HEADER TRANSPORT PROTEIN 25-SEP-23 8UBZ TITLE CHOLINE-BOUND FLVCR1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEME TRANSPORTER FLVCR1; COMPND 3 CHAIN: A; 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: FLVCR1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS CHOLINE, ETHANOLAMINE, MEMBRANE TRANSPORT, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR R.K.HITE,Y.SON REVDAT 3 15-MAY-24 8UBZ 1 JRNL REVDAT 2 01-MAY-24 8UBZ 1 JRNL REVDAT 1 27-MAR-24 8UBZ 0 JRNL AUTH Y.SON,T.C.KENNY,A.KHAN,K.BIRSOY,R.K.HITE JRNL TITL STRUCTURAL BASIS OF LIPID HEAD GROUP ENTRY TO THE KENNEDY JRNL TITL 2 PATHWAY BY FLVCR1. JRNL REF NATURE 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 38693265 JRNL DOI 10.1038/S41586-024-07374-4 REMARK 2 REMARK 2 RESOLUTION. 3.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM, CRYOSPARC, CRYOSPARC, REMARK 3 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 : REAL REMARK 3 REFINEMENT PROTOCOL : BACKBONE TRACE REMARK 3 REFINEMENT TARGET : FSC 0.5 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) : 3.020 REMARK 3 NUMBER OF PARTICLES : 36781 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 8UBZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000277638. 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 FLVCR1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 6.00 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) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 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) : 6600.00 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 ARG A 3 REMARK 465 PRO A 4 REMARK 465 ASP A 5 REMARK 465 ASP A 6 REMARK 465 GLU A 7 REMARK 465 GLU A 8 REMARK 465 GLY A 9 REMARK 465 ALA A 10 REMARK 465 ALA A 11 REMARK 465 VAL A 12 REMARK 465 ALA A 13 REMARK 465 PRO A 14 REMARK 465 GLY A 15 REMARK 465 HIS A 16 REMARK 465 PRO A 17 REMARK 465 LEU A 18 REMARK 465 ALA A 19 REMARK 465 LYS A 20 REMARK 465 GLY A 21 REMARK 465 TYR A 22 REMARK 465 LEU A 23 REMARK 465 PRO A 24 REMARK 465 LEU A 25 REMARK 465 PRO A 26 REMARK 465 ARG A 27 REMARK 465 GLY A 28 REMARK 465 ALA A 29 REMARK 465 PRO A 30 REMARK 465 VAL A 31 REMARK 465 GLY A 32 REMARK 465 LYS A 33 REMARK 465 GLU A 34 REMARK 465 SER A 35 REMARK 465 VAL A 36 REMARK 465 GLU A 37 REMARK 465 LEU A 38 REMARK 465 GLN A 39 REMARK 465 ASN A 40 REMARK 465 GLY A 41 REMARK 465 PRO A 42 REMARK 465 LYS A 43 REMARK 465 ALA A 44 REMARK 465 GLY A 45 REMARK 465 THR A 46 REMARK 465 PHE A 47 REMARK 465 PRO A 48 REMARK 465 VAL A 49 REMARK 465 ASN A 50 REMARK 465 GLY A 51 REMARK 465 ALA A 52 REMARK 465 PRO A 53 REMARK 465 ARG A 54 REMARK 465 ASP A 55 REMARK 465 SER A 56 REMARK 465 LEU A 57 REMARK 465 ALA A 58 REMARK 465 ALA A 59 REMARK 465 ALA A 60 REMARK 465 SER A 61 REMARK 465 GLY A 62 REMARK 465 VAL A 63 REMARK 465 LEU A 64 REMARK 465 GLY A 65 REMARK 465 GLY A 