HEADER MEMBRANE PROTEIN 28-APR-25 9UPM TITLE CRYO-EM STRUCTURE OF MACAQUE RED CONE PIGMENT WITH Q114N MUTATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LW OPSIN,SOLUBLE CYTOCHROME B562; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME B-562; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MACACA FASCICULARIS, ESCHERICHIA COLI; SOURCE 3 ORGANISM_COMMON: CRAB-EATING MACAQUE; SOURCE 4 ORGANISM_TAXID: 9541, 562; SOURCE 5 GENE: CYBC; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS CONE PIGMENT, GPCR, RHODOPSIN, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.OHASHI,A.KOJIMA,M.FUKUDA,S.KIM,H.E.KATO,H.KANDORI,K.KATAYAMA REVDAT 1 24-JUN-26 9UPM 0 JRNL AUTH S.OHASHI,A.KOJIMA,X.YANG,M.FUKUDA,F.SACCHETTA,Y.SUGITA, JRNL AUTH 2 N.NUEMKET,S.KIM,K.KOBAYASHI,H.IMAI,S.IWATA,E.NANGO, JRNL AUTH 3 T.KOBAYASHI,T.NODA,M.OLIVUCCI,H.E.KATO,H.KANDORI JRNL TITL STRUCTURAL INSIGHTS INTO SPECTRAL TUNING AND RETINAL JRNL TITL 2 EXCHANGE IN CONE VISUAL PIGMENTS JRNL REF SCIENCE 2026 JRNL REFN ESSN 1095-9203 JRNL DOI 10.1126/SCIENCE.ADZ3996 REMARK 2 REMARK 2 RESOLUTION. 3.21 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) : 3.210 REMARK 3 NUMBER OF PARTICLES : 256022 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9UPM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300058756. 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 : MR REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : JEC-3000FC REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 15824 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 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) : 4690.00 REMARK 245 ILLUMINATION MODE : OTHER 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 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 GLN A 3 REMARK 465 GLN A 4 REMARK 465 TRP A 5 REMARK 465 SER A 6 REMARK 465 LEU A 7 REMARK 465 GLN A 8 REMARK 465 ARG A 9 REMARK 465 LEU A 10 REMARK 465 ALA A 11 REMARK 465 GLY A 12 REMARK 465 ARG A 13 REMARK 465 HIS A 14 REMARK 465 PRO A 15 REMARK 465 GLN A 16 REMARK 465 ASP A 17 REMARK 465 SER A 18 REMARK 465 TYR A 19 REMARK 465 GLU A 20 REMARK 465 ASP A 21 REMARK 465 SER A 22 REMARK 465 THR A 23 REMARK 465 GLN A 24 REMARK 465 SER A 25 REMARK 465 SER A 26 REMARK 465 ILE A 27 REMARK 465 PHE A 28 REMARK 465 THR A 29 REMARK 465 TYR A 30 REMARK 465 THR A 31 REMARK 465 ASN A 32 REMARK 465 SER A 33 REMARK 465 ASN A 34 REMARK 465 SER A 35 REMARK 465 THR A 36 REMARK 465 ARG A 37 REMARK 465 ALA A 251 REMARK 465 ASP A 252 REMARK 465 