HEADER MEMBRANE PROTEIN 19-MAR-25 9U4J TITLE CRYO-EM STRUCTURE OF THE HGPR4-APO RECEPTOR IN PH 7.8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: G-PROTEIN COUPLED RECEPTOR 4,SOLUBLE CYTOCHROME B562; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: G-PROTEIN COUPLED RECEPTOR 6C.L,GPR6C.L,CYTOCHROME B-562; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, ESCHERICHIA COLI O157:H7; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606, 83334; SOURCE 5 GENE: GPR4, CYBC, Z5846, ECS5213; SOURCE 6 EXPRESSION_SYSTEM: MAMMALIAN EXPRESSION VECTOR FLAG-MCS-PCDNA3.1; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 2021188 KEYWDS PH7.8, HGPR4, APO, MEMBRANE PROTEIN/IMMUNE SYSTEM, MEMBRANE PROTEIN- KEYWDS 2 IMMUNE SYSTEM, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.N.ZHONG,Z.L.LIU,L.L.GUO,J.P.SUN,F.YANG REVDAT 1 25-MAR-26 9U4J 0 JRNL AUTH Y.N.ZHONG,Z.L.LIU,F.YANG,J.P.SUN,F.YANG JRNL TITL CRYO-EM STRUCTURE OF THE HGPR4 APO-BRIL FAB RECEPTOR IN PH JRNL TITL 2 7.8 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.40 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 127493 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 9U4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 25-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300057691. 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 : CRYO-EM STRUCTURE OF THE REMARK 245 RECEPTOR OF THE HGPR4 APO-BRIL REMARK 245 FAB COMPLEX IN PH 7.8 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 : 7.80 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : DIFFRACTION REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 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: 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 SER A 213 REMARK 465 THR A 214 REMARK 465 PRO A 255 REMARK 465 TRP A 256 REMARK 465 ASP A 257 REMARK 465 CYS A 258 REMARK 465 ARG A 295 REMARK 465 GLN A 296 REMARK 465 LEU A 297 REMARK 465 ALA A 298 REMARK 465 ASP A 299 REMARK 465 LEU A 300 REMARK 465 GLU A 301 REMARK 465 ASP A 302 REMARK 465 ASN A 303 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 ASP A 16 CG OD1 OD2 REMARK 470 PHE A 19 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 23 CG CD1 CD2 REMARK 470 ILE A 25 CG1 CG2 CD1 REMARK 470 ILE A 28 CG1 CG2 CD1 REMARK 470 LEU A 32 CG CD1 CD2 REMARK 470 CYS A 36 SG REMARK 470 LEU A 37 CG CD1 CD2 REMARK 470 LEU A 39 CG CD1 CD2 REMARK 470 GLN A 45 CG CD OE1 NE2 REMARK 470 GLU A 51 CG CD OE1 OE2 REMARK 470 MET A 57 CG SD CE REMARK 470 ILE A 61 CG1 CG2 CD1 REMARK 470 LEU A 64 CG CD1 CD2 REMARK 470 THR A 69 OG1 CG2 REMARK 470 LEU A 72 CG CD1 CD2 REMARK 470 VAL A 74 CG1 CG2 REMARK 470 TYR A 76 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 78 CG CD1 CD2 REMARK 470 ASP A 81 CG OD1 OD2 REMARK 470 ASN A 82 CG OD1 ND2 REMARK 470 TRP A 83 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 83 CZ3 CH2 REMARK 470 HIS A 85 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 91 CG CD CE NZ REMARK 470 LEU A 92 CG CD1 CD2 REMARK 470 CYS A 110 SG REMARK 470 LEU A 117 CG CD1 CD2 REMARK 470 LEU A 123 CG CD1 CD2 REMARK 470 ARG A 124 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 125 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 127 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 128 CG CD1 CD2 REMARK 470 ARG A 129 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 135 CG1 CG2 REMARK 470 ASN A 149 CG OD1 ND2 REMARK 470 SER A 150 OG REMARK 470 HIS A 155 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 156 CG OD1 OD2 REMARK 470 PHE A 159 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 162 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 163 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN A 164 CG OD1 ND2 REMARK 470 THR A 166 OG1 CG2 REMARK 470 CYS A 168 SG REMARK 470 PHE A 169 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 