HEADER TRANSPORT PROTEIN 17-JUN-21 7N98 TITLE CRYO-EM STRUCTURE OF MFSD2A COMPND MOL_ID: 1; COMPND 2 MOLECULE: SODIUM-DEPENDENT LYSOPHOSPHATIDYLCHOLINE SYMPORTER 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NLS1,SODIUM-DEPENDENT LPC SYMPORTER 1,MAJOR FACILITATOR COMPND 5 SUPERFAMILY DOMAIN-CONTAINING PROTEIN 2A; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MFSD2A, MFSD2, NLS1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS MEMBRANE PROTEIN, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.ZHANG,L.FENG REVDAT 3 01-SEP-21 7N98 1 JRNL REVDAT 2 25-AUG-21 7N98 1 JRNL REVDAT 1 04-AUG-21 7N98 0 JRNL AUTH C.A.P.WOOD,J.ZHANG,D.AYDIN,Y.XU,B.J.ANDREONE,U.H.LANGEN, JRNL AUTH 2 R.O.DROR,C.GU,L.FENG JRNL TITL STRUCTURE AND MECHANISM OF BLOOD-BRAIN-BARRIER LIPID JRNL TITL 2 TRANSPORTER MFSD2A. JRNL REF NATURE V. 596 444 2021 JRNL REFN ESSN 1476-4687 JRNL PMID 34349262 JRNL DOI 10.1038/S41586-021-03782-Y REMARK 2 REMARK 2 RESOLUTION. 3.50 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 90577 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 7N98 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000257612. 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 : MEMBRANE PROTEIN COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 5.00 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 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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: 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 ALA A 2 REMARK 465 LYS A 3 REMARK 465 GLY A 4 REMARK 465 GLU A 5 REMARK 465 GLY A 6 REMARK 465 ALA A 7 REMARK 465 GLU A 8 REMARK 465 SER A 9 REMARK 465 GLY A 10 REMARK 465 SER A 11 REMARK 465 ALA A 12 REMARK 465 ALA A 13 REMARK 465 GLY A 14 REMARK 465 LEU A 15 REMARK 465 LEU A 16 REMARK 465 PRO A 17 REMARK 465 THR A 18 REMARK 465 SER A 19 REMARK 465 ILE A 20 REMARK 465 LEU A 21 REMARK 465 GLN A 22 REMARK 465 ALA A 23 REMARK 465 SER A 24 REMARK 465 GLU A 25 REMARK 465 ARG A 26 REMARK 465 PRO A 27 REMARK 465 VAL A 28 REMARK 465 GLN A 29 REMARK 465 VAL A 30 REMARK 465 LYS A 31 REMARK 465 LYS A 32 REMARK 465 GLU A 33 REMARK 465 PRO A 34 REMARK 465 LYS A 35 REMARK 465 LYS A 36 REMARK 465 LYS A 37 REMARK 465 GLN A 38 REMARK 465 ALA A 512 REMARK 465 LEU A 513 REMARK 465 ARG A 514 REMARK 465 GLU A 515 REMARK 465 GLU A 516 REMARK 465 ALA A 517 REMARK 465 SER A 518 REMARK 465 SER A 519 REMARK 465 SER A 520 REMARK 465 GLY A 521 REMARK 465 CYS A 522 REMARK 465 SER A 523 REMARK 465 ASP A 524 REMARK 465 THR A 525 REMARK 465 ASP A 526 REMARK 465 SER A 527 REMARK 465 THR A 528 REMARK 465 GLU A 529 REMARK 465 LEU A 530 REMARK 465 ALA A 531 REMARK 465 SER A 532 REMARK 465 ILE A 533 REMARK 465 LEU A 534 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 GLN A 211 CG CD OE1 NE2 REMARK 470 LEU A 217 CG CD1 CD2 REMARK 470 