LEU A 253 REMARK 465 GLU A 254 REMARK 465 ASP A 255 REMARK 465 ASN A 256 REMARK 465 TRP A 257 REMARK 465 GLU A 258 REMARK 465 THR A 259 REMARK 465 LEU A 260 REMARK 465 ASN A 261 REMARK 465 ASP A 262 REMARK 465 ASN A 263 REMARK 465 LEU A 264 REMARK 465 LYS A 265 REMARK 465 VAL A 266 REMARK 465 ILE A 267 REMARK 465 GLU A 268 REMARK 465 LYS A 269 REMARK 465 ALA A 270 REMARK 465 ASP A 271 REMARK 465 ASN A 272 REMARK 465 ALA A 273 REMARK 465 ALA A 274 REMARK 465 GLN A 275 REMARK 465 VAL A 276 REMARK 465 LYS A 277 REMARK 465 ASP A 278 REMARK 465 ALA A 279 REMARK 465 LEU A 280 REMARK 465 THR A 281 REMARK 465 LYS A 282 REMARK 465 MET A 283 REMARK 465 ARG A 284 REMARK 465 ALA A 285 REMARK 465 ALA A 286 REMARK 465 ALA A 287 REMARK 465 LEU A 288 REMARK 465 ASP A 289 REMARK 465 ALA A 290 REMARK 465 GLY A 291 REMARK 465 SER A 292 REMARK 465 GLY A 293 REMARK 465 SER A 294 REMARK 465 GLY A 295 REMARK 465 HIS A 296 REMARK 465 GLY A 297 REMARK 465 PHE A 298 REMARK 465 ASP A 299 REMARK 465 ILE A 300 REMARK 465 LEU A 301 REMARK 465 VAL A 302 REMARK 465 GLY A 303 REMARK 465 GLN A 304 REMARK 465 ILE A 305 REMARK 465 ASP A 306 REMARK 465 ASP A 307 REMARK 465 ALA A 308 REMARK 465 LEU A 309 REMARK 465 LYS A 310 REMARK 465 LEU A 311 REMARK 465 ALA A 312 REMARK 465 ASN A 313 REMARK 465 GLU A 314 REMARK 465 GLY A 315 REMARK 465 LYS A 316 REMARK 465 VAL A 317 REMARK 465 LYS A 318 REMARK 465 GLU A 319 REMARK 465 ALA A 320 REMARK 465 GLN A 321 REMARK 465 ALA A 322 REMARK 465 ALA A 323 REMARK 465 ALA A 324 REMARK 465 GLU A 325 REMARK 465 GLN A 326 REMARK 465 LEU A 327 REMARK 465 LYS A 328 REMARK 465 THR A 329 REMARK 465 THR A 330 REMARK 465 ILE A 331 REMARK 465 ASN A 332 REMARK 465 ALA A 333 REMARK 465 TYR A 334 REMARK 465 ILE A 335 REMARK 465 GLN A 336 REMARK 465 LYS A 337 REMARK 465 TYR A 338 REMARK 465 GLY A 339 REMARK 465 LYS A 421 REMARK 465 LYS A 422 REMARK 465 VAL A 423 REMARK 465 ASP A 424 REMARK 465 ASP A 425 REMARK 465 GLY A 426 REMARK 465 SER A 427 REMARK 465 GLU A 428 REMARK 465 LEU A 429 REMARK 465 SER A 430 REMARK 465 SER A 431 REMARK 465 ALA A 432 REMARK 465 SER A 433 REMARK 465 LYS A 434 REMARK 465 THR A 435 REMARK 465 GLU A 436 REMARK 465 VAL A 437 REMARK 465 SER A 438 REMARK 465 SER A 439 REMARK 465 VAL A 440 REMARK 465 SER A 441 REMARK 465 SER A 442 REMARK 465 VAL A 443 REMARK 465 SER A 444 REMARK 465 PRO A 445 REMARK 465 ALA A 446 REMARK 465 LEU A 447 REMARK 465 GLU A 448 REMARK 465 VAL A 449 REMARK 465 LEU A 450 REMARK 465 PHE A 451 REMARK 465 GLN A 452 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 ILE A 105 -74.12 -102.40 REMARK 500 LYS A 157 70.79 51.48 REMARK 500 ASP A 165 -124.55 50.67 REMARK 500 ALA A 166 -33.78 -142.96 REMARK 500 TRP A 191 -133.01 53.72 REMARK 500 CYS A 227 13.33 -140.11 REMARK 500 CYS A 228 -51.26 -137.