66 REMARK 465 PRO A 67 REMARK 465 GLN A 68 REMARK 465 THR A 69 REMARK 465 PRO A 70 REMARK 465 LEU A 71 REMARK 465 ALA A 72 REMARK 465 PRO A 73 REMARK 465 GLU A 74 REMARK 465 GLU A 75 REMARK 465 GLU A 76 REMARK 465 THR A 77 REMARK 465 GLN A 78 REMARK 465 ALA A 79 REMARK 465 ARG A 80 REMARK 465 LEU A 81 REMARK 465 LEU A 82 REMARK 465 PRO A 83 REMARK 465 ALA A 84 REMARK 465 GLY A 85 REMARK 465 ALA A 86 REMARK 465 GLY A 87 REMARK 465 ALA A 88 REMARK 465 GLU A 89 REMARK 465 THR A 90 REMARK 465 PRO A 91 REMARK 465 GLY A 92 REMARK 465 ALA A 93 REMARK 465 GLU A 94 REMARK 465 SER A 95 REMARK 465 SER A 96 REMARK 465 PRO A 97 REMARK 465 LEU A 98 REMARK 465 ASP A 514 REMARK 465 LEU A 515 REMARK 465 ARG A 516 REMARK 465 ARG A 517 REMARK 465 HIS A 518 REMARK 465 ASN A 519 REMARK 465 ILE A 520 REMARK 465 ASN A 521 REMARK 465 ILE A 522 REMARK 465 GLY A 523 REMARK 465 ILE A 524 REMARK 465 THR A 525 REMARK 465 ASN A 526 REMARK 465 VAL A 527 REMARK 465 ASP A 528 REMARK 465 VAL A 529 REMARK 465 LYS A 530 REMARK 465 ALA A 531 REMARK 465 ILE A 532 REMARK 465 PRO A 533 REMARK 465 ALA A 534 REMARK 465 ASP A 535 REMARK 465 SER A 536 REMARK 465 PRO A 537 REMARK 465 THR A 538 REMARK 465 ASP A 539 REMARK 465 GLN A 540 REMARK 465 GLU A 541 REMARK 465 PRO A 542 REMARK 465 LYS A 543 REMARK 465 THR A 544 REMARK 465 VAL A 545 REMARK 465 MET A 546 REMARK 465 LEU A 547 REMARK 465 SER A 548 REMARK 465 LYS A 549 REMARK 465 GLN A 550 REMARK 465 SER A 551 REMARK 465 GLU A 552 REMARK 465 SER A 553 REMARK 465 ALA A 554 REMARK 465 ILE A 555 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ILE A 415 OG1 THR A 419 2.04 REMARK 500 REMARK 500 REMARK: NULL 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 THR A 454 30.99 -94.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-42110 RELATED DB: EMDB REMARK 900 CHOLINE-BOUND FLVCR1 DBREF 8UBZ A 1 555 UNP Q9Y5Y0 FLVC1_HUMAN 1 555 SEQRES 1 A 555 MET ALA ARG PRO ASP ASP GLU GLU GLY ALA ALA VAL ALA SEQRES 2 A 555 PRO GLY HIS PRO LEU ALA LYS GLY TYR LEU PRO LEU PRO SEQRES 3 A 555 ARG GLY ALA PRO VAL GLY LYS GLU SER VAL GLU LEU GLN SEQRES 4 A 555 ASN GLY PRO LYS ALA GLY THR PHE PRO VAL ASN GLY ALA SEQRES 5 A 555 PRO ARG ASP SER LEU ALA ALA ALA SER GLY VAL LEU GLY SEQRES 6 A 555 GLY PRO GLN THR PRO LEU ALA PRO GLU GLU GLU THR GLN SEQRES 7 A 555 ALA ARG LEU LEU PRO ALA GLY ALA GLY ALA GLU THR PRO SEQRES 8 A 555 GLY ALA GLU SER SER PRO LEU PRO LEU THR ALA LEU SER SEQRES 9 A 555 PRO ARG ARG PHE VAL VAL LEU LEU ILE PHE SER LEU TYR SEQRES 10 A 555 SER LEU VAL ASN ALA PHE GLN TRP ILE GLN TYR SER ILE SEQRES 11 A 555 ILE SER ASN VAL PHE GLU GLY PHE TYR GLY VAL THR LEU SEQRES 12 A 555 LEU HIS ILE ASP TRP LEU SER MET VAL TYR MET LEU ALA SEQRES 13 A 555 TYR VAL PRO LEU ILE PHE PRO ALA THR TRP LEU LEU ASP SEQRES 14 A 555 THR ARG GLY LEU ARG LEU THR ALA LEU LEU GLY SER GLY SEQRES 15 A 555 