HEADER ELECTRON TRANSPORT 20-AUG-24 9J7W TITLE CHANNEL RHODOSPIN FROM KLEBSORMIDIUM NITENS (KNCHR) COMPND MOL_ID: 1; COMPND 2 MOLECULE: KNCHR; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSORMIDIUM NITENS; SOURCE 3 ORGANISM_TAXID: 105231; SOURCE 4 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS BLUE-LIGHT ABSORBING, ELECTRON TRANSPORT EXPDTA ELECTRON MICROSCOPY AUTHOR Y.Z.WANG,H.AKASAKA,T.TANAKA,F.K.SANO,W.SHIHOYA,O.NUREKI REVDAT 2 09-JUL-25 9J7W 1 JRNL REVDAT 1 02-JUL-25 9J7W 0 JRNL AUTH Y.Z.WANG,K.NATSUME,T.TANAKA,S.HOSOSHIMA,R.TASHIRO,F.K.SANO, JRNL AUTH 2 H.AKASAKA,S.P.TSUNODA,W.SHIHOYA,H.KANDORI,O.NUREKI JRNL TITL CRYO-EM STRUCTURE OF A BLUE-SHIFTED CHANNELRHODOPSIN FROM JRNL TITL 2 KLEBSORMIDIUM NITENS. JRNL REF NAT COMMUN V. 16 5297 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40533461 JRNL DOI 10.1038/S41467-025-59299-9 REMARK 2 REMARK 2 RESOLUTION. 2.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 PHENIX, CRYOSPARC, COOT 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) : 2.690 REMARK 3 NUMBER OF PARTICLES : 164260 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 9J7W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1300050236. 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 : 6-S-CIS RETINAL 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 : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 8554 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 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) : 4926.30 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : 105000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER A 137 OE1 GLU A 139 1.97 REMARK 500 OG SER C 137 OE1 GLU C 139 1.97 REMARK 500 OH TYR C 49 O HOH C 401 2.05 REMARK 500 OH TYR A 49 O HOH A 401 2.05 REMARK 500 O HOH A 402 O HOH A 412 2.05 REMARK 500 O HOH C 402 O HOH C 412 2.05 REMARK 500 OE2 GLU C 94 O HOH C 402 2.07 REMARK 500 OE2 GLU A 94 O HOH A 402 2.07 REMARK 500 OE2 GLU A 53 O HOH A 401 2.16 REMARK 500 OE2 GLU C 53 O HOH C 401 2.16 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 ARG A 287 -169.01 -161.25 REMARK 500 MET A 290 -109.38 57.16 REMARK 500 ARG C 287 -169.00 -161.23 REMARK 500 MET C 290 -109.32 57.07 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 PC1 A 301 REMARK 610 PC1 C 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61212 RELATED DB: EMDB REMARK 900 CHANNEL RHODOSPIN FROM KLEBSORMIDIUM NITENS (KNCHR) DBREF1 9J7W A 27 291 UNP A0A1Y1HT90_KLENI DBREF2 9J7W A A0A1Y1HT90 27 291 DBREF1 9J7W C 27 291 UNP A0A1Y1HT90_KLENI DBREF2 9J7W C A0A1Y1HT90 27 291 SEQRES 1 A 265 SER CYS TYR VAL ALA ASP PHE LEU GLY MET HIS HIS GLU SEQRES 2 A 265 SER HIS GLU GLY ALA LEU TYR SER VAL TYR LYS SER LEU SEQRES 3 A 265 GLU TRP GLY CYS PHE LEU ILE SER ILE GLY LEU PHE VAL SEQRES 4 A 265 PHE TYR LEU GLN GLN TYR ARG LYS LYS THR ALA GLY TRP SEQRES 5 A 265 GLU VAL ILE TYR ILE ALA PHE ILE GLU SER PHE LYS TYR SEQRES 6 A 265 ILE PHE GLU ILE PHE TRP PRO HIS ASN ASN PRO ALA GLN SEQRES 7 A 265 LEU ASN ILE TYR GLY VAL ASN LYS SER VAL PRO TRP VAL SEQRES 8 A 265 ARG TYR MET