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-64397 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF MONKEY RED CONE PIGMENT WITH Q114N MUTATION DBREF 9UPM A 1 250 UNP Q9XSX4 Q9XSX4_MACFA 1 250 DBREF 9UPM A 251 290 UNP P0ABE7 C562_ECOLX 23 62 DBREF 9UPM A 296 338 UNP P0ABE7 C562_ECOLX 85 127 DBREF 9UPM A 340 446 UNP Q9XSX4 Q9XSX4_MACFA 258 364 SEQADV 9UPM ASN A 114 UNP Q9XSX4 GLN 114 ENGINEERED MUTATION SEQADV 9UPM TRP A 257 UNP P0ABE7 MET 29 ENGINEERED MUTATION SEQADV 9UPM GLY A 291 UNP P0ABE7 LINKER SEQADV 9UPM SER A 292 UNP P0ABE7 LINKER SEQADV 9UPM GLY A 293 UNP P0ABE7 LINKER SEQADV 9UPM SER A 294 UNP P0ABE7 LINKER SEQADV 9UPM GLY A 295 UNP P0ABE7 LINKER SEQADV 9UPM ILE A 331 UNP P0ABE7 ARG 120 ENGINEERED MUTATION SEQADV 9UPM ILE A 335 UNP P0ABE7 HIS 124 ENGINEERED MUTATION SEQADV 9UPM GLY A 339 UNP P0ABE7 LINKER SEQADV 9UPM LEU A 447 UNP Q9XSX4 EXPRESSION TAG SEQADV 9UPM GLU A 448 UNP Q9XSX4 EXPRESSION TAG SEQADV 9UPM VAL A 449 UNP Q9XSX4 EXPRESSION TAG SEQADV 9UPM LEU A 450 UNP Q9XSX4 EXPRESSION TAG SEQADV 9UPM PHE A 451 UNP Q9XSX4 EXPRESSION TAG SEQADV 9UPM GLN A 452 UNP Q9XSX4 EXPRESSION TAG SEQRES 1 A 452 MET ALA GLN GLN TRP SER LEU GLN ARG LEU ALA GLY ARG SEQRES 2 A 452 HIS PRO GLN ASP SER TYR GLU ASP SER THR GLN SER SER SEQRES 3 A 452 ILE PHE THR TYR THR ASN SER ASN SER THR ARG GLY PRO SEQRES 4 A 452 PHE GLU GLY PRO ASN TYR HIS ILE ALA PRO ARG TRP VAL SEQRES 5 A 452 TYR HIS LEU THR SER VAL TRP MET ILE PHE VAL VAL THR SEQRES 6 A 452 ALA SER VAL PHE THR ASN GLY LEU VAL LEU ALA ALA THR SEQRES 7 A 452 MET LYS PHE LYS LYS LEU ARG HIS PRO LEU ASN TRP ILE SEQRES 8 A 452 LEU VAL ASN LEU ALA VAL ALA ASP LEU ALA GLU THR VAL SEQRES 9 A 452 ILE ALA SER THR ILE SER VAL VAL ASN ASN VAL SER GLY SEQRES 10 A 452 TYR PHE VAL LEU GLY HIS PRO MET CYS VAL LEU GLU GLY SEQRES 11 A 452 PHE THR VAL SER LEU CYS GLY ILE THR GLY LEU TRP SER SEQRES 12 A 452 LEU ALA ILE ILE SER TRP GLU ARG TRP LEU VAL VAL CYS SEQRES 13 A 452 LYS PRO PHE GLY ASN VAL ARG PHE ASP ALA LYS LEU ALA SEQRES 14 A 452 ILE VAL GLY ILE ALA PHE SER TRP ILE TRP SER ALA VAL SEQRES 15 A 452 TRP THR ALA PRO PRO ILE PHE GLY TRP SER ARG TYR TRP SEQRES 16 A 452 PRO HIS GLY LEU LYS THR SER CYS GLY PRO ASP VAL PHE SEQRES 17 A 