HEADER MEMBRANE PROTEIN 26-OCT-25 9YWU TITLE HISTAMINE-BOUND STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MFS-TYPE TRANSPORTER SLC18B1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SOLUTE CARRIER FAMILY 18 MEMBER B1,VESICULAR POLYAMINE COMPND 5 TRANSPORTER,VPAT; COMPND 6 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: SLC18B1, C6ORF192; SOURCE 6 EXPRESSION_SYSTEM: INSECTA ENVIRONMENTAL SAMPLE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 2588572 KEYWDS MEMBRANE TRANSPORTER, NEUROTRANSMITTER TRANSPORTER, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR M.LU,B.LIU REVDAT 1 07-OCT-26 9YWU 0 JRNL AUTH Y.GUO,G.YANG,J.CHAI,J.SHANKLIN,B.LIU,M.LU JRNL TITL COOPERATIVE MECHANISM OF NEUROTRANSMITTER RECOGNITION AND JRNL TITL 2 TRANSPORT BY THE HUMAN VESICULAR POLYAMINE TRANSPORTER. JRNL REF NAT COMMUN V. 17 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 42463709 JRNL DOI 10.1038/S41467-026-75564-X REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, COOT, CRYOSPARC, PHENIX 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 : AB INITIO MODEL 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 : 127728 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 9YWU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1000301510. 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 TRANSPORT PROTEIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOCONTINUUM (6K X REMARK 245 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 : 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 GLU A 2 REMARK 465 ALA A 3 REMARK 465 LEU A 4 REMARK 465 GLY A 5 REMARK 465 ASP A 6 REMARK 465 LEU A 7 REMARK 465 GLU A 8 REMARK 465 GLY A 9 REMARK 465 PRO A 10 REMARK 465 ARG A 11 REMARK 465 ALA A 12 REMARK 465 PRO A 13 REMARK 465 GLY A 14 REMARK 465 GLY A 15 REMARK 465 ASP A 16 REMARK 465 ASP A 17 REMARK 465 PRO A 18 REMARK 465 ALA A 19 REMARK 465 GLY A 20 REMARK 465 SER A 21 REMARK 465 ALA A 22 REMARK 465 GLY A 23 REMARK 465 GLU A 24 REMARK 465 PRO A 56 REMARK 465 PHE A 57 REMARK 465 PHE A 58 REMARK 465 PRO A 59 REMARK 465 LYS A 60 REMARK 465 GLU A 61 REMARK 465 ALA A 62 REMARK 465 GLU A 63 REMARK 465 LYS A 64 REMARK 465 LYS A 65 REMARK 465 GLY A 66 REMARK 465 ALA A 67 REMARK 465 SER A 68 REMARK 465 ASN A 69 REMARK 465 THR A 70 REMARK 465 ILE A 71 REMARK 465 ARG A 432 REMARK 465 ARG A 433 REMARK 465 LYS A 434 REMARK 465 ARG A 435 REMARK 465 SER A 436 REMARK 465 LYS A 437 REMARK 465 SER A 438 REMARK 465 GLN A 439 REMARK 465 ASN A 440 REMARK 465 ILE A 441 REMARK 465 LEU A 442 REMARK 465 SER A 443 REMARK 465 THR A 444 REMARK 465 GLU A 445 REMARK 465 GLU A 446 REMARK 465 GLU A 447 REMARK 465 ARG A 448 REMARK 465 THR A 449 REMARK 465 THR A 450 REMARK 465 LEU A 451 REMARK 465 LEU A 452 REMARK 465 PRO A 453 REMARK 465 ASN A 454 REMARK 465 GLU A 455 REMARK 465 THR A 456 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 139 C ASP A 140 N 0.164 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 50 C - N - CA ANGL. DEV. = -15.5 DEGREES REMARK 500 TYR A 51 CA - C - N ANGL. DEV. = -18.4 DEGREES REMARK 500 TYR A 51 O - C - N ANGL. DEV. = 18.6 DEGREES REMARK 500 SER A 52 C - N - CA ANGL. DEV. = -19.3 DEGREES 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 SER A 52 -6.73 -55.47 REMARK 500 VAL A 163 -61.24 -95.02 REMARK 500 PRO A 256 37.80 -92.45 REMARK 500 THR A 257 -30.90 -131.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 CYS A 50 -11.