GLN A 218 CG CD OE1 NE2 REMARK 470 ASP A 219 CG OD1 OD2 REMARK 470 SER A 223 OG REMARK 470 VAL A 224 CG1 CG2 REMARK 470 VAL A 225 CG1 CG2 REMARK 470 VAL A 226 CG1 CG2 REMARK 470 SER A 227 OG REMARK 470 GLU A 228 CG CD OE1 OE2 REMARK 470 VAL A 229 CG1 CG2 REMARK 470 ASN A 231 CG OD1 ND2 REMARK 470 ARG A 232 CG CD NE CZ NH1 NH2 REMARK 470 THR A 233 OG1 CG2 REMARK 470 GLN A 234 CG CD OE1 NE2 REMARK 470 SER A 235 OG REMARK 470 ARG A 269 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 270 CG CD OE1 OE2 REMARK 470 GLN A 271 CG CD OE1 NE2 REMARK 470 ARG A 272 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 273 CG CD OE1 OE2 REMARK 470 LEU A 274 CG CD1 CD2 REMARK 470 TYR A 275 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 276 CG CD OE1 OE2 REMARK 470 SER A 277 OG REMARK 470 GLN A 278 CG CD OE1 NE2 REMARK 470 GLN A 279 CG CD OE1 NE2 REMARK 470 GLU A 281 CG CD OE1 OE2 REMARK 470 SER A 282 OG REMARK 470 MET A 283 CG SD CE 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 LEU A 66 47.41 -82.50 REMARK 500 VAL A 73 -61.52 -109.70 REMARK 500 LYS A 75 97.12 -69.55 REMARK 500 PRO A 139 43.51 -86.75 REMARK 500 SER A 177 -8.82 70.27 REMARK 500 SER A 223 147.65 -173.98 REMARK 500 MET A 283 73.54 63.56 REMARK 500 PRO A 284 -174.78 -66.58 REMARK 500 CYS A 323 49.20 -84.85 REMARK 500 THR A 324 -30.14 -134.81 REMARK 500 ASP A 328 -157.48 -77.88 REMARK 500 PHE A 329 27.66 84.64 REMARK 500 LYS A 360 74.14 59.52 REMARK 500 LYS A 361 -3.41 84.48 REMARK 500 ARG A 383 69.14 60.17 REMARK 500 LEU A 385 -7.23 67.75 REMARK 500 PRO A 422 -169.47 -71.42 REMARK 500 SER A 424 76.62 52.28 REMARK 500 PRO A 425 -36.48 -36.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-24252 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF A MEMBRANE PROTEIN DBREF 7N98 A 1 534 UNP Q9DA75 NLS1_MOUSE 1 534 SEQADV 7N98 HIS A 67 UNP Q9DA75 GLN 67 ENGINEERED MUTATION SEQRES 1 A 534 MET ALA LYS GLY GLU GLY ALA GLU SER GLY SER ALA ALA SEQRES 2 A 534 GLY LEU LEU PRO THR SER ILE LEU GLN ALA SER GLU ARG SEQRES 3 A 534 PRO VAL GLN VAL LYS LYS GLU PRO LYS LYS LYS GLN GLN SEQRES 4 A 534 LEU SER ILE CYS ASN LYS LEU CYS TYR ALA VAL GLY GLY SEQRES 5 A 534 ALA PRO TYR GLN LEU THR GLY CYS ALA LEU GLY PHE PHE SEQRES 6 A 534 LEU HIS ILE TYR LEU LEU ASP VAL ALA LYS VAL GLU PRO SEQRES 7 A 534 LEU PRO ALA SER ILE ILE LEU PHE VAL GLY ARG ALA TRP SEQRES 8 A 534 ASP ALA PHE THR ASP PRO LEU VAL GLY PHE CYS ILE SER SEQRES 9 A 534 LYS SER SER TRP THR ARG LEU GLY ARG LEU MET PRO TRP SEQRES 10 A 534 ILE ILE PHE SER THR PRO LEU ALA ILE ILE ALA TYR PHE SEQRES 11 A 534 LEU ILE TRP PHE VAL PRO ASP PHE PRO SER GLY THR GLU SEQRES 12 A 534 SER SER HIS GLY PHE LEU TRP TYR LEU LEU PHE TYR CYS SEQRES 13 A 534 LEU PHE GLU THR LEU VAL THR CYS PHE HIS VAL PRO TYR SEQRES 14 A 534 SER ALA LEU THR MET PHE ILE SER THR GLU GLN SER GLU SEQRES 