HEADER MEMBRANE PROTEIN 03-JUL-24 9CIB TITLE CRYOEM STRUCTURE OF HCA2 DREADD GI1 IN COMPLEX WITH FCH-2296413 (LOCAL TITLE 2 REFINEMENT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROXYCARBOXYLIC ACID RECEPTOR 2; COMPND 3 CHAIN: R; COMPND 4 SYNONYM: G-PROTEIN COUPLED RECEPTOR 109,G-PROTEIN COUPLED RECEPTOR COMPND 5 109A,G-PROTEIN COUPLED RECEPTOR HM74,NIACIN RECEPTOR 1,NICOTINIC ACID COMPND 6 RECEPTOR,PROTEIN PUMA-G; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: PROTEIN STARTS AT M1, GTT SEQUENCE FROM PROTEASE COMPND 10 CLEAVAGE SITE, MUTATION D120A, MUTATION R108K TO CONVERT WT TO COMPND 11 DREADD. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: HCAR2, GPR109, GPR109A, GPR109B, NIACR1, PUMAG; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS GPCR, HCA2, MEMBRANE PROTEIN, DREADD EXPDTA ELECTRON MICROSCOPY AUTHOR B.E.KRUMM,H.J.KANG,J.F.DIBERTO,N.J.KAPOLKA,R.H.GUMPPER,R.H.J.OLSEN, AUTHOR 2 X.P.HUANG,S.ZHANG,J.F.FAY,B.L.ROTH REVDAT 1 14-MAY-25 9CIB 0 JRNL AUTH H.J.KANG,B.E.KRUMM,A.TASSOU,M.GERON,J.F.DIBERTO,N.J.KAPOLKA, JRNL AUTH 2 R.H.GUMPPER,K.SAKAMOTO,D.DEWRAN KOCAK,R.H.J.OLSEN,X.P.HUANG, JRNL AUTH 3 S.ZHANG,K.L.HUANG,S.A.ZAIDI,M.T.NGUYEN,M.J.JO,V.KATRITCH, JRNL AUTH 4 J.F.FAY,G.SCHERRER,B.L.ROTH JRNL TITL STRUCTURE-GUIDED DESIGN OF A PERIPHERALLY RESTRICTED JRNL TITL 2 CHEMOGENETIC SYSTEM. JRNL REF CELL V. 187 7433 2024 JRNL REFN ISSN 1097-4172 JRNL PMID 39631393 JRNL DOI 10.1016/J.CELL.2024.11.001 REMARK 2 REMARK 2 RESOLUTION. 2.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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 : FLEXIBLE FIT 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) : 2.620 REMARK 3 NUMBER OF PARTICLES : 250000 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 9CIB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1000285584. 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 : MOUSE HCAD-GAI1 IN COMPLEX WITH REMARK 245 FCH-2296413 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.50 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 TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1300.00 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) : 4700.00 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) : 200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 PHE R 51 REMARK 465 HIS R 52 REMARK 465 LEU R 53 REMARK 465 LYS R 54 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 TRP R 47 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP R 47 CZ3 CH2 REMARK 470 TRP R 56 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP R 56 CZ3 CH2 REMARK 470 ARG R 139 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 SER R 175 130.04 -175.58 REMARK 500 ARG R 219 30.50 -147.03 REMARK 500 ARG R 261 -39.69 -135.36 REMARK 500 CYS R 263 4.46 -67.50 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 R 207 0.29 SIDE CHAIN REMARK 500 ARG R 261 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8UUJ RELATED DB: PDB REMARK 900 FULL COMPLEX REMARK 900 RELATED ID: EMD-45616 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF HCA2 DREADD GI1 IN COMPLEX WITH FCH-2296413 REMARK 900 (LOCAL REFINEMENT) DBREF 9CIB R 4 297 UNP Q9EP66 HCAR2_MOUSE 4 297 SEQADV 9CIB LYS R 108 UNP Q9EP66 ARG 108 ENGINEERED MUTATION SEQADV 9CIB ALA R 121 UNP Q9EP66 ASP 121 ENGINEERED MUTATION SEQRES 1 R 294 SER ASP HIS PHE LEU VAL ILE ASN GLY LYS ASN CYS CYS SEQRES 2 R 294 VAL PHE ARG ASP GLU ASN ILE ALA LYS VAL LEU PRO PRO SEQRES 3 R 294 VAL LEU GLY LEU GLU PHE VAL PHE GLY LEU LEU GLY ASN SEQRES 4 R 294 GLY LEU ALA LEU TRP ILE PHE CYS PHE HIS LEU LYS SER SEQRES 5 R 294 TRP LYS SER SER ARG ILE PHE LEU PHE ASN LEU ALA VAL SEQRES 6 R 294 ALA ASP PHE LEU LEU ILE ILE CYS LEU PRO PHE LEU THR SEQRES 7 R 294 ASP ASN TYR VAL HIS ASN TRP ASP TRP ARG PHE GLY GLY SEQRES 8 R 294 ILE PRO CYS ARG VAL MET LEU PHE MET LEU ALA MET ASN SEQRES 9 R 294 LYS GLN GLY SER ILE ILE PHE LEU THR VAL VAL ALA VAL SEQRES 10 R 294 ALA ARG TYR PHE ARG VAL VAL HIS PRO HIS HIS PHE LEU SEQRES 11 R 294 ASN LYS ILE SER ASN ARG THR ALA ALA ILE ILE SER CYS SEQRES 12 R 294 PHE LEU TRP GLY LEU THR ILE GLY LEU THR VAL HIS LEU SEQRES 13 R 294 LEU TYR THR ASN MET MET THR LYS ASN GLY GLU ALA TYR SEQRES 14 R 294 LEU CYS SER SER PHE SER ILE CYS TYR ASN PHE ARG TRP SEQRES 15 R 294 HIS ASP ALA MET PHE LEU LEU GLU PHE PHE LEU PRO LEU SEQRES 16 R 294 ALA ILE ILE LEU PHE CYS SER GLY ARG ILE ILE TRP SER SEQRES 17 R 294 LEU ARG GLN ARG GLN MET ASP ARG HIS ALA LYS ILE LYS SEQRES 18 R 294 ARG ALA ILE ASN PHE ILE MET VAL VAL ALA ILE VAL PHE SEQRES 19 R 294 ILE ILE CYS PHE LEU PRO SER VAL ALA VAL ARG ILE ARG SEQRES 20 R 294 ILE PHE TRP LEU LEU TYR LYS TYR ASN VAL ARG ASN CYS SEQRES 21 R 294 ASP ILE TYR SER SER VAL ASP LEU ALA PHE PHE THR THR SEQRES 22 R 294 LEU SER PHE THR TYR MET ASN SER MET LEU ASP PRO VAL SEQRES 23 R 294 VAL TYR TYR PHE SER SER PRO SER HET XI9 R 401 14 HETNAM XI9 (3M,4AR,5AR)-3-(1H-TETRAZOL-5-YL)-4,4A,5,5A-TETRAHYDRO- HETNAM 2 XI9 1H-CYCLOPROPA[4,5]CYCLOPENTA[1,2-C]PYRAZOLE FORMUL 2 XI9 C8 H8 N6 HELIX 1 AA1 ASP R 20 ILE R 48 1 29 HELIX 2 AA2 LYS R 57 CYS R 76 1 20 HELIX 3 AA3 CYS R 76 HIS R 86 1 11 HELIX 4 AA4 GLY R 93 HIS R 128 1 36 HELIX 5 AA5 HIS R 131 ILE R 136 5 6 HELIX 6 AA6 SER R 137 VAL R 157 1 21 HELIX 7 AA7 VAL R 157 THR R 162 1 6 HELIX 8 AA8 ARG R 184 GLN R 214 1 31 HELIX 9 AA9 ARG R 219 TYR R 258 1 40 HELIX 10 AB1 ASN R 262 ILE R 265 5 4 HELIX 11 AB2 TYR R 266 TYR R 292 1 27 SHEET 1 AA1 2 PHE R 7 ILE R 10 0 SHEET 2 AA1 2 LYS R 13 CYS R 16 -1 O CYS R 15 N LEU R 8 SHEET 1 AA2 2 MET R 165 ASN R 168 0 SHEET 2 AA2 2 ALA R 171 CYS R 174 -1 O LEU R 173 N THR R 166 SSBOND 1 CYS R 15 CYS R 180 1555 1555 2.03 SSBOND 2 CYS R 16 CYS R 263 1555 1555 2.03 SSBOND 3 CYS R 97 CYS R 174 1555 1555 2.02 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 93 1363 CONECT 99 2079 CONECT 708 1320 CONECT 1320 708 CONECT 1363 93 CONECT 2079 99 CONECT 2356 2357 2360 CONECT 2357 2356 2358 2363 CONECT 2358 2357 2359 2363 CONECT 2359 2358 2360 2364 CONECT 2360 2356 2359 2361 CONECT 2361 2360 2362 2365 CONECT 2362 2361 2366 2369 CONECT 2363 2357 2358 CONECT 2364 2359 2365 CONECT 2365 2361 2364 CONECT 2366 2362 2367 CONECT 2367 2366 2368 CONECT 2368 2367 2369 CONECT 2369 2362 2368 MASTER 163 0 1 11 4 0 0 6 2368 1 20 23 END