HEADER TRANSPORT PROTEIN 10-NOV-22 8HFE TITLE CRYO-EM STRUCTURE OF HUMAN NOREPINEPHRINE TRANSPORTER NET IN AN TITLE 2 INWARD-OPEN STATE AT RESOLUTION OF 2.5 ANGSTROM COMPND MOL_ID: 1; COMPND 2 MOLECULE: SODIUM-DEPENDENT NORADRENALINE TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NOREPINEPHRINE TRANSPORTER,NET,SOLUTE CARRIER FAMILY 6 COMPND 5 MEMBER 2; 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: SLC6A2, NAT1, NET1, SLC6A5; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS NOREPINEPHRINE TRANSPORTER, NET, SLC6A2, NOREPINEPHRINE, DOPAMINE, KEYWDS 2 NEUROTRANSMITTER, DESIPRAMINE, BUPROPION, ANTIDEPRESSANT., TRANSPORT KEYWDS 3 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.TAN,Y.XIAO,F.KONG,J.LEI,Y.YUAN,C.YAN REVDAT 3 07-AUG-24 8HFE 1 JRNL REVDAT 2 31-JUL-24 8HFE 1 JRNL REVDAT 1 15-MAY-24 8HFE 0 JRNL AUTH J.TAN,Y.XIAO,F.KONG,X.ZHANG,H.XU,A.ZHU,Y.LIU,J.LEI,B.TIAN, JRNL AUTH 2 Y.YUAN,C.YAN JRNL TITL MOLECULAR BASIS OF HUMAN NORADRENALINE TRANSPORTER REUPTAKE JRNL TITL 2 AND INHIBITION. JRNL REF NATURE 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 39048818 JRNL DOI 10.1038/S41586-024-07719-Z REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, 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) : 2.500 REMARK 3 NUMBER OF PARTICLES : 360911 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 8HFE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 15-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1300033539. 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 : NET REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 10.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1400.00 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 LEU A 2 REMARK 465 LEU A 3 REMARK 465 ALA A 4 REMARK 465 ARG A 5 REMARK 465 MET A 6 REMARK 465 ASN A 7 REMARK 465 PRO A 8 REMARK 465 GLN A 9 REMARK 465 VAL A 10 REMARK 465 GLN A 11 REMARK 465 PRO A 12 REMARK 465 GLU A 13 REMARK 465 ASN A 14 REMARK 465 ASN A 15 REMARK 465 GLY A 16 REMARK 465 ALA A 17 REMARK 465 ASP A 18 REMARK 465 THR A 19 REMARK 465 GLY A 20 REMARK 465 PRO A 21 REMARK 465 GLU A 22 REMARK 465 GLN A 23 REMARK 465 PRO A 24 REMARK 465 LEU A 25 REMARK 465 ARG A 26 REMARK 465 ALA A 27 REMARK 465 ARG A 28 REMARK 465 LYS A 29 REMARK 465 THR A 30 REMARK 465 ALA A 31 REMARK 465 GLU A 32 REMARK 465 LEU A 33 REMARK 465 LEU A 34 REMARK 465 VAL A 35 REMARK 465 VAL A 36 REMARK 465 LYS A 37 REMARK 465 GLU A 38 REMARK 465 ARG A 39 REMARK 465 ASN A 40 REMARK 465 GLY A 41 REMARK 465 VAL A 42 REMARK 465 GLN A 43 REMARK 465 CYS A 44 REMARK 465 LEU A 45 REMARK 465 LEU A 46 REMARK 465 ALA A 47 REMARK 465 PRO A 48 REMARK 465 ARG A 49 REMARK 465 ASP A 50 REMARK 465 GLY A 51 REMARK 465 ASP A 52 REMARK 465 ALA A 53 REMARK 465 GLN A 54 REMARK 465 PRO A 55 REMARK 465 ARG A 56 REMARK 465 GLU A 57 REMARK 465 THR A 58 