HEADER MEMBRANE PROTEIN 10-OCT-23 8QSM TITLE CRYO-EM STRUCTURE OF HUMAN SLC15A4 MONOMER IN OUTWARD OPEN STATE IN TITLE 2 LMNG COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 15 MEMBER 4; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SLC15A4; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS SOLUTE CARRIER, TRANSPORTER, SLC, MFS, MAJOR FACILITATOR SUPERFAMILY, KEYWDS 2 LYSOSOME, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.REHAN,R.MATSUOKA,A.JAZAYERI,K.L.DUERR REVDAT 1 25-OCT-23 8QSM 0 JRNL AUTH S.REHAN,R.MATSUOKA,A.JAZAYERI,K.L.DUERR JRNL TITL CRYO-EM STRUCTURE OF HUMAN SLC15A4 MONOMER IN OUTWARD OPEN JRNL TITL 2 STATE IN LMNG JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, 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) : 3.690 REMARK 3 NUMBER OF PARTICLES : 215786 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 8QSM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1292133886. 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 : SLC15A4 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 : 6.50 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) : 2000.00 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) : 4000.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 GLY A 5 REMARK 465 GLY A 6 REMARK 465 GLY A 7 REMARK 465 ALA A 8 REMARK 465 GLY A 9 REMARK 465 GLU A 10 REMARK 465 ARG A 11 REMARK 465 ALA A 12 REMARK 465 PRO A 13 REMARK 465 ALA A 14 REMARK 465 ALA A 15 REMARK 465 GLY A 16 REMARK 465 ALA A 17 REMARK 465 ARG A 18 REMARK 465 ARG A 19 REMARK 465 ALA A 20 REMARK 465 ALA A 21 REMARK 465 ALA A 22 REMARK 465 ALA A 23 REMARK 465 ALA A 24 REMARK 465 ALA A 25 REMARK 465 ALA A 26 REMARK 465 ALA A 27 REMARK 465 LEU A 123 REMARK 465 ALA A 124 REMARK 465 ALA A 125 REMARK 465 PRO A 126 REMARK 465 ALA A 127 REMARK 465 THR A 128 REMARK 465 ARG A 129 REMARK 465 ALA A 130 REMARK 465 ALA A 131 REMARK 465 LEU A 132 REMARK 465 CYS A 133 REMARK 465 GLY A 134 REMARK 465 SER A 135 REMARK 465 ALA A 136 REMARK 465 ARG A 137 REMARK 465 LEU A 138 REMARK 465 LEU A 139 REMARK 465 ASN A 140 REMARK 465 CYS A 141 REMARK 465 THR A 142 REMARK 465 ALA A 143 REMARK 465 PRO A 144 REMARK 465 GLY A 145 REMARK 465 PRO A 146 REMARK 465 ASP A 147 REMARK 465 ALA A 148 REMARK 465 ALA A 149 REMARK 465 ALA A 150 REMARK 465 ARG A 151 REMARK 465 CYS A 152 REMARK 465 CYS A 153 REMARK 465 SER A 154 REMARK 465 SER A 274 REMARK 465 GLY A 275 REMARK 465 GLU A 276 REMARK 465 ARG A 277 REMARK 465 GLN A 278 REMARK 465 SER A 279 REMARK 465 ASN A 280 REMARK 465 GLY A 281 REMARK 465 GLU A 282 REMARK 465 GLY A 283 REMARK 465 ILE A 284 REMARK 465 