HEADER MEMBRANE PROTEIN 08-NOV-21 7SRQ TITLE 5-HT2B RECEPTOR BOUND TO LSD OBTAINED BY CRYO-ELECTRON MICROSCOPY TITLE 2 (CRYOEM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5-HYDROXYTRYPTAMINE RECEPTOR 2B; COMPND 3 CHAIN: R; COMPND 4 SYNONYM: 5-HT-2B,5-HT2B,SEROTONIN RECEPTOR 2B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HTR2B; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS 5-HT2B RECEPTOR, SEROTONIN RECEPTOR, GPCR, LYSERGIC ACID KEYWDS 2 DIETHYLAMIDE, LSD, CRYOEM, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR X.BARROS-ALVAREZ,C.CAO,O.PANOVA,B.L.ROTH,G.SKINIOTIS REVDAT 3 19-OCT-22 7SRQ 1 JRNL REVDAT 2 05-OCT-22 7SRQ 1 HETSYN REVDAT 1 21-SEP-22 7SRQ 0 JRNL AUTH C.CAO,X.BARROS-ALVAREZ,S.ZHANG,K.KIM,M.A.DAMGEN,O.PANOVA, JRNL AUTH 2 C.M.SUOMIVUORI,J.F.FAY,X.ZHONG,B.E.KRUMM,R.H.GUMPPER, JRNL AUTH 3 A.B.SEVEN,M.J.ROBERTSON,N.J.KROGAN,R.HUTTENHAIN,D.E.NICHOLS, JRNL AUTH 4 R.O.DROR,G.SKINIOTIS,B.L.ROTH JRNL TITL SIGNALING SNAPSHOTS OF A SEROTONIN RECEPTOR ACTIVATED BY THE JRNL TITL 2 PROTOTYPICAL PSYCHEDELIC LSD. JRNL REF NEURON V. 110 3154 2022 JRNL REFN ISSN 0896-6273 JRNL PMID 36087581 JRNL DOI 10.1016/J.NEURON.2022.08.006 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC 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) : 2.700 REMARK 3 NUMBER OF PARTICLES : 665475 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 7SRQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1000260921. 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 : 5-HT2B RECEPTOR BOUND TO LSD REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 6.50 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 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 123.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : 55000 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: R 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 THR R 36 REMARK 465 GLU R 37 REMARK 465 SER R 38 REMARK 465 ILE R 39 REMARK 465 PRO R 40 REMARK 465 GLU R 41 REMARK 465 GLU R 42 REMARK 465 MET R 43 REMARK 465 LYS R 44 REMARK 465 GLN R 45 REMARK 465 ILE R 46 REMARK 465 VAL R 47 REMARK 465 GLU R 48 REMARK 465 GLU R 49 REMARK 465 GLN R 50 REMARK 465 GLY R 51 REMARK 465 ASN R 52 REMARK 465 LYS R 53 REMARK 465 LEU R 54 REMARK 465 HIS R 55 REMARK 465 ILE R 161 REMARK 465 GLN R 162 REMARK 465 ALA R 163 REMARK 465 ASN R 164 REMARK 465 GLN R 165 REMARK 465 TYR R 166 REMARK 465 ASN R 167 REMARK 465 LEU R 303 REMARK 465 GLN R 304 REMARK 465 LYS R 305 REMARK 465 VAL R 306 REMARK 465 ARG R 307 REMARK 465 LEU R 308 REMARK 465 LEU R 309 REMARK 465 SER R 310 REMARK 465 GLY R 311 REMARK 465 SER R 312 REMARK 465 ARG R 313 REMARK 465 GLN R 314 REMARK 465 THR R 315 REMARK 465 ILE R 316 REMARK 465 SER R 317 REMARK 465 ASN R 318 REMARK 465 GLU R 319 REMARK 465 GLN R 320 REMARK 465 ARG R 321 REMARK 465 ILE R 395 REMARK 465 THR R 396 REMARK 465 CYS R 397 REMARK 465 ASN R 398 REMARK 465 TYR R 399 REMARK 465 ARG R 400 REMARK 465 ALA R 401 REMARK 465 THR R 402 REMARK 465 LYS R 403 REMARK 465 SER R 404 REMARK 465 VAL R 405 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU R 59 CG CD1 CD2 REMARK 470 LEU R 60 CG CD1 CD2 REMARK 470 LEU R 62 CG