REMARK 465 TRP A 59 REMARK 465 GLY A 193 REMARK 465 SER A 194 REMARK 465 VAL A 195 REMARK 465 LEU A 196 REMARK 465 GLY A 197 REMARK 465 LYS A 257 REMARK 465 THR A 258 REMARK 465 SER A 259 REMARK 465 GLY A 260 REMARK 465 LYS A 261 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 OE1 GLU A 113 O HOH A 801 2.08 REMARK 500 O ALA A 384 O HOH A 802 2.09 REMARK 500 O HOH A 813 O HOH A 822 2.15 REMARK 500 O HOH A 814 O HOH A 817 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 480 CA SER A 480 CB -0.094 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 200 -125.65 -3.65 REMARK 500 TYR A 202 43.25 -140.05 REMARK 500 ALA A 305 -11.84 76.27 REMARK 500 ALA A 477 71.08 -151.87 REMARK 500 ASP A 546 -110.97 59.57 REMARK 500 LEU A 615 30.33 -99.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34718 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN NOREPINEPHRINE TRANSPORTER NET IN AN REMARK 900 INWARD-OPEN STATE AT RESOLUTION OF 2.5 ANGSTROM DBREF 8HFE A 1 617 UNP P23975 SC6A2_HUMAN 1 617 SEQRES 1 A 617 MET LEU LEU ALA ARG MET ASN PRO GLN VAL GLN PRO GLU SEQRES 2 A 617 ASN ASN GLY ALA ASP THR GLY PRO GLU GLN PRO LEU ARG SEQRES 3 A 617 ALA ARG LYS THR ALA GLU LEU LEU VAL VAL LYS GLU ARG SEQRES 4 A 617 ASN GLY VAL GLN CYS LEU LEU ALA PRO ARG ASP GLY ASP SEQRES 5 A 617 ALA GLN PRO ARG GLU THR TRP GLY LYS LYS ILE ASP PHE SEQRES 6 A 617 LEU LEU SER VAL VAL GLY PHE ALA VAL ASP LEU ALA ASN SEQRES 7 A 617 VAL TRP ARG PHE PRO TYR LEU CYS TYR LYS ASN GLY GLY SEQRES 8 A 617 GLY ALA PHE LEU ILE PRO TYR THR LEU PHE LEU ILE ILE SEQRES 9 A 617 ALA GLY MET PRO LEU PHE TYR MET GLU LEU ALA LEU GLY SEQRES 10 A 617 GLN TYR ASN ARG GLU GLY ALA ALA THR VAL TRP LYS ILE SEQRES 11 A 617 CYS PRO PHE PHE LYS GLY VAL GLY TYR ALA VAL ILE LEU SEQRES 12 A 617 ILE ALA LEU TYR VAL GLY PHE TYR TYR ASN VAL ILE ILE SEQRES 13 A 617 ALA TRP SER LEU TYR TYR LEU PHE SER SER PHE THR LEU SEQRES 14 A 617 ASN LEU PRO TRP THR ASP CYS GLY HIS THR TRP ASN SER SEQRES 15 A 617 PRO ASN CYS THR ASP PRO LYS LEU LEU ASN GLY SER VAL SEQRES 16 A 617 LEU GLY ASN HIS THR LYS TYR SER LYS TYR LYS PHE THR SEQRES 17 A 617 PRO ALA ALA GLU PHE TYR GLU ARG GLY VAL LEU HIS LEU SEQRES 18 A 617 HIS GLU SER SER GLY ILE HIS ASP ILE GLY LEU PRO GLN SEQRES 19 A 617 TRP GLN LEU LEU LEU CYS LEU MET VAL VAL VAL ILE VAL SEQRES 20 A 617 LEU TYR PHE SER LEU TRP LYS GLY VAL LYS THR SER GLY SEQRES 21 A 617 LYS VAL VAL TRP ILE THR ALA THR LEU PRO TYR PHE VAL SEQRES 22 A 617 LEU PHE VAL LEU LEU VAL HIS GLY VAL THR LEU PRO GLY SEQRES 23 A 617 ALA SER ASN GLY ILE ASN ALA TYR LEU HIS ILE ASP PHE SEQRES 24 A 617 TYR ARG LEU LYS GLU ALA THR VAL TRP ILE ASP ALA ALA SEQRES 25 A 617 THR GLN ILE PHE PHE SER LEU GLY ALA GLY PHE GLY VAL SEQRES 26 A 617 LEU ILE ALA PHE ALA SER TYR ASN LYS PHE ASP ASN ASN SEQRES 27 A 617 CYS TYR ARG ASP ALA LEU LEU THR SER SER ILE