GLY A 285 REMARK 465 VAL A 286 REMARK 465 PHE A 287 REMARK 465 GLN A 288 REMARK 465 GLN A 289 REMARK 465 SER A 290 REMARK 465 SER A 291 REMARK 465 LYS A 292 REMARK 465 GLN A 293 REMARK 465 SER A 294 REMARK 465 LEU A 295 REMARK 465 ARG A 350 REMARK 465 ILE A 351 REMARK 465 PRO A 352 REMARK 465 GLU A 353 REMARK 465 ILE A 354 REMARK 465 SER A 355 REMARK 465 ASN A 356 REMARK 465 ILE A 357 REMARK 465 THR A 358 REMARK 465 THR A 359 REMARK 465 THR A 360 REMARK 465 PRO A 361 REMARK 465 HIS A 362 REMARK 465 THR A 363 REMARK 465 LEU A 364 REMARK 465 ARG A 561 REMARK 465 ASP A 562 REMARK 465 HIS A 563 REMARK 465 GLN A 564 REMARK 465 ARG A 565 REMARK 465 SER A 566 REMARK 465 ARG A 567 REMARK 465 ALA A 568 REMARK 465 ASN A 569 REMARK 465 GLY A 570 REMARK 465 VAL A 571 REMARK 465 PRO A 572 REMARK 465 THR A 573 REMARK 465 SER A 574 REMARK 465 ARG A 575 REMARK 465 ARG A 576 REMARK 465 ALA A 577 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 ILE A 248 40.89 33.30 REMARK 500 LYS A 250 71.96 51.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-18636 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN SLC15A4 MONOMER IN OUTWARD OPEN STATE IN REMARK 900 LMNG DBREF 8QSM A 1 577 UNP Q8N697 S15A4_HUMAN 1 577 SEQADV 8QSM ALA A 14 UNP Q8N697 LEU 14 ENGINEERED MUTATION SEQADV 8QSM ALA A 15 UNP Q8N697 LEU 15 ENGINEERED MUTATION SEQRES 1 A 577 MET GLU GLY SER GLY GLY GLY ALA GLY GLU ARG ALA PRO SEQRES 2 A 577 ALA ALA GLY ALA ARG ARG ALA ALA ALA ALA ALA ALA ALA SEQRES 3 A 577 ALA GLY ALA PHE ALA GLY ARG ARG ALA ALA CYS GLY ALA SEQRES 4 A 577 VAL LEU LEU THR GLU LEU LEU GLU ARG ALA ALA PHE TYR SEQRES 5 A 577 GLY ILE THR SER ASN LEU VAL LEU PHE LEU ASN GLY ALA SEQRES 6 A 577 PRO PHE CYS TRP GLU GLY ALA GLN ALA SER GLU ALA LEU SEQRES 7 A 577 LEU LEU PHE MET GLY LEU THR TYR LEU GLY SER PRO PHE SEQRES 8 A 577 GLY GLY TRP LEU ALA ASP ALA ARG LEU GLY ARG ALA ARG SEQRES 9 A 577 ALA ILE LEU LEU SER LEU ALA LEU TYR LEU LEU GLY MET SEQRES 10 A 577 LEU ALA PHE PRO LEU LEU ALA ALA PRO ALA THR ARG ALA SEQRES 11 A 577 ALA LEU CYS GLY SER ALA ARG LEU LEU ASN CYS THR ALA SEQRES 12 A 577 PRO GLY PRO ASP ALA ALA ALA ARG CYS CYS SER PRO ALA SEQRES 13 A 577 THR PHE ALA GLY LEU VAL LEU VAL GLY LEU GLY VAL ALA SEQRES 14 A 577 THR VAL LYS ALA ASN ILE THR PRO PHE GLY ALA ASP GLN SEQRES 15 A 577 VAL LYS ASP ARG GLY PRO GLU ALA THR ARG ARG PHE PHE SEQRES 16 A 577 ASN TRP PHE TYR TRP SER ILE ASN LEU GLY ALA ILE LEU SEQRES 17 A 577 SER LEU GLY GLY ILE ALA TYR ILE GLN GLN ASN VAL SER SEQRES 18 A 577 PHE VAL THR GLY TYR ALA ILE PRO THR VAL CYS VAL GLY SEQRES 19 A 577 LEU ALA PHE VAL VAL PHE LEU CYS GLY