LEU ASN CYS LEU GLY ALA TRP ILE LYS CYS GLY SER VAL SEQRES 16 A 555 GLN GLN HIS LEU PHE TRP VAL THR MET LEU GLY GLN CYS SEQRES 17 A 555 LEU CYS SER VAL ALA GLN VAL PHE ILE LEU GLY LEU PRO SEQRES 18 A 555 SER ARG ILE ALA SER VAL TRP PHE GLY PRO LYS GLU VAL SEQRES 19 A 555 SER THR ALA CYS ALA THR ALA VAL LEU GLY ASN GLN LEU SEQRES 20 A 555 GLY THR ALA VAL GLY PHE LEU LEU PRO PRO VAL LEU VAL SEQRES 21 A 555 PRO ASN THR GLN ASN ASP THR ASN LEU LEU ALA CYS ASN SEQRES 22 A 555 ILE SER THR MET PHE TYR GLY THR SER ALA VAL ALA THR SEQRES 23 A 555 LEU LEU PHE ILE LEU THR ALA ILE ALA PHE LYS GLU LYS SEQRES 24 A 555 PRO ARG TYR PRO PRO SER GLN ALA GLN ALA ALA LEU GLN SEQRES 25 A 555 ASP SER PRO PRO GLU GLU TYR SER TYR LYS LYS SER ILE SEQRES 26 A 555 ARG ASN LEU PHE LYS ASN ILE PRO PHE VAL LEU LEU LEU SEQRES 27 A 555 ILE THR TYR GLY ILE MET THR GLY ALA PHE TYR SER VAL SEQRES 28 A 555 SER THR LEU LEU ASN GLN MET ILE LEU THR TYR TYR GLU SEQRES 29 A 555 GLY GLU GLU VAL ASN ALA GLY ARG ILE GLY LEU THR LEU SEQRES 30 A 555 VAL VAL ALA GLY MET VAL GLY SER ILE LEU CYS GLY LEU SEQRES 31 A 555 TRP LEU ASP TYR THR LYS THR TYR LYS GLN THR THR LEU SEQRES 32 A 555 ILE VAL TYR ILE LEU SER PHE ILE GLY MET VAL ILE PHE SEQRES 33 A 555 THR PHE THR LEU ASP LEU ARG TYR ILE ILE ILE VAL PHE SEQRES 34 A 555 VAL THR GLY GLY VAL LEU GLY PHE PHE MET THR GLY TYR SEQRES 35 A 555 LEU PRO LEU GLY PHE GLU PHE ALA VAL GLU ILE THR TYR SEQRES 36 A 555 PRO GLU SER GLU GLY THR SER SER GLY LEU LEU ASN ALA SEQRES 37 A 555 SER ALA GLN ILE PHE GLY ILE LEU PHE THR LEU ALA GLN SEQRES 38 A 555 GLY LYS LEU THR SER ASP TYR GLY PRO LYS ALA GLY ASN SEQRES 39 A 555 ILE PHE LEU CYS VAL TRP MET PHE ILE GLY ILE ILE LEU SEQRES 40 A 555 THR ALA LEU ILE LYS SER ASP LEU ARG ARG HIS ASN ILE SEQRES 41 A 555 ASN ILE GLY ILE THR ASN VAL ASP VAL LYS ALA ILE PRO SEQRES 42 A 555 ALA ASP SER PRO THR ASP GLN GLU PRO LYS THR VAL MET SEQRES 43 A 555 LEU SER LYS GLN SER GLU SER ALA ILE HET Y01 A 601 84 HET Y01 A 602 84 HET Y01 A 603 84 HET CHT A 604 21 HETNAM Y01 CHOLESTEROL HEMISUCCINATE HETNAM CHT CHOLINE ION FORMUL 2 Y01 3(C31 H50 O4) FORMUL 5 CHT C5 H14 N O 1+ FORMUL 6 HOH *26(H2 O) HELIX 1 AA1 PRO A 105 ILE A 131 1 27 HELIX 2 AA2 ILE A 131 GLY A 140 1 10 HELIX 3 AA3 THR A 142 ARG A 171 1 30 HELIX 4 AA4 GLY A 172 GLY A 193 1 22 HELIX 5 AA5 LEU A 199 GLY A 219 1 21 HELIX 6 AA6 GLY A 219 PHE A 229 1 11 HELIX 7 AA7 GLU A 233 VAL A 260 1 28 HELIX 8 AA8 ASP A 266 PHE A 296 1 31 HELIX 9 AA9 SER A 305 SER A 314 1 10 HELIX 10 AB1 SER A 320 ASN A 331 1 12 HELIX 11 AB2 ASN A 331 TYR A 363 1 33 HELIX 12 AB3 GLU A 366 LYS A 396 1 31 HELIX 13 AB4 LYS A 399 LEU A 420 1 22 HELIX 14 AB5 ASP A 421 ARG A 423 5 3 HELIX 15 AB6 TYR A 424 THR A 454 1 31 HELIX 16 AB7 SER A 458 GLY A 489 1 32 HELIX 17 AB8 GLY A 489 ILE A 511 1 23 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