15 A 534 ARG ASP SER ALA THR ALA TYR ARG MET THR VAL GLU VAL SEQRES 16 A 534 LEU GLY THR VAL ILE GLY THR ALA ILE GLN GLY GLN ILE SEQRES 17 A 534 VAL GLY GLN ALA LYS ALA PRO CYS LEU GLN ASP GLN ASN SEQRES 18 A 534 GLY SER VAL VAL VAL SER GLU VAL ALA ASN ARG THR GLN SEQRES 19 A 534 SER THR ALA SER LEU LYS ASP THR GLN ASN ALA TYR LEU SEQRES 20 A 534 LEU ALA ALA GLY ILE ILE ALA SER ILE TYR VAL LEU CYS SEQRES 21 A 534 ALA PHE ILE LEU ILE LEU GLY VAL ARG GLU GLN ARG GLU SEQRES 22 A 534 LEU TYR GLU SER GLN GLN ALA GLU SER MET PRO PHE PHE SEQRES 23 A 534 GLN GLY LEU ARG LEU VAL MET GLY HIS GLY PRO TYR VAL SEQRES 24 A 534 LYS LEU ILE ALA GLY PHE LEU PHE THR SER LEU ALA PHE SEQRES 25 A 534 MET LEU VAL GLU GLY ASN PHE ALA LEU PHE CYS THR TYR SEQRES 26 A 534 THR LEU ASP PHE ARG ASN GLU PHE GLN ASN LEU LEU LEU SEQRES 27 A 534 ALA ILE MET LEU SER ALA THR PHE THR ILE PRO ILE TRP SEQRES 28 A 534 GLN TRP PHE LEU THR ARG PHE GLY LYS LYS THR ALA VAL SEQRES 29 A 534 TYR ILE GLY ILE SER SER ALA VAL PRO PHE LEU ILE LEU SEQRES 30 A 534 VAL ALA LEU MET GLU ARG ASN LEU ILE VAL THR TYR VAL SEQRES 31 A 534 VAL ALA VAL ALA ALA GLY VAL SER VAL ALA ALA ALA PHE SEQRES 32 A 534 LEU LEU PRO TRP SER MET LEU PRO ASP VAL ILE ASP ASP SEQRES 33 A 534 PHE HIS LEU LYS HIS PRO HIS SER PRO GLY THR GLU PRO SEQRES 34 A 534 ILE PHE PHE SER PHE TYR VAL PHE PHE THR LYS PHE ALA SEQRES 35 A 534 SER GLY VAL SER LEU GLY VAL SER THR LEU SER LEU ASP SEQRES 36 A 534 PHE ALA ASN TYR GLN ARG GLN GLY CYS SER GLN PRO GLU SEQRES 37 A 534 GLN VAL LYS PHE THR LEU LYS MET LEU VAL THR MET ALA SEQRES 38 A 534 PRO ILE ILE LEU ILE LEU LEU GLY LEU LEU LEU PHE LYS SEQRES 39 A 534 LEU TYR PRO ILE ASP GLU GLU LYS ARG ARG GLN ASN LYS SEQRES 40 A 534 LYS ALA LEU GLN ALA LEU ARG GLU GLU ALA SER SER SER SEQRES 41 A 534 GLY CYS SER ASP THR ASP SER THR GLU LEU ALA SER ILE SEQRES 42 A 534 LEU HELIX 1 AA1 SER A 41 GLY A 51 1 11 HELIX 2 AA2 GLY A 52 PHE A 64 1 13 HELIX 3 AA3 ILE A 68 VAL A 73 1 6 HELIX 4 AA4 GLU A 77 LYS A 105 1 29 HELIX 5 AA5 MET A 115 PHE A 120 1 6 HELIX 6 AA6 SER A 121 TRP A 133 1 13 HELIX 7 AA7 GLU A 143 PHE A 148 1 6 HELIX 8 AA8 PHE A 148 LEU A 172 1 25 HELIX 9 AA9 THR A 173 PHE A 175 5 3 HELIX 10 AB1 GLU A 179 VAL A 209 1 31 HELIX 11 AB2 SER A 235 LEU A 266 1 32 HELIX 12 AB3 GLY A 288 MET A 293 1 6 HELIX 13 AB4 GLY A 296 CYS A 323 1 28 HELIX 14 AB5 GLU A 332 ALA A 344 1 13 HELIX 15 AB6 THR A 347 ARG A 357 1 11 HELIX 16 AB7 ALA A 363 ALA A 379 1 17 HELIX 17 AB8 ILE A 386 MET A 409 1 24 HELIX 18 AB9 MET A 409 LYS A 420 1 12 HELIX 19 AC1 THR A 427 PHE A 456 1 30 HELIX 20 AC2 GLN A 469 PHE A 493 1 25 HELIX 21 AC3 ILE A 498 ALA A 509 1 12 SHEET 1 AA1 2 CYS A 216 GLN A 218 0 SHEET 2 AA1 2 VAL A 224 VAL A 226 -1 O VAL A 225 N LEU A 217 SSBOND 1 CYS A 216 CYS A 464 1555 1555 2.03 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