ASN CYS SEQRES 28 A 617 ILE THR SER PHE VAL SER GLY PHE ALA ILE PHE SER ILE SEQRES 29 A 617 LEU GLY TYR MET ALA HIS GLU HIS LYS VAL ASN ILE GLU SEQRES 30 A 617 ASP VAL ALA THR GLU GLY ALA GLY LEU VAL PHE ILE LEU SEQRES 31 A 617 TYR PRO GLU ALA ILE SER THR LEU SER GLY SER THR PHE SEQRES 32 A 617 TRP ALA VAL VAL PHE PHE VAL MET LEU LEU ALA LEU GLY SEQRES 33 A 617 LEU ASP SER SER MET GLY GLY MET GLU ALA VAL ILE THR SEQRES 34 A 617 GLY LEU ALA ASP ASP PHE GLN VAL LEU LYS ARG HIS ARG SEQRES 35 A 617 LYS LEU PHE THR PHE GLY VAL THR PHE SER THR PHE LEU SEQRES 36 A 617 LEU ALA LEU PHE CYS ILE THR LYS GLY GLY ILE TYR VAL SEQRES 37 A 617 LEU THR LEU LEU ASP THR PHE ALA ALA GLY THR SER ILE SEQRES 38 A 617 LEU PHE ALA VAL LEU MET GLU ALA ILE GLY VAL SER TRP SEQRES 39 A 617 PHE TYR GLY VAL ASP ARG PHE SER ASN ASP ILE GLN GLN SEQRES 40 A 617 MET MET GLY PHE ARG PRO GLY LEU TYR TRP ARG LEU CYS SEQRES 41 A 617 TRP LYS PHE VAL SER PRO ALA PHE LEU LEU PHE VAL VAL SEQRES 42 A 617 VAL VAL SER ILE ILE ASN PHE LYS PRO LEU THR TYR ASP SEQRES 43 A 617 ASP TYR ILE PHE PRO PRO TRP ALA ASN TRP VAL GLY TRP SEQRES 44 A 617 GLY ILE ALA LEU SER SER MET VAL LEU VAL PRO ILE TYR SEQRES 45 A 617 VAL ILE TYR LYS PHE LEU SER THR GLN GLY SER LEU TRP SEQRES 46 A 617 GLU ARG LEU ALA TYR GLY ILE THR PRO GLU ASN GLU HIS SEQRES 47 A 617 HIS LEU VAL ALA GLN ARG ASP ILE ARG GLN PHE GLN LEU SEQRES 48 A 617 GLN HIS TRP LEU ALA ILE HET CL A 701 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- FORMUL 3 HOH *22(H2 O) HELIX 1 AA1 GLY A 60 VAL A 74 1 15 HELIX 2 AA2 ASP A 75 ASN A 89 1 15 HELIX 3 AA3 PHE A 94 ALA A 105 1 12 HELIX 4 AA4 ALA A 105 ARG A 121 1 17 HELIX 5 AA5 ALA A 125 ILE A 130 5 6 HELIX 6 AA6 CYS A 131 PHE A 133 5 3 HELIX 7 AA7 PHE A 134 SER A 166 1 33 HELIX 8 AA8 THR A 208 GLY A 217 1 10 HELIX 9 AA9 HIS A 220 SER A 224 5 5 HELIX 10 AB1 GLN A 234 TRP A 253 1 20 HELIX 11 AB2 TRP A 264 THR A 283 1 20 HELIX 12 AB3 GLY A 286 LEU A 295 1 10 HELIX 13 AB4 ASP A 298 LYS A 303 1 6 HELIX 14 AB5 ALA A 305 GLY A 320 1 16 HELIX 15 AB6 GLY A 324 SER A 331 1 8 HELIX 16 AB7 ASN A 338 LYS A 373 1 36 HELIX 17 AB8 GLY A 385 SER A 396 1 12 HELIX 18 AB9 GLY A 400 PHE A 435 1 36 HELIX 19 AC1 PHE A 435 ARG A 440 1 6 HELIX 20 AC2 HIS A 441 PHE A 459 1 19 HELIX 21 AC3 GLY A 464 ALA A 476 1 13 HELIX 22 AC4 GLY A 478 TRP A 494 1 17 HELIX 23 AC5 GLY A 497 GLY A 510 1 14 HELIX 24 AC6 GLY A 514 PHE A 523 1 10 HELIX 25 AC7 PHE A 523 ASN A 539 1 17 HELIX 26 AC8 PRO A 551 VAL A 567 1 17 HELIX 27 AC9 VAL A 567 THR A 580 1 14 HELIX 28 AD1 SER A 583 THR A 593 1 11 HELIX 29 AD2 PRO A 594 ARG A 604 5 11 HELIX 30 AD3 ILE A 606 PHE A 609 5 4 HELIX 31 AD4 GLN A 610 LEU A 615 1 6 SHEET 1 AA1 2 THR A 544 TYR A 545 0 SHEET 2 AA1 2 TYR A 548 ILE A 549 -1 O TYR A 548 N TYR A 545 SSBOND 1 CYS A 176 CYS A 185 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