GLU TRP MET ILE THR CYS PRO VAL ILE LEU SEQRES 9 A 265 MET ALA LEU SER ASN ILE SER GLY GLU GLU GLY GLU TYR SEQRES 10 A 265 THR HIS ARG SER MET GLN LEU LEU ALA THR ASP GLN GLY SEQRES 11 A 265 ALA ILE LEU CYS ALA ILE THR ALA ALA ALA SER GLU GLY SEQRES 12 A 265 ALA ILE SER ALA VAL PHE TYR ALA ILE GLY VAL CYS TYR SEQRES 13 A 265 GLY ILE CYS THR PHE TYR PHE CYS LEU GLN ILE TYR ILE SEQRES 14 A 265 GLU ALA TYR PHE THR LEU PRO GLU THR CYS HIS SER ALA SEQRES 15 A 265 VAL LYS TRP MET ALA VAL ILE PHE TYR ALA GLY TRP LEU SEQRES 16 A 265 CYS TYR PRO CYS PHE PHE LEU ALA GLY SER GLU GLY TRP SEQRES 17 A 265 GLY ASN LEU SER TYR GLU GLY SER ALA ILE GLY HIS CYS SEQRES 18 A 265 ILE ALA ASP LEU LEU SER LYS ASN ALA TRP GLY VAL MET SEQRES 19 A 265 HIS TRP TRP ILE ARG CYS GLN LEU GLU GLU TYR LYS HIS SEQRES 20 A 265 THR HIS ASN GLY GLN LEU PRO HIS TYR SER LEU GLU THR SEQRES 21 A 265 ARG ALA LYS MET ARG SEQRES 1 C 265 SER CYS TYR VAL ALA ASP PHE LEU GLY MET HIS HIS GLU SEQRES 2 C 265 SER HIS GLU GLY ALA LEU TYR SER VAL TYR LYS SER LEU SEQRES 3 C 265 GLU TRP GLY CYS PHE LEU ILE SER ILE GLY LEU PHE VAL SEQRES 4 C 265 PHE TYR LEU GLN GLN TYR ARG LYS LYS THR ALA GLY TRP SEQRES 5 C 265 GLU VAL ILE TYR ILE ALA PHE ILE GLU SER PHE LYS TYR SEQRES 6 C 265 ILE PHE GLU ILE PHE TRP PRO HIS ASN ASN PRO ALA GLN SEQRES 7 C 265 LEU ASN ILE TYR GLY VAL ASN LYS SER VAL PRO TRP VAL SEQRES 8 C 265 ARG TYR MET GLU TRP MET ILE THR CYS PRO VAL ILE LEU SEQRES 9 C 265 MET ALA LEU SER ASN ILE SER GLY GLU GLU GLY GLU TYR SEQRES 10 C 265 THR HIS ARG SER MET GLN LEU LEU ALA THR ASP GLN GLY SEQRES 11 C 265 ALA ILE LEU CYS ALA ILE THR ALA ALA ALA SER GLU GLY SEQRES 12 C 265 ALA ILE SER ALA VAL PHE TYR ALA ILE GLY VAL CYS TYR SEQRES 13 C 265 GLY ILE CYS THR PHE TYR PHE CYS LEU GLN ILE TYR ILE SEQRES 14 C 265 GLU ALA TYR PHE THR LEU PRO GLU THR CYS HIS SER ALA SEQRES 15 C 265 VAL LYS TRP MET ALA VAL ILE PHE TYR ALA GLY TRP LEU SEQRES 16 C 265 CYS TYR PRO CYS PHE PHE LEU ALA GLY SER GLU GLY TRP SEQRES 17 C 265 GLY ASN LEU SER TYR GLU GLY SER ALA ILE GLY HIS CYS SEQRES 18 C 265 ILE ALA ASP LEU LEU SER LYS ASN ALA TRP GLY VAL MET SEQRES 19 C 265 HIS TRP TRP ILE ARG CYS GLN LEU GLU GLU TYR LYS HIS SEQRES 20 C 265 THR HIS ASN GLY GLN LEU PRO HIS TYR SER LEU GLU THR SEQRES 21 C 265 ARG ALA LYS MET ARG HET PC1 A 301 32 HET RET A 302 20 HET PC1 C 301 32 HET RET C 302 20 HETNAM PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE HETNAM RET RETINAL HETSYN PC1 3-SN-PHOSPHATIDYLCHOLINE FORMUL 3 PC1 2(C44 H88 N O8 P) FORMUL 4 RET 2(C20 H28 O) FORMUL 7 HOH *36(H2 O) HELIX 1 AA1 GLY A 43 TYR A 71 1 29 HELIX 2 AA2 ARG A 72 LYS A 74 5 3 HELIX 3 AA3 GLY A 77 TRP A 97 1 21 HELIX 4 AA4 TRP A 116 ASN A 135 1 20 HELIX 5 AA5 THR A 144 SER A 167 1 24 HELIX 6 AA6 GLY A 169 LEU A 201 1 33 HELIX 7 AA7 PRO A 202 THR A 204 5 3 HELIX 8 AA8 CYS A 205 LEU A 221 1 17 HELIX 9 AA9 LEU A 221 GLY A 230 1 10 HELIX 10 AB1 SER A 238 LYS A 254 1 17 HELIX 11 AB2 LYS A 254 HIS A 275 1 22 HELIX 12 AB3 GLY C 43 TYR C 71 1 29 HELIX 13 AB4 ARG C 72 LYS C 74 5 3 HELIX 14 AB5 GLY C 77 TRP C 97 1 21 HELIX 