452 SER GLY SER SER TYR PRO GLY VAL GLN SER TYR MET ILE SEQRES 18 A 452 VAL LEU MET VAL THR CYS CYS ILE ILE PRO LEU ALA ILE SEQRES 19 A 452 ILE VAL LEU CYS TYR LEU GLN VAL TRP LEU ALA ILE ARG SEQRES 20 A 452 ALA VAL ALA ALA ASP LEU GLU ASP ASN TRP GLU THR LEU SEQRES 21 A 452 ASN ASP ASN LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA SEQRES 22 A 452 ALA GLN VAL LYS ASP ALA LEU THR LYS MET ARG ALA ALA SEQRES 23 A 452 ALA LEU ASP ALA GLY SER GLY SER GLY HIS GLY PHE ASP SEQRES 24 A 452 ILE LEU VAL GLY GLN ILE ASP ASP ALA LEU LYS LEU ALA SEQRES 25 A 452 ASN GLU GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA GLU SEQRES 26 A 452 GLN LEU LYS THR THR ILE ASN ALA TYR ILE GLN LYS TYR SEQRES 27 A 452 GLY SER THR GLN LYS ALA GLU LYS GLU VAL THR ARG MET SEQRES 28 A 452 VAL MET VAL MET ILE PHE ALA TYR CYS VAL CYS TRP GLY SEQRES 29 A 452 PRO TYR THR PHE PHE ALA CYS PHE ALA ALA ALA ASN PRO SEQRES 30 A 452 GLY TYR ALA PHE HIS PRO LEU MET ALA ALA LEU PRO ALA SEQRES 31 A 452 TYR PHE ALA LYS SER ALA THR ILE TYR ASN PRO ILE ILE SEQRES 32 A 452 TYR VAL PHE MET ASN ARG GLN PHE ARG ASN CYS ILE LEU SEQRES 33 A 452 GLN LEU PHE GLY LYS LYS VAL ASP ASP GLY SER GLU LEU SEQRES 34 A 452 SER SER ALA SER LYS THR GLU VAL SER SER VAL SER SER SEQRES 35 A 452 VAL SER PRO ALA LEU GLU VAL LEU PHE GLN HET RET A 500 21 HETNAM RET RETINAL FORMUL 2 RET C20 H28 O HELIX 1 AA1 PRO A 49 PHE A 81 1 33 HELIX 2 AA2 LYS A 82 ARG A 85 5 4 HELIX 3 AA3 HIS A 86 ILE A 105 1 20 HELIX 4 AA4 ILE A 105 GLY A 117 1 13 HELIX 5 AA5 GLY A 122 VAL A 155 1 34 HELIX 6 AA6 ALA A 169 ALA A 185 1 17 HELIX 7 AA7 ALA A 185 GLY A 190 1 6 HELIX 8 AA8 GLY A 215 CYS A 228 1 14 HELIX 9 AA9 CYS A 228 ALA A 250 1 23 HELIX 10 AB1 THR A 341 ASN A 376 1 36 HELIX 11 AB2 HIS A 382 ALA A 393 1 12 HELIX 12 AB3 LYS A 394 ALA A 396 5 3 HELIX 13 AB4 ILE A 398 ASN A 408 1 11 HELIX 14 AB5 ASN A 408 GLY A 420 1 13 SSBOND 1 CYS A 126 CYS A 203 1555 1555 2.03 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 696 1314 CONECT 1314 696 CONECT 2319 2320 2324 2335 2336 CONECT 2320 2319 2321 CONECT 2321 2320 2322 CONECT 2322 2321 2323 CONECT 2323 2322 2324 2337 CONECT 2324 2319 2323 2325 CONECT 2325 2324 2326 CONECT 2326 2325 2327 CONECT 2327 2326 2328 2338 CONECT 2328 2327 2329 CONECT 2329 2328 2330 CONECT 2330 2329 2331 CONECT 2331 2330 2332 2339 CONECT 2332 2331 2333 CONECT 2333 2332 2334 CONECT 2334 2333 CONECT 2335 2319 CONECT 2336 2319 CONECT 2337 2323 CONECT 2338 2327 CONECT 2339 2331 MASTER 286 0 1 14 0 0 0 6 2338 1 23 35 END