HEADER MEMBRANE PROTEIN 21-OCT-22 8H86 TITLE CRYO-EM STRUCTURE OF THE POTASSIUM-SELECTIVE CHANNELRHODOPSIN HCKCR1 TITLE 2 IN LIPID NANODISC COMPND MOL_ID: 1; COMPND 2 MOLECULE: HCKCR1; 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: SPODOPTERA FRUGIPERDA; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS MEMBRANE PROTEIN, CRYO-EM EXPDTA ELECTRON MICROSCOPY AUTHOR S.TAJIMA,Y.KIM,K.YAMASHITA,M.FUKUDA,K.DEISSEROTH,H.E.KATO REVDAT 2 01-MAY-24 8H86 1 JRNL REVDAT 1 06-SEP-23 8H86 0 JRNL AUTH S.TAJIMA,Y.S.KIM,M.FUKUDA,Y.JO,P.Y.WANG,J.M.PAGGI,M.INOUE, JRNL AUTH 2 E.F.X.BYRNE,K.E.KISHI,S.NAKAMURA,C.RAMAKRISHNAN, JRNL AUTH 3 S.TAKARAMOTO,T.NAGATA,M.KONNO,M.SUGIURA,K.KATAYAMA, JRNL AUTH 4 T.E.MATSUI,K.YAMASHITA,S.KIM,H.IKEDA,J.KIM,H.KANDORI, JRNL AUTH 5 R.O.DROR,K.INOUE,K.DEISSEROTH,H.E.KATO JRNL TITL STRUCTURAL BASIS FOR ION SELECTIVITY IN POTASSIUM-SELECTIVE JRNL TITL 2 CHANNELRHODOPSINS. JRNL REF CELL V. 186 4325 2023 JRNL REFN ISSN 1097-4172 JRNL PMID 37652010 JRNL DOI 10.1016/J.CELL.2023.08.009 REMARK 2 REMARK 2 RESOLUTION. 2.56 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) : 2.560 REMARK 3 NUMBER OF PARTICLES : 801114 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 8H86 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1300033026. 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 : HCKCR1 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 K3 (6K 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 : 2.70 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 : 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 168.88687 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 45.25310 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 45.25310 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 168.88687 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 PRO A 2 REMARK 465 PHE A 3 REMARK 465 TYR A 4 REMARK 465 ASP A 5 REMARK 465 PRO A 261 REMARK 465 GLU A 262 REMARK 465 THR A 263 REMARK 465 LEU A 264 REMARK 465 SER A 265 REMARK 465 LEU A 266 REMARK 465 GLU A 267 REMARK 465 VAL A 268 REMARK 465 LEU A 269 REMARK 465 PHE A 270 REMARK 465 GLN A 271 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 PHE A 96 70.10 -108.55 REMARK 500 TYR A 103 -8.16 87.27 REMARK 500 ASP A 122 41.17 72.84 REMARK 500 LYS A 233 -64.04 -105.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 62 0.10 SIDE CHAIN 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 PSC A 302 REMARK 610 PSC A 303 REMARK 610 PLM A 304 REMARK 610 PLM A 305 REMARK 610 PSC A 306 REMARK 610 PLM A 307 REMARK 610 PLM A 308 REMARK 610 PLM A 309 REMARK 610 PSC A 310 REMARK 610 PSC A 311 REMARK 610 PSC A 312 REMARK 610 PSC A 313 REMARK 610 PSC A 314 REMARK 610 PSC A 315 REMARK 610 PSC A 316 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34530 RELATED DB: EMDB REMARK 900 