15 AB6 TRP C 116 ASN C 135 1 20 HELIX 16 AB7 THR C 144 SER C 167 1 24 HELIX 17 AB8 GLY C 169 LEU C 201 1 33 HELIX 18 AB9 PRO C 202 THR C 204 5 3 HELIX 19 AC1 CYS C 205 LEU C 221 1 17 HELIX 20 AC2 LEU C 221 GLY C 230 1 10 HELIX 21 AC3 SER C 238 LYS C 254 1 17 HELIX 22 AC4 LYS C 254 HIS C 275 1 22 SHEET 1 AA1 2 GLN A 104 ILE A 107 0 SHEET 2 AA1 2 LYS A 112 PRO A 115 -1 O LYS A 112 N ILE A 107 SHEET 1 AA2 2 GLN C 104 ILE C 107 0 SHEET 2 AA2 2 LYS C 112 PRO C 115 -1 O LYS C 112 N ILE C 107 LINK NZ LYS A 254 C15 RET A 302 1555 1555 1.34 LINK NZ LYS C 254 C15 RET C 302 1555 1555 1.33 CISPEP 1 ASN A 101 PRO A 102 0 7.68 CISPEP 2 ASN C 101 PRO C 102 0 7.69 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 1820 4359 CONECT 3976 4411 CONECT 4313 4314 CONECT 4314 4313 4315 4316 4323 CONECT 4315 4314 CONECT 4316 4314 4317 CONECT 4317 4316 4318 CONECT 4318 4317 4319 CONECT 4319 4318 4320 4321 4322 CONECT 4320 4319 CONECT 4321 4319 CONECT 4322 4319 CONECT 4323 4314 4324 CONECT 4324 4323 4325 CONECT 4325 4324 4326 4335 CONECT 4326 4325 4327 CONECT 4327 4326 4328 4329 CONECT 4328 4327 CONECT 4329 4327 4330 CONECT 4330 4329 4331 CONECT 4331 4330 4332 CONECT 4332 4331 4333 CONECT 4333 4332 4334 CONECT 4334 4333 CONECT 4335 4325 4336 CONECT 4336 4335 4337 CONECT 4337 4336 4338 4339 CONECT 4338 4337 CONECT 4339 4337 4340 CONECT 4340 4339 4341 CONECT 4341 4340 4342 CONECT 4342 4341 4343 CONECT 4343 4342 4344 CONECT 4344 4343 CONECT 4345 4346 4350 4360 4361 CONECT 4346 4345 4347 CONECT 4347 4346 4348 CONECT 4348 4347 4349 CONECT 4349 4348 4350 4362 CONECT 4350 4345 4349 4351 CONECT 4351 4350 4352 CONECT 4352 4351 4353 CONECT 4353 4352 4354 4363 CONECT 4354 4353 4355 CONECT 4355 4354 4356 CONECT 4356 4355 4357 CONECT 4357 4356 4358 4364 CONECT 4358 4357 4359 CONECT 4359 1820 4358 CONECT 4360 4345 CONECT 4361 4345 CONECT 4362 4349 CONECT 4363 4353 CONECT 4364 4357 CONECT 4365 4366 CONECT 4366 4365 4367 4368 4375 CONECT 4367 4366 CONECT 4368 4366 4369 CONECT 4369 4368 4370 CONECT 4370 4369 4371 CONECT 4371 4370 4372 4373 4374 CONECT 4372 4371 CONECT 4373 4371 CONECT 4374 4371 CONECT 4375 4366 4376 CONECT 4376 4375 4377 CONECT 4377 4376 4378 4387 CONECT 4378 4377 4379 CONECT 4379 4378 4380 4381 CONECT 4380 4379 CONECT 4381 4379 4382 CONECT 4382 4381 4383 CONECT 4383 4382 4384 CONECT 4384 4383 4385 CONECT 4385 4384 4386 CONECT 4386 4385 CONECT 4387 4377 4388 CONECT 4388 4387 4389 CONECT 4389 4388 4390 4391 CONECT 4390 4389 CONECT 4391 4389 4392 CONECT 4392 4391 4393 CONECT 4393 4392 4394 CONECT 4394 4393 4395 CONECT 4395 4394 4396 CONECT 4396 4395 CONECT 4397 4398 4402 4412 4413 CONECT 4398 4397 4399 CONECT 4399 4398 4400 CONECT 4400 4399 4401 CONECT 4401 4400 4402 4414 CONECT 4402 4397 4401 4403 CONECT 4403 4402 4404 CONECT 4404 4403 4405 CONECT 4405 4404 4406 4415 CONECT 4406 4405 4407 CONECT 4407 4406 4408 CONECT 4408 4407 4409 CONECT 4409 4408 4410 4416 CONECT 4410 4409 4411 CONECT 4411 3976 4410 CONECT 4412 4397 CONECT 4413 4397 CONECT 4414 4401 CONECT 4415 4405 CONECT 4416 4409 MASTER 148 0 4 22 4 0 0 6 4428 2 106 42 END