HEADER MEMBRANE PROTEIN 06-DEC-23 8XBI TITLE HUMAN GPR34 -GI COMPLEX BOUND TO M1, RECEPTOR FOCUSED COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE G-PROTEIN COUPLED RECEPTOR 34; COMPND 3 CHAIN: R; COMPND 4 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: GPR34; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS GPCR, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR R.KAWAHARA,W.SHIHOYA,O.NUREKI REVDAT 2 15-MAY-24 8XBI 1 SOURCE JRNL REVDAT 1 27-DEC-23 8XBI 0 JRNL AUTH T.IZUME,R.KAWAHARA,A.UWAMIZU,L.CHEN,S.YAGINUMA,J.OMI, JRNL AUTH 2 H.KAWANA,F.HOU,F.K.SANO,T.TANAKA,K.KOBAYASHI,H.H.OKAMOTO, JRNL AUTH 3 Y.KISE,T.OHWADA,J.AOKI,W.SHIHOYA,O.NUREKI JRNL TITL STRUCTURAL BASIS FOR LYSOPHOSPHATIDYLSERINE RECOGNITION BY JRNL TITL 2 GPR34. JRNL REF NAT COMMUN V. 15 902 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38326347 JRNL DOI 10.1038/S41467-024-45046-Z REMARK 2 REMARK 2 RESOLUTION. 3.06 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) : 3.060 REMARK 3 NUMBER OF PARTICLES : 236096 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 8XBI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1300042064. 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 : HUMAN GPR34-GI COMPLEX BOUND TO REMARK 245 M1,RECEPTOR FOCUSED REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 12.00 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 : 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) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 5000.00 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 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 ASP R -8 REMARK 465 TYR R -7 REMARK 465 LYS R -6 REMARK 465 ASP R -5 REMARK 465 ASP R -4 REMARK 465 ASP R -3 REMARK 465 ASP R -2 REMARK 465 ALA R -1 REMARK 465 MET R 0 REMARK 465 GLY R 1 REMARK 465 ARG R 2 REMARK 465 SER R 3 REMARK 465 HIS R 4 REMARK 465 THR R 5 REMARK 465 ILE R 6 REMARK 465 THR R 7 REMARK 465 MET R 8 REMARK 465 THR R 9 REMARK 465 THR R 10 REMARK 465 THR R 11 REMARK 465 SER R 12 REMARK 465 VAL R 13 REMARK 465 SER R 14 REMARK 465 SER R 15 REMARK 465 TRP R 16 REMARK 465 PRO R 17 REMARK 465 TYR R 18 REMARK 465 SER R 19 REMARK 465 SER R 20 REMARK 465 HIS R 21 REMARK 465 ARG R 22 REMARK 465 MET R 23 REMARK 465 ARG R 24 REMARK 465 PHE R 25 REMARK 465 ILE R 26 REMARK 465 THR R 27 REMARK 465 ASN R 28 REMARK 465 HIS R 29 REMARK 465 SER R 30 REMARK 465 ASP R 31 REMARK 465 GLN R 32 REMARK 465 PRO R 33 REMARK 465 PRO R 34 REMARK 465 GLN R 35 REMARK 465 ASN R 36 REMARK 465 PHE R 37 REMARK 465 SER R 38 REMARK 465 ALA R 39 REMARK 465 THR R 40 REMARK 465 PRO R 41 REMARK 465 ASN R 42 REMARK 465 VAL R 43 REMARK 465 THR R 44 REMARK 465 PHE R 343 REMARK 465 ARG R 344 REMARK 465 ARG R 345 REMARK 465 PHE R 346 REMARK 465 GLN R 347 REMARK 465 GLY R 348 REMARK 465 GLU R 349 REMARK 465 PRO R 350 REMARK 465 SER R 351 REMARK 465 ARG R 352 REMARK 465 SER R 353 REMARK 465 GLU R 354 REMARK 465 SER R 355 REMARK 465 THR R 356 REMARK 465 SER R 357 REMARK 465 GLU R 358 REMARK 465 PHE R 359 REMARK 465 LYS R 360 REMARK 465 PRO R 361 REMARK 465 GLY R 362 REMARK 465 TYR R 363 REMARK 465 SER R 364 REMARK 465 LEU R 365 REMARK 465 HIS R 366 REMARK 465 ASP R 367 REMARK 465 THR R 368 REMARK 465 SER R 369 REMARK 465 VAL R 370 REMARK 465 ALA R 371 REMARK 465 VAL R 372 REMARK 465 LYS R 373 REMARK 465 ILE R 374 REMARK 465 GLN R 375 REMARK 465 SER R 376 REMARK 465 SER R 377 REMARK 465 SER R 378 REMARK 465 LYS R 379 REMARK 465 SER R 380 REMARK 465 THR R 381 REMARK 465 GLU R 382 REMARK 465 ASN R 383 REMARK 465 LEU R 384 REMARK 465 TYR R 385 REMARK 465 PHE R 386 REMARK 465 GLN R 387 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 ASN R 116 -73.21 -63.61 REMARK 500 GLN R 117 15.85 -146.47 REMARK 500 GLN R 162 -177.96 -176.44 REMARK 500 ASN R 257 43.24 37.