MEMBRANE PROTEIN A DBREF 8H86 A -1 271 PDB 8H86 8H86 -1 271 SEQRES 1 A 273 GLY PRO MET PRO PHE TYR ASP SER ARG PRO PRO GLU GLY SEQRES 2 A 273 TRP PRO LYS GLY SER ILE ASN ASP MET ASP TYR PRO LEU SEQRES 3 A 273 LEU GLY SER ILE CYS ALA VAL CYS CYS VAL PHE VAL ALA SEQRES 4 A 273 GLY SER GLY ILE TRP MET LEU TYR ARG LEU ASP LEU GLY SEQRES 5 A 273 MET GLY TYR SER CYS LYS PRO TYR LYS SER GLY ARG ALA SEQRES 6 A 273 PRO GLU VAL ASN SER LEU SER GLY ILE ILE CYS LEU LEU SEQRES 7 A 273 CYS GLY THR MET TYR ALA ALA LYS SER PHE ASP PHE PHE SEQRES 8 A 273 ASP GLY GLY GLY THR PRO PHE SER LEU ASN TRP TYR TRP SEQRES 9 A 273 TYR LEU ASP TYR VAL PHE THR CYS PRO LEU LEU ILE LEU SEQRES 10 A 273 ASP PHE ALA PHE THR LEU ASP LEU PRO HIS LYS ILE ARG SEQRES 11 A 273 TYR PHE PHE ALA VAL PHE LEU THR LEU TRP CYS GLY VAL SEQRES 12 A 273 ALA ALA PHE VAL THR PRO SER ALA TYR ARG PHE ALA TYR SEQRES 13 A 273 TYR ALA LEU GLY CYS CYS TRP PHE THR PRO PHE ALA LEU SEQRES 14 A 273 SER LEU MET ARG HIS VAL LYS GLU ARG TYR LEU VAL TYR SEQRES 15 A 273 PRO PRO LYS CYS GLN ARG TRP LEU PHE TRP ALA CYS VAL SEQRES 16 A 273 ILE PHE PHE GLY PHE TRP PRO MET PHE PRO ILE LEU PHE SEQRES 17 A 273 ILE PHE SER TRP LEU GLY THR GLY HIS ILE SER GLN GLN SEQRES 18 A 273 ALA PHE TYR ILE ILE HIS ALA PHE LEU ASP LEU THR CYS SEQRES 19 A 273 LYS SER ILE PHE GLY ILE LEU MET THR VAL PHE ARG LEU SEQRES 20 A 273 GLU LEU GLU GLU HIS THR GLU VAL GLN GLY LEU PRO LEU SEQRES 21 A 273 ASN GLU PRO GLU THR LEU SER LEU GLU VAL LEU PHE GLN HET RET A 301 20 HET PSC A 302 27 HET PSC A 303 30 HET PLM A 304 10 HET PLM A 305 9 HET PSC A 306 4 HET PLM A 307 11 HET PLM A 308 12 HET PLM A 309 11 HET PSC A 310 27 HET PSC A 311 16 HET PSC A 312 9 HET PSC A 313 15 HET PSC A 314 21 HET PSC A 315 14 HET PSC A 316 13 HETNAM RET RETINAL HETNAM PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7- HETNAM 2 PSC [(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA- HETNAM 3 PSC 17,20-DIEN-1-AMINIUM 4-OXIDE HETNAM PLM PALMITIC ACID HETSYN PSC PHOSPHATIDYLCHOLINE; 2-LINOLEOYL-1-PALMITOYL-SN- HETSYN 2 PSC GYCEROL-3-PHOSPHOCHOLINE FORMUL 2 RET C20 H28 O FORMUL 3 PSC 10(C42 H81 N O8 P 1+) FORMUL 5 PLM 5(C16 H32 O2) FORMUL 18 HOH *21(H2 O) HELIX 1 AA1 ASP A 21 LEU A 49 1 29 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 ASP A 122 1 20 HELIX 5 AA5 HIS A 125 THR A 146 1 22 HELIX 6 AA6 ALA A 149 TYR A 177 1 29 HELIX 7 AA7 PRO A 181 TRP A 199 1 19 HELIX 8 AA8 PRO A 200 SER A 209 1 10 HELIX 9 AA9 SER A 217 GLU A 252 1 36 LINK NZ LYS A 233 C15 RET A 301 1555 1555 1.26 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 168.88688 MTRIX2 2 0.866025 -0.500000 0.000000 45.25310 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 MTRIX1 3 -0.500000 0.866025 0.000000 45.25310 MTRIX2 3 -0.866025 -0.500000 0.000000 168.88688 MTRIX3 3 0.000000 0.000000 1.000000 0.00000