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-73561 RELATED DB: EMDB REMARK 900 HISTAMINE-BOUND STRUCTURE DBREF 9YWU A 1 456 UNP Q6NT16 S18B1_HUMAN 1 456 SEQRES 1 A 456 MET GLU ALA LEU GLY ASP LEU GLU GLY PRO ARG ALA PRO SEQRES 2 A 456 GLY GLY ASP ASP PRO ALA GLY SER ALA GLY GLU THR PRO SEQRES 3 A 456 GLY TRP LEU SER ARG GLU GLN VAL PHE VAL LEU ILE SER SEQRES 4 A 456 ALA ALA SER VAL ASN LEU GLY SER MET MET CYS TYR SER SEQRES 5 A 456 ILE LEU GLY PRO PHE PHE PRO LYS GLU ALA GLU LYS LYS SEQRES 6 A 456 GLY ALA SER ASN THR ILE ILE GLY MET ILE PHE GLY CYS SEQRES 7 A 456 PHE ALA LEU PHE GLU LEU LEU ALA SER LEU VAL PHE GLY SEQRES 8 A 456 ASN TYR LEU VAL HIS ILE GLY ALA LYS PHE MET PHE VAL SEQRES 9 A 456 ALA GLY MET PHE VAL SER GLY GLY VAL THR ILE LEU PHE SEQRES 10 A 456 GLY VAL LEU ASP ARG VAL PRO ASP GLY PRO VAL PHE ILE SEQRES 11 A 456 ALA MET CYS PHE LEU VAL ARG VAL MET ASP ALA VAL SER SEQRES 12 A 456 PHE ALA ALA ALA MET THR ALA SER SER SER ILE LEU ALA SEQRES 13 A 456 LYS ALA PHE PRO ASN ASN VAL ALA THR VAL LEU GLY SER SEQRES 14 A 456 LEU GLU THR PHE SER GLY LEU GLY LEU ILE LEU GLY PRO SEQRES 15 A 456 PRO VAL GLY GLY PHE LEU TYR GLN SER PHE GLY TYR GLU SEQRES 16 A 456 VAL PRO PHE ILE VAL LEU GLY CYS VAL VAL LEU LEU MET SEQRES 17 A 456 VAL PRO LEU ASN MET TYR ILE LEU PRO ASN TYR GLU SER SEQRES 18 A 456 ASP PRO GLY GLU HIS SER PHE TRP LYS LEU ILE ALA LEU SEQRES 19 A 456 PRO LYS VAL GLY LEU ILE ALA PHE VAL ILE ASN SER LEU SEQRES 20 A 456 SER SER CYS PHE GLY PHE LEU ASP PRO THR LEU SER LEU SEQRES 21 A 456 PHE VAL LEU GLU LYS PHE ASN LEU PRO ALA GLY TYR VAL SEQRES 22 A 456 GLY LEU VAL PHE LEU GLY MET ALA LEU SER TYR ALA ILE SEQRES 23 A 456 SER SER PRO LEU PHE GLY LEU LEU SER ASP LYS ARG PRO SEQRES 24 A 456 PRO LEU ARG LYS TRP LEU LEU VAL PHE GLY ASN LEU ILE SEQRES 25 A 456 THR ALA GLY CYS TYR MET LEU LEU GLY PRO VAL PRO ILE SEQRES 26 A 456 LEU HIS ILE LYS SER GLN LEU TRP LEU LEU VAL LEU ILE SEQRES 27 A 456 LEU VAL VAL SER GLY LEU SER ALA GLY MET SER ILE ILE SEQRES 28 A 456 PRO THR PHE PRO GLU ILE LEU SER CYS ALA HIS GLU ASN SEQRES 29 A 456 GLY PHE GLU GLU GLY LEU SER THR LEU GLY LEU VAL SER SEQRES 30 A 456 GLY LEU PHE SER ALA MET TRP SER ILE GLY ALA PHE MET SEQRES 31 A 456 GLY PRO THR LEU GLY GLY PHE LEU TYR GLU LYS ILE GLY SEQRES 32 A 456 PHE GLU TRP ALA ALA ALA ILE GLN GLY LEU TRP ALA LEU SEQRES 33 A 456 ILE SER GLY LEU ALA MET GLY LEU PHE TYR LEU LEU GLU SEQRES 34 A 456 TYR SER ARG ARG LYS ARG SER LYS SER GLN ASN ILE LEU SEQRES 35 A 456 SER THR GLU GLU GLU ARG THR THR LEU LEU PRO ASN GLU SEQRES 36 A 456 THR HET HSM A 501 8 HET HSM A 502 8 HET HSM A 503 8 HETNAM HSM HISTAMINE FORMUL 2 HSM 3(C5 H9 N3) FORMUL 5 HOH *2(H2 O) HELIX 1 AA1 SER A 30 LEU A 54 1 25 HELIX 2 AA2 GLY A 73 TYR A 93 1 21 HELIX 3 AA3 ALA A 99 GLY A 118 1 20 HELIX 4 AA4 GLY A 126 PHE A 159 1 34 HELIX 5 AA5 VAL A 163 PHE A 192 1 30 HELIX 6 AA6 GLU A 195 LEU A 216 1 22 HELIX 7 AA7 PHE A 228 ALA A 233 1 6 HELIX 8 AA8 LEU A 234 PHE A 266 1 33 HELIX 9 AA9 PRO A 269 ARG A 298 1 30 HELIX 10 AB1 LEU A 301 LEU A 319 1 19 HELIX 11 AB2 GLN A 331 ILE A 350 1 20 HELIX 12 AB3 PRO A 352 ASN A 364 1 13 HELIX 13 AB4 GLY A 369 MET A 390 1 22 HELIX 14 AB5 GLY A 391 ILE A 402 1 12 HELIX 15 AB6 GLY A 403 LEU A 427 1 25 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 CONECT 2955 2956 CONECT 2956 2955 2957 CONECT 2957 2956 2958 CONECT 2958 2957 2959 2960 CONECT 2959 2958 2961 CONECT 2960 2958 2962 CONECT 2961 2959 2962 CONECT 2962 2960 2961 CONECT 2963 2964 CONECT 2964 2963 2965 CONECT 2965 2964 2966 CONECT 2966 2965 2967 2968 CONECT 2967 2966 2969 CONECT 2968 2966 2970 CONECT 2969 2967 2970 CONECT 2970 2968 2969 CONECT 2971 2972 CONECT 2972 2971 2973 CONECT 2973 2972 2974 CONECT 2974 2973 2975 2976 CONECT 2975 2974 2977 CONECT 2976 2974 2978 CONECT 2977 2975 2978 CONECT 2978 2976 2977 MASTER 246 0 3 15 0 0 0 6 2979 1 24 36 END