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38219 RELATED DB: EMDB REMARK 900 HUMAN GPR34 -GI COMPLEX BOUND TO M1, RECEPTOR FOCUSED DBREF 8XBI R 2 381 UNP Q9UPC5 GPR34_HUMAN 2 381 SEQADV 8XBI ASP R -8 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI TYR R -7 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI LYS R -6 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI ASP R -5 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI ASP R -4 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI ASP R -3 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI ASP R -2 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI ALA R -1 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI MET R 0 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI GLY R 1 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI GLU R 382 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI ASN R 383 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI LEU R 384 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI TYR R 385 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI PHE R 386 UNP Q9UPC5 EXPRESSION TAG SEQADV 8XBI GLN R 387 UNP Q9UPC5 EXPRESSION TAG SEQRES 1 R 396 ASP TYR LYS ASP ASP ASP ASP ALA MET GLY ARG SER HIS SEQRES 2 R 396 THR ILE THR MET THR THR THR SER VAL SER SER TRP PRO SEQRES 3 R 396 TYR SER SER HIS ARG MET ARG PHE ILE THR ASN HIS SER SEQRES 4 R 396 ASP GLN PRO PRO GLN ASN PHE SER ALA THR PRO ASN VAL SEQRES 5 R 396 THR THR CYS PRO MET ASP GLU LYS LEU LEU SER THR VAL SEQRES 6 R 396 LEU THR THR SER TYR SER VAL ILE PHE ILE VAL GLY LEU SEQRES 7 R 396 VAL GLY ASN ILE ILE ALA LEU TYR VAL PHE LEU GLY ILE SEQRES 8 R 396 HIS ARG LYS ARG ASN SER ILE GLN ILE TYR LEU LEU ASN SEQRES 9 R 396 VAL ALA ILE ALA ASP LEU LEU LEU ILE PHE CYS LEU PRO SEQRES 10 R 396 PHE ARG ILE MET TYR HIS ILE ASN GLN ASN LYS TRP THR SEQRES 11 R 396 LEU GLY VAL ILE LEU CYS LYS VAL VAL GLY THR LEU PHE SEQRES 12 R 396 TYR MET ASN MET TYR ILE SER ILE ILE LEU LEU GLY PHE SEQRES 13 R 396 ILE SER LEU ASP ARG TYR ILE LYS ILE ASN ARG SER ILE SEQRES 14 R 396 GLN GLN ARG LYS ALA ILE THR THR LYS GLN SER ILE TYR SEQRES 15 R 396 VAL CYS CYS ILE VAL TRP MET LEU ALA LEU GLY GLY PHE SEQRES 16 R 396 LEU THR MET ILE ILE LEU THR LEU LYS LYS GLY GLY HIS SEQRES 17 R 396 ASN SER THR MET CYS PHE HIS TYR ARG ASP LYS HIS ASN SEQRES 18 R 396 ALA LYS GLY GLU ALA ILE PHE ASN PHE ILE LEU VAL VAL SEQRES 19 R 396 MET PHE TRP LEU ILE PHE LEU LEU ILE ILE LEU SER TYR SEQRES 20 R 396 ILE LYS ILE GLY LYS ASN LEU LEU ARG ILE SER LYS ARG SEQRES 21 R 396 ARG SER LYS PHE PRO ASN SER GLY LYS TYR ALA THR THR SEQRES 22 R 396 ALA ARG ASN SER PHE ILE VAL LEU ILE ILE PHE THR ILE SEQRES 23 R 396 CYS PHE VAL PRO TYR HIS ALA PHE ARG PHE ILE TYR ILE SEQRES 24 R 396 SER SER GLN LEU ASN VAL SER SER CYS TYR TRP LYS GLU SEQRES 25 R 396 ILE VAL HIS LYS THR ASN GLU ILE MET LEU VAL LEU SER SEQRES 26 R 396 SER PHE ASN SER CYS LEU ASP PRO VAL MET TYR PHE LEU SEQRES 27 R 396 MET SER SER ASN ILE ARG LYS ILE MET CYS GLN LEU LEU SEQRES 28 R 396 PHE ARG ARG PHE GLN GLY GLU PRO SER ARG SER GLU SER SEQRES 29 R 396 THR SER GLU PHE LYS PRO GLY TYR SER LEU HIS ASP THR SEQRES 30 R 396 SER VAL ALA VAL LYS ILE GLN SER SER SER LYS SER THR SEQRES 31 R 396 GLU ASN LEU TYR PHE GLN HET KW3 R 401 43 HETNAM KW3 (2~{S})-2-AZANYL-3-[[(2~{R})-1-ETHOXY-3-[3-[2-[(3- HETNAM 2 KW3 PHENOXYPHENYL)METHOXY]PHENYL]PROPANOYLOXY]PROPAN-2- HETNAM 3 KW3 YL]OXY-OXIDANYL-PHOSPHORYL]OXY-PROPANOIC ACID FORMUL 2 KW3 C30 H36 N O11 P HELIX 1 AA1 GLU R 50 ILE R 82 1 33 HELIX 2 AA2 ASN R 87 GLN R 117 1 31 HELIX 3 AA3 GLY R 123 ASN R 157 1 35 HELIX 4 AA4 THR R 167 GLY R 197 1 31 HELIX 5 AA5 ALA R 213 ARG R 252 1 40 HELIX 6 AA6 GLY R 259 LEU R 294 1 36 HELIX 7 AA7 SER R 298 SER R 331 1 34 HELIX 8 AA8 SER R 331 LEU R 342 1 12 SSBOND 1 CYS R 46 CYS R 299 1555 1555 2.04 SSBOND 2 CYS R 127 CYS R 204 1555 1555 2.08 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