 1 17 HELIX 13 AB4 LYS A 257 ARG A 277 1 21 LINK NZ LYS A 257 C15 RET A 401 1555 1555 1.33 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 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.500000 -0.866025 0.000000 180.75898 MTRIX2 2 0.866025 -0.500000 0.000000 48.43422 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 MTRIX1 3 -0.500000 0.866025 0.000000 48.43422 MTRIX2 3 -0.866025 -0.500000 0.000000 180.75898 MTRIX3 3 0.000000 0.000000 1.000000 0.00000