HEADER MEMBRANE PROTEIN 21-OCT-22 8H87 TITLE CRYO-EM STRUCTURE OF THE POTASSIUM-SELECTIVE CHANNELRHODOPSIN HCKCR2 TITLE 2 IN LIPID NANODISC COMPND MOL_ID: 1; COMPND 2 MOLECULE: HCKCR2; 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 8H87 1 JRNL REVDAT 1 06-SEP-23 8H87 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. 2.53 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) : 2.530 REMARK 3 NUMBER OF PARTICLES : 682797 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 8H87 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_1300033031. 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 : HCKCR2 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) : 5100.00 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 166.92311 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 44.72691 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 44.72692 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 166.92311 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 261 REMARK 465 LYS A 262 REMARK 465 VAL A 263 REMARK 465 MET A 264 REMARK 465 ASP A 265 REMARK 465 ALA A 266 REMARK 465 ALA A 267 REMARK 465 ALA A 268 REMARK 465 LYS A 269 REMARK 465 SER A 270 REMARK 465 ARG A 271 REMARK 465 ILE A 272 REMARK 465 THR A 273 REMARK 465 SER A 274 REMARK 465 GLU A 275 REMARK 465 GLY A 276 REMARK 465 GLU A 277 REMARK 465 TYR A 278 REMARK 465 ILE A 279 REMARK 465 PRO A 280 REMARK 465 LEU A 281 REMARK 465 ASP A 282 REMARK 465 GLN A 283 REMARK 465 ILE A 284 REMARK 465 ASP A 285 REMARK 465 ILE A 286 REMARK 465 ASN A 287 REMARK 465 VAL A 288 REMARK 465 GLY A 289 REMARK 465 ALA A 290 REMARK 465 PRO A 291 REMARK 465 GLY A 292 REMARK 465 SER A 293 REMARK 465 SER A 294 REMARK 465 LEU A 295 REMARK 465 GLU A 296 REMARK 465 VAL A 297 REMARK 465 LEU A 298 REMARK 465 PHE A 299 REMARK 465 GLN A 300 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 103 -2.22 73.47 REMARK 500 GLN A 125 61.10 65.28 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 244 0.08 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 402 REMARK 610 PSC A 403 REMARK 610 PSC A 404 REMARK 610 PSC A 405 REMARK 610 PSC A 406 REMARK 610 PSC A 407 REMARK 610 PLM A 408 REMARK 610 PLM A 410 REMARK 610 PLM A 411 REMARK 610 PLM A 412 REMARK 610 PLM A 413 REMARK 610 PLM A 414 REMARK 610 PLM A 415 REMARK 610 PLM A 416 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34531 RELATED DB: EMDB REMARK 900 MEMBRANE PROTEIN B DBREF 8H87 A 1 300 PDB 8H87 8H87 1 300 SEQRES 1 A 300 MET PRO PHE TYR ASP SER ARG PRO PRO GLU GLY TRP PRO SEQRES 2 A 300 ARG GLY SER VAL ASN ASP MET ASP TYR PRO LEU LEU GLY SEQRES 3 A 300 SER ILE CYS ALA ILE SER ALA ILE ALA ILE ALA GLY SER SEQRES 4 A 300 GLY ILE TRP MET LEU TYR ARG LEU ASP LEU GLY MET GLY SEQRES 5 A 300 TYR SER CYS LYS PRO TYR LYS SER GLY ARG ALA PRO GLU SEQRES 6 A 300 VAL ASN SER ILE SER GLY ILE VAL CYS LEU LEU CYS GLY SEQRES 7 A 300 THR MET TYR ALA ALA LYS SER PHE ASP PHE PHE ASP GLY SEQRES 8 A 300 GLY GLY THR PRO PHE SER LEU ASN TRP TYR TRP TYR LEU SEQRES 9 A 300 ASP TYR VAL PHE THR CYS PRO LEU LEU ILE VAL ASP PHE SEQRES 10 A 300 ALA PHE THR LEU ASP ILE PRO GLN LYS LEU ARG TYR SER SEQRES 11 A 300 ILE ALA VAL PHE VAL ALA LEU TRP CYS ALA VAL ALA ALA SEQRES 12 A 300 PHE ALA THR PRO SER ALA PHE ARG PHE ALA TYR TYR ALA SEQRES 13 A 300 LEU GLY CYS CYS TRP PHE ILE PRO LEU SER LEU PHE LEU SEQRES 14 A 300 ILE ARG ASP VAL LYS LYS ARG TYR GLN VAL TYR PRO PRO SEQRES 15 A 300 LYS CYS GLN ARG LEU LEU PHE TRP ALA CYS VAL VAL PHE SEQRES 16 A 300 PHE GLY PHE TRP PRO LEU PHE PRO LEU LEU PHE ILE PHE SEQRES 17 A 300 SER TRP GLN GLY SER GLY HIS ILE SER ARG GLN ALA TYR SEQRES 18 A 300 TYR ILE ILE HIS ALA PHE LEU ASP LEU VAL CYS LYS SER SEQRES 19 A 300 ILE PHE GLY PHE LEU MET THR PHE PHE ARG LEU GLU LEU SEQRES 20 A 300 GLU GLU HIS THR GLU VAL GLN GLY LEU PRO LEU LYS GLU SEQRES 21 A 300 PRO LYS VAL MET ASP ALA ALA ALA LYS SER ARG ILE THR SEQRES 22 A 300 SER GLU GLY GLU TYR ILE PRO LEU ASP GLN ILE ASP ILE SEQRES 23 A 300 ASN VAL GLY ALA PRO GLY SER SER LEU GLU VAL LEU PHE SEQRES 24 A 300 GLN HET RET A 401 20 HET PSC A 402 43 HET PSC A 403 9 HET PSC A 404 10 HET PSC A 405 31 HET PSC A 406 6 HET PSC A 407 14 HET PLM A 408 12 HET PLM A 409 18 HET PLM A 410 9 HET PLM A 411 9 HET PLM A 412 8 HET PLM A 413 9 HET PLM A 414 5 HET PLM A 415 6 HET PLM A 416 6 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 6(C42 H81 N O8 P 1+) FORMUL 9 PLM 9(C16 H32 O2) FORMUL 18 HOH *49(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 ASP A 105 ASP A 122 1 18 HELIX 5 AA5 GLN 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 ILE A 207 1 8 HELIX 9 AA9 SER A 217 LYS A 233 1 17 HELIX 10 AB1 LYS A 233 GLU A 252 1 20 LINK NZ LYS A 233 C15 RET A 401 1555 1555 1.27 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 166.92311 MTRIX2 2 0.866025 -0.500000 0.000000 44.72691 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 MTRIX1 3 -0.500000 0.866025 0.000000 44.72691 MTRIX2 3 -0.866025 -0.500000 0.000000 166.92311 MTRIX3 3 0.000000 0.000000 1.000000 0.00000