GLN SER VAL PHE SEQRES 20 A 577 ILE THR LYS PRO PRO ASP GLY SER ALA PHE THR ASP MET SEQRES 21 A 577 PHE LYS ILE LEU THR TYR SER CYS CYS SER GLN LYS ARG SEQRES 22 A 577 SER GLY GLU ARG GLN SER ASN GLY GLU GLY ILE GLY VAL SEQRES 23 A 577 PHE GLN GLN SER SER LYS GLN SER LEU PHE ASP SER CYS SEQRES 24 A 577 LYS MET SER HIS GLY GLY PRO PHE THR GLU GLU LYS VAL SEQRES 25 A 577 GLU ASP VAL LYS ALA LEU VAL LYS ILE VAL PRO VAL PHE SEQRES 26 A 577 LEU ALA LEU ILE PRO TYR TRP THR VAL TYR PHE GLN MET SEQRES 27 A 577 GLN THR THR TYR VAL LEU GLN SER LEU HIS LEU ARG ILE SEQRES 28 A 577 PRO GLU ILE SER ASN ILE THR THR THR PRO HIS THR LEU SEQRES 29 A 577 PRO ALA ALA TRP LEU THR MET PHE ASP ALA VAL LEU ILE SEQRES 30 A 577 LEU LEU LEU ILE PRO LEU LYS ASP LYS LEU VAL ASP PRO SEQRES 31 A 577 ILE LEU ARG ARG HIS GLY LEU LEU PRO SER SER LEU LYS SEQRES 32 A 577 ARG ILE ALA VAL GLY MET PHE PHE VAL MET CYS SER ALA SEQRES 33 A 577 PHE ALA ALA GLY ILE LEU GLU SER LYS ARG LEU ASN LEU SEQRES 34 A 577 VAL LYS GLU LYS THR ILE ASN GLN THR ILE GLY ASN VAL SEQRES 35 A 577 VAL TYR HIS ALA ALA ASP LEU SER LEU TRP TRP GLN VAL SEQRES 36 A 577 PRO GLN TYR LEU LEU ILE GLY ILE SER GLU ILE PHE ALA SEQRES 37 A 577 SER ILE ALA GLY LEU GLU PHE ALA TYR SER ALA ALA PRO SEQRES 38 A 577 LYS SER MET GLN SER ALA ILE MET GLY LEU PHE PHE PHE SEQRES 39 A 577 PHE SER GLY VAL GLY SER PHE VAL GLY SER GLY LEU LEU SEQRES 40 A 577 ALA LEU VAL SER ILE LYS ALA ILE GLY TRP MET SER SER SEQRES 41 A 577 HIS THR ASP PHE GLY ASN ILE ASN GLY CYS TYR LEU ASN SEQRES 42 A 577 TYR TYR PHE PHE LEU LEU ALA ALA ILE GLN GLY ALA THR SEQRES 43 A 577 LEU LEU LEU PHE LEU ILE ILE SER VAL LYS TYR ASP HIS SEQRES 44 A 577 HIS ARG ASP HIS GLN ARG SER ARG ALA ASN GLY VAL PRO SEQRES 45 A 577 THR SER ARG ARG ALA HELIX 1 AA1 ARG A 33 ASN A 57 1 25 HELIX 2 AA2 ASN A 57 ALA A 65 1 9 HELIX 3 AA3 GLU A 70 ALA A 98 1 29 HELIX 4 AA4 ARG A 102 LEU A 118 1 17 HELIX 5 AA5 ALA A 156 VAL A 183 1 28 HELIX 6 AA6 GLY A 187 GLN A 218 1 32 HELIX 7 AA7 SER A 221 VAL A 246 1 26 HELIX 8 AA8 ALA A 256 ARG A 273 1 18 HELIX 9 AA9 ASP A 297 GLY A 305 1 9 HELIX 10 AB1 THR A 308 LEU A 347 1 40 HELIX 11 AB2 HIS A 348 LEU A 349 5 2 HELIX 12 AB3 PRO A 365 ALA A 366 5 2 HELIX 13 AB4 ALA A 367 GLY A 396 1 30 HELIX 14 AB5 SER A 400 LYS A 431 1 32 HELIX 15 AB6 SER A 450 TRP A 453 5 4 HELIX 16 AB7 GLN A 454 ALA A 468 1 15 HELIX 17 AB8 ALA A 468 ALA A 479 1 12 HELIX 18 AB9 MET A 484 VAL A 510 1 27 HELIX 19 AC1 TYR A 531 HIS A 560 1 30 SHEET 1 AA1 2 ILE A 435 ILE A 439 0 SHEET 2 AA1 2 VAL A 442 ALA A 446 -1 O ALA A 446 N ILE A 435 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