CD1 CD2 REMARK 470 LEU R 77 CG CD1 CD2 REMARK 470 LEU R 81 CG CD1 CD2 REMARK 470 GLU R 82 CG CD OE1 OE2 REMARK 470 LYS R 83 CG CD CE NZ REMARK 470 LYS R 84 CG CD CE NZ REMARK 470 GLU R 118 CG CD OE1 OE2 REMARK 470 LYS R 159 CG CD CE NZ REMARK 470 ARG R 169 CG CD NE CZ NH1 NH2 REMARK 470 ILE R 176 CG1 CG2 CD1 REMARK 470 PHE R 238 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS R 324 CG CD CE NZ REMARK 470 VAL R 325 CG1 CG2 REMARK 470 VAL R 329 CG1 CG2 REMARK 470 PHE R 333 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP R 351 CG OD1 OD2 REMARK 470 MET R 360 CG SD CE REMARK 470 GLU R 363 CG CD OE1 OE2 REMARK 470 LEU R 378 CG CD1 CD2 REMARK 470 ARG R 393 CG CD NE CZ NH1 NH2 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 GLU R 118 97.94 -68.13 REMARK 500 LYS R 324 -61.07 -93.39 REMARK 500 LEU R 335 -35.50 -36.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-25401 RELATED DB: EMDB REMARK 900 5-HT2B RECEPTOR BOUND TO LSD OBTAINED BY CRYO-ELECTRON MICROSCOPY REMARK 900 (CRYOEM) DBREF 7SRQ R 36 405 UNP P41595 5HT2B_HUMAN 36 405 SEQADV 7SRQ TRP R 144 UNP P41595 MET 144 CONFLICT SEQADV 7SRQ R UNP P41595 LYS 246 DELETION SEQADV 7SRQ R UNP P41595 LYS 247 DELETION SEQADV 7SRQ R UNP P41595 ALA 248 DELETION SEQADV 7SRQ R UNP P41595 TYR 249 DELETION SEQADV 7SRQ R UNP P41595 LEU 250 DELETION SEQADV 7SRQ R UNP P41595 VAL 251 DELETION SEQADV 7SRQ R UNP P41595 LYS 252 DELETION SEQADV 7SRQ R UNP P41595 ASN 253 DELETION SEQADV 7SRQ R UNP P41595 LYS 254 DELETION SEQADV 7SRQ R UNP P41595 PRO 255 DELETION SEQADV 7SRQ R UNP P41595 PRO 256 DELETION SEQADV 7SRQ R UNP P41595 GLN 257 DELETION SEQADV 7SRQ R UNP P41595 ARG 258 DELETION SEQADV 7SRQ R UNP P41595 LEU 259 DELETION SEQADV 7SRQ R UNP P41595 THR 260 DELETION SEQADV 7SRQ R UNP P41595 TRP 261 DELETION SEQADV 7SRQ R UNP P41595 LEU 262 DELETION SEQADV 7SRQ R UNP P41595 THR 263 DELETION SEQADV 7SRQ R UNP P41595 VAL 264 DELETION SEQADV 7SRQ R UNP P41595 SER 265 DELETION SEQADV 7SRQ R UNP P41595 THR 266 DELETION SEQADV 7SRQ R UNP P41595 VAL 267 DELETION SEQADV 7SRQ R UNP P41595 PHE 268 DELETION SEQADV 7SRQ R UNP P41595 GLN 269 DELETION SEQADV 7SRQ R UNP P41595 ARG 270 DELETION SEQADV 7SRQ R UNP P41595 ASP 271 DELETION SEQADV 7SRQ R UNP P41595 GLU 272 DELETION SEQADV 7SRQ R UNP P41595 THR 273 DELETION SEQADV 7SRQ R UNP P41595 PRO 274 DELETION SEQADV 7SRQ R UNP P41595 CYS 275 DELETION SEQADV 7SRQ R UNP P41595 SER 276 DELETION SEQADV 7SRQ R UNP P41595 SER 277 DELETION SEQADV 7SRQ R UNP P41595 PRO 278 DELETION SEQADV 7SRQ R UNP P41595 GLU 279 DELETION SEQADV 7SRQ ARG R 307 UNP P41595 ALA 282 CONFLICT SEQADV 7SRQ LEU R 308 UNP P41595 MET 283 CONFLICT SEQADV 7SRQ SER R 310 UNP P41595 ASP 285 CONFLICT SEQADV 7SRQ R UNP P41595 LYS 289 DELETION SEQADV 7SRQ R UNP P41595 ASP 290 DELETION SEQADV 7SRQ R UNP P41595 LYS 291 DELETION SEQADV 7SRQ R UNP P41595 ALA 292 DELETION SEQADV 7SRQ R UNP P41595 LEU 293 DELETION SEQADV 7SRQ R UNP P41595 PRO 294 DELETION SEQADV 7SRQ R UNP P41595 ASN 295 DELETION SEQADV 7SRQ R UNP P41595 SER 296 DELETION SEQADV 7SRQ R UNP P41595 GLY 297 DELETION SEQADV 7SRQ R UNP P41595 ASP 298 DELETION SEQADV 7SRQ R UNP P41595 GLU 299 DELETION SEQADV 7SRQ R UNP