HEADER TRANSPORT PROTEIN 13-MAR-23 8GI9 TITLE CATION CHANNELRHODOPSIN FROM HYPHOCHYTRIUM CATENOIDES (HCCCR) EMBEDDED TITLE 2 IN PEPTIDISC COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATION CHANNELRHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HYPHOCHYTRIUM CATENOIDES; SOURCE 3 ORGANISM_TAXID: 42384; SOURCE 4 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: SMD1168; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: HCCCR_PPICZALPHA-A KEYWDS RETINAL PROTEIN, CHANNELRHODOPSIN, CATION CHANNEL, PEPTIDISC, KEYWDS 2 OPTOGENETICS, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR T.MORIZUMI,K.KIM,H.LI,J.L.SPUDICH,O.P.ERNST REVDAT 3 01-MAY-24 8GI9 1 JRNL REVDAT 2 24-APR-24 8GI9 1 REMARK REVDAT 1 26-JUL-23 8GI9 0 JRNL AUTH T.MORIZUMI,K.KIM,H.LI,E.G.GOVORUNOVA,O.A.SINESHCHEKOV, JRNL AUTH 2 Y.WANG,L.ZHENG,E.BERTALAN,A.N.BONDAR,A.ASKARI,L.S.BROWN, JRNL AUTH 3 J.L.SPUDICH,O.P.ERNST JRNL TITL STRUCTURES OF CHANNELRHODOPSIN PARALOGS IN PEPTIDISCS JRNL TITL 2 EXPLAIN THEIR CONTRASTING K + AND NA + SELECTIVITIES. JRNL REF NAT COMMUN V. 14 4365 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37474513 JRNL DOI 10.1038/S41467-023-40041-2 REMARK 2 REMARK 2 RESOLUTION. 2.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, PHENIX, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : CROSS CORRELATION COEFFICENT REMARK 3 OVERALL ANISOTROPIC B VALUE : 151.100 REMARK 3 REMARK 3 FITTING PROCEDURE : INITIAL FITTING DONE IN PHENIX 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) : 2.840 REMARK 3 NUMBER OF PARTICLES : 298957 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 8GI9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000272950. 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 : CATION CHANNELRHODOPSIN TRIMER REMARK 245 RECONSTITUTED IN PEPTIDISC REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.35 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 : 5902 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : OTHER REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : 75000 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 292.39678 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 78.42584 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 78.27962 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 292.43596 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 PRO A 2 REMARK 465 PHE A 3 REMARK 465 CYS A 4 REMARK 465 GLY A 5 REMARK 465 GLY A 6 REMARK 465 ARG A 7 REMARK 465 PRO A 8 REMARK 465 GLU A 9 REMARK 465 ASP A 10 REMARK 465 GLY A 11 REMARK 465 TRP A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 GLY A 15 REMARK 465 SER A 16 REMARK 465 PRO A 257 REMARK 465 LEU A 258 REMARK 465 ASN A 259 REMARK 465 GLU A 260 REMARK 465 PRO A 261 REMARK 465 LYS A 262 REMARK 465 GLY A 263 REMARK 465 LYS A 264 REMARK 465 HIS A 265 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 62 -63.05 -96.66 REMARK 500 TYR A 103 -3.32 70.57 REMARK 500 PRO A 124 -179.00 -67.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-40063 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-40062 RELATED DB: EMDB DBREF 8GI9 A 1 265 PDB 8GI9 8GI9 1 265 SEQRES 1 A 265 MET PRO PHE CYS GLY GLY ARG PRO GLU ASP GLY TRP HIS SEQRES 2 A 265 HIS GLY SER ILE HIS ASP MET ASP TYR PRO LEU LEU GLY SEQRES 3 A 265 ALA MET ALA ALA ILE CYS SER VAL PHE ILE GLY GLY SER SEQRES 4 A 265 GLY ALA TRP MET LEU TYR ARG LEU ASP LEU GLY LEU GLY SEQRES 5 A 265 TYR SER CYS LYS PRO HIS HIS SER GLY TYR ALA PRO GLU SEQRES 6 A 265 ALA ASN SER PHE SER ALA LEU SER CYS LEU VAL SER GLY SEQRES 7 A 265 THR ILE TYR ALA ALA LYS THR PHE ASP PHE PHE ASP GLY SEQRES 8 A 265 GLY GLY THR PRO PHE SER PHE ASN TRP TYR TRP TYR LEU SEQRES 9 A 265 ASP TYR VAL PHE THR CYS PRO LEU ILE LEU LEU ASP VAL SEQRES 10 A 265 LEU TYR THR LEU GLU ILE PRO HIS LYS LEU ARG PHE VAL SEQRES 11 A 265 PHE ALA VAL ILE ILE THR LEU TRP CYS GLY VAL ALA ALA SEQRES 12 A 265 PHE VAL THR PRO SER ALA PHE ARG PHE GLY TYR TYR ALA SEQRES 13 A 265 VAL GLY CYS VAL TRP PHE VAL PRO PHE SER PHE SER LEU SEQRES 14 A 265 LEU ARG HIS VAL LYS GLN ARG TYR GLN VAL TYR PRO PRO SEQRES 15 A 265 LYS CYS GLN LYS LEU LEU PHE TRP ALA CYS THR ILE PHE SEQRES 16 A 265 PHE GLY PHE TRP PRO LEU PHE PRO ILE LEU PHE LEU PHE SEQRES 17 A 265 SER TRP LEU GLY THR GLY HIS ILE ASP GLN GLN ALA PHE SEQRES 18 A 265 THR ILE ILE HIS ALA PHE LEU ASP LEU PHE CYS LYS THR SEQRES 19 A 265 VAL PHE GLY LEU ILE MET THR PHE PHE ARG LEU GLU LEU SEQRES 20 A 265 GLU GLU HIS THR GLU VAL LEU GLY LEU PRO LEU ASN GLU SEQRES 21 A 265 PRO LYS GLY LYS HIS HET RET A 301 20 HET NA A 302 1 HET NA A 303 1 HET NA A 304 1 HET CLR A 305 28 HET CLR A 306 28 HET CLR A 307 28 HET CLR A 308 28 HET CLR A 309 28 HET CLR A 310 28 HET CLR A 311 28 HET PEE A 312 51 HET PEE A 313 51 HETNAM RET RETINAL HETNAM NA SODIUM ION HETNAM CLR CHOLESTEROL HETNAM PEE 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE HETSYN PEE DOPE FORMUL 2 RET C20 H28 O FORMUL 3 NA 3(NA 1+) FORMUL 6 CLR 7(C27 H46 O) FORMUL 13 PEE 2(C41 H78 N O8 P) FORMUL 15 HOH *15(H2 O) HELIX 1 AA1 ASP A 21 ASP A 48 1 28 HELIX 2 AA2 PRO A 64 ASN A 67 5 4 HELIX 3 AA3 SER A 68 ASP A 90 1 23 HELIX 4 AA4 TYR A 103 PHE A 108 1 6 HELIX 5 AA5 THR A 109 GLU A 122 1 14 HELIX 6 AA6 HIS A 125 THR A 146 1 22 HELIX 7 AA7 PHE A 150 TYR A 177 1 28 HELIX 8 AA8 PRO A 181 TRP A 199 1 19 HELIX 9 AA9 PRO A 200 SER A 209 1 10 HELIX 10 AB1 ASP A 217 LYS A 233 1 17 HELIX 11 AB2 LYS A 233 GLU A 252 1 20 LINK NZ LYS A 233 C15 RET A 301 1555 1555 1.43 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