170 CG CD OE1 OE2 REMARK 470 LYS A 171 CG CD CE NZ REMARK 470 PHE A 172 CG CD1 CD2 CE1 CE2 CZ REMARK 470 MET A 174 CG SD CE REMARK 470 GLU A 175 CG CD OE1 OE2 REMARK 470 VAL A 178 CG1 CG2 REMARK 470 TRP A 180 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 180 CZ3 CH2 REMARK 470 MET A 181 CG SD CE REMARK 470 ARG A 185 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 206 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 216 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 245 CG CD1 CD2 REMARK 470 SER A 246 OG REMARK 470 ARG A 247 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 251 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 254 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 262 CG CD OE1 OE2 REMARK 470 PHE A 265 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER A 271 OG REMARK 470 LEU A 272 CG CD1 CD2 REMARK 470 LEU A 277 CG CD1 CD2 REMARK 470 CYS A 279 SG REMARK 470 TYR A 286 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 CYS A 287 SG REMARK 470 GLU A 291 CG CD OE1 OE2 REMARK 470 ARG A 294 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 HIS A 121 70.30 57.44 REMARK 500 VAL A 131 38.47 39.11 REMARK 500 GLU A 157 44.54 38.68 REMARK 500 PHE A 172 72.55 52.68 REMARK 500 TYR A 268 -56.90 -122.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-63848 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE HGPR4-APO RECEPTOR IN PH 7.8 DBREF 9U4J A 16 294 UNP P46093 GPR4_HUMAN 16 294 DBREF 9U4J A 298 303 UNP P0ABE8 C562_ECO57 23 28 SEQADV 9U4J ARG A 295 UNP P46093 LINKER SEQADV 9U4J GLN A 296 UNP P46093 LINKER SEQADV 9U4J LEU A 297 UNP P46093 LINKER SEQRES 1 A 288 ASP HIS LEU PHE PRO PRO SER LEU TYR ILE PHE VAL ILE SEQRES 2 A 288 GLY VAL GLY LEU PRO THR ASN CYS LEU ALA LEU TRP ALA SEQRES 3 A 288 ALA TYR ARG GLN VAL GLN GLN ARG ASN GLU LEU GLY VAL SEQRES 4 A 288 TYR LEU MET ASN LEU SER ILE ALA ASP LEU LEU TYR ILE SEQRES 5 A 288 CYS THR LEU PRO LEU TRP VAL ASP TYR PHE LEU HIS HIS SEQRES 6 A 288 ASP ASN TRP ILE HIS GLY PRO GLY SER CYS LYS LEU PHE SEQRES 7 A 288 GLY PHE ILE PHE TYR THR ASN ILE TYR ILE SER ILE ALA SEQRES 8 A 288 PHE LEU CYS CYS ILE SER VAL ASP ARG TYR LEU ALA VAL SEQRES 9 A 288 ALA HIS PRO LEU ARG PHE ALA ARG LEU ARG ARG VAL LYS SEQRES 10 A 288 THR ALA VAL ALA VAL SER SER VAL VAL TRP ALA THR GLU SEQRES 11 A 288 LEU GLY ALA ASN SER ALA PRO LEU PHE HIS ASP GLU LEU SEQRES 12 A 288 PHE ARG ASP ARG TYR ASN HIS THR PHE CYS PHE GLU LYS SEQRES 13 A 288 PHE PRO MET GLU GLY TRP VAL ALA TRP MET ASN LEU TYR SEQRES 14 A 288 ARG VAL PHE VAL GLY PHE LEU PHE PRO TRP ALA LEU MET SEQRES 15 A 288 LEU LEU SER TYR ARG GLY ILE LEU ARG ALA VAL ARG GLY SEQRES 16 A 288 SER VAL SER THR GLU ARG GLN GLU LYS ALA LYS ILE LYS SEQRES 17 A 288 ARG LEU ALA LEU SER LEU ILE ALA ILE VAL LEU VAL CYS SEQRES 18 A 288 PHE ALA PRO TYR HIS VAL LEU LEU LEU SER ARG SER ALA SEQRES 19 A 288 ILE TYR LEU GLY ARG PRO TRP ASP CYS GLY PHE GLU GLU SEQRES 20 A 288 ARG VAL PHE SER ALA TYR HIS SER SER LEU ALA PHE THR SEQRES 21 A 288 SER LEU ASN CYS VAL ALA ASP PRO ILE LEU TYR CYS LEU SEQRES 22 A 288 VAL ASN GLU GLY ALA ARG ARG GLN LEU ALA ASP LEU GLU SEQRES 23 A 288 ASP ASN HELIX 1 AA1 LEU A 18 VAL A 46 1 29 HELIX 2 AA2 GLN A 47 ARG A 49 5 3 HELIX 3 AA3 LEU A 52 THR A 69 1 18 HELIX 4 AA4 PRO A 71 TYR A 76 1 6 HELIX 5 AA5 GLY A 86 ALA A 120 1 35 HELIX 6 AA6 ARG A 129 THR A 133 5 5 HELIX 7 AA7 VAL A 135 ALA A 151 1 17 HELIX 8 AA8 PRO A 152 LEU A 158 5 7 HELIX 9 AA9 GLU A 175 PHE A 190 1 16 HELIX 10 AB1 PHE A 190 VAL A 212 1 23 HELIX 11 AB2 ARG A 216 ARG A 254 1 39 HELIX 12 AB3 PHE A 260 PHE A 265 1 6 HELIX 13 AB4 TYR A 268 ALA A 273 1 6 HELIX 14 AB5 PHE A 274 SER A 276 5 3 HELIX 15 AB6 LEU A 277 LEU A 285 1 9 HELIX 16 AB7 LEU A 285 ASN A 290 1 6 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 MASTER 221 0 0 16 0 0 0 6 1937 1 0 23 END