P41595 THR 300 DELETION SEQADV 7SRQ R UNP P41595 LEU 301 DELETION SEQADV 7SRQ R UNP P41595 MET 302 DELETION SEQADV 7SRQ R UNP P41595 ARG 303 DELETION SEQADV 7SRQ R UNP P41595 ARG 304 DELETION SEQADV 7SRQ R UNP P41595 THR 305 DELETION SEQADV 7SRQ R UNP P41595 SER 306 DELETION SEQADV 7SRQ R UNP P41595 THR 307 DELETION SEQADV 7SRQ R UNP P41595 ILE 308 DELETION SEQADV 7SRQ R UNP P41595 GLY 309 DELETION SEQADV 7SRQ R UNP P41595 LYS 310 DELETION SEQADV 7SRQ R UNP P41595 LYS 311 DELETION SEQADV 7SRQ R UNP P41595 SER 312 DELETION SEQADV 7SRQ R UNP P41595 VAL 313 DELETION SEQRES 1 R 311 THR GLU SER ILE PRO GLU GLU MET LYS GLN ILE VAL GLU SEQRES 2 R 311 GLU GLN GLY ASN LYS LEU HIS TRP ALA ALA LEU LEU ILE SEQRES 3 R 311 LEU MET VAL ILE ILE PRO THR ILE GLY GLY ASN THR LEU SEQRES 4 R 311 VAL ILE LEU ALA VAL SER LEU GLU LYS LYS LEU GLN TYR SEQRES 5 R 311 ALA THR ASN TYR PHE LEU MET SER LEU ALA VAL ALA ASP SEQRES 6 R 311 LEU LEU VAL GLY LEU PHE VAL MET PRO ILE ALA LEU LEU SEQRES 7 R 311 THR ILE MET PHE GLU ALA MET TRP PRO LEU PRO LEU VAL SEQRES 8 R 311 LEU CYS PRO ALA TRP LEU PHE LEU ASP VAL LEU PHE SER SEQRES 9 R 311 THR ALA SER ILE TRP HIS LEU CYS ALA ILE SER VAL ASP SEQRES 10 R 311 ARG TYR ILE ALA ILE LYS LYS PRO ILE GLN ALA ASN GLN SEQRES 11 R 311 TYR ASN SER ARG ALA THR ALA PHE ILE LYS ILE THR VAL SEQRES 12 R 311 VAL TRP LEU ILE SER ILE GLY ILE ALA ILE PRO VAL PRO SEQRES 13 R 311 ILE LYS GLY ILE GLU THR ASP VAL ASP ASN PRO ASN ASN SEQRES 14 R 311 ILE THR CYS VAL LEU THR LYS GLU ARG PHE GLY ASP PHE SEQRES 15 R 311 MET LEU PHE GLY SER LEU ALA ALA PHE PHE THR PRO LEU SEQRES 16 R 311 ALA ILE MET ILE VAL THR TYR PHE LEU THR ILE HIS ALA SEQRES 17 R 311 LEU GLN LYS VAL ARG LEU LEU SER GLY SER ARG GLN THR SEQRES 18 R 311 ILE SER ASN GLU GLN ARG ALA SER LYS VAL LEU GLY ILE SEQRES 19 R 311 VAL PHE PHE LEU PHE LEU LEU MET TRP CYS PRO PHE PHE SEQRES 20 R 311 ILE THR ASN ILE THR LEU VAL LEU CYS ASP SER CYS ASN SEQRES 21 R 311 GLN THR THR LEU GLN MET LEU LEU GLU ILE PHE VAL TRP SEQRES 22 R 311 ILE GLY TYR VAL SER SER GLY VAL ASN PRO LEU VAL TYR SEQRES 23 R 311 THR LEU PHE ASN LYS THR PHE ARG ASP ALA PHE GLY ARG SEQRES 24 R 311 TYR ILE THR CYS ASN TYR ARG ALA THR LYS SER VAL HET NAG R 501 14 HET 7LD R 502 24 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM 7LD (8ALPHA)-N,N-DIETHYL-6-METHYL-9,10-DIDEHYDROERGOLINE-8- HETNAM 2 7LD CARBOXAMIDE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN 7LD LYSERGIC ACID DIETHYLAMIDE FORMUL 2 NAG C8 H15 N O6 FORMUL 3 7LD C20 H25 N3 O HELIX 1 AA1 TRP R 56 GLU R 82 1 27 HELIX 2 AA2 TYR R 87 PHE R 117 1 31 HELIX 3 AA3 VAL R 126 LYS R 159 1 34 HELIX 4 AA4 ARG R 169 ILE R 188 1 20 HELIX 5 AA5 ILE R 188 LYS R 193 1 6 HELIX 6 AA6 ASN R 201 ILE R 205 5 5 HELIX 7 AA7 GLY R 215 PHE R 226 1 12 HELIX 8 AA8 PHE R 226 HIS R 242 1 17 HELIX 9 AA9 SER R 323 PHE R 333 1 11 HELIX 10 AB1 LEU R 334 MET R 336 5 3 HELIX 11 AB2 TRP R 337 CYS R 350 1 14 HELIX 12 AB3 ASN R 354 LEU R 382 1 29 HELIX 13 AB4 ASN R 384 TYR R 394 1 11 SSBOND 1 CYS R 128 CYS R 207 1555 1555 2.03 SSBOND 2 CYS R 350 CYS R 353 1555 1555 2.03 LINK ND2 ASN R 204 C1 NAG R 501 1555 1555 1.44 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