HEADER MEMBRANE PROTEIN 26-OCT-24 9H76 TITLE BACTERIAL LAT TRANSPORTER BASC IN COMPLEX WITH L-ALA AND NB53 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE AMINO ACID/POLYAMINE TRANSPORT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NANOBODY NB53; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CARNOBACTERIUM SP. AT7; SOURCE 3 ORGANISM_TAXID: 333990; SOURCE 4 GENE: CAT7_03719; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 9 ORGANISM_TAXID: 9844; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSPORTER, NANOBODY, AMINOACID TRANSPORTER, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.FORT,M.PALACIN REVDAT 3 02-JUL-25 9H76 1 REMARK REVDAT 2 19-FEB-25 9H76 1 JRNL REVDAT 1 01-JAN-25 9H76 0 JRNL AUTH J.FORT,A.NICOLAS-ARAGO,L.MAGGI,M.MARTINEZ-MOLLEDO,D.KAPIKI, JRNL AUTH 2 P.GONZALEZ-NOVOA,P.GOMEZ-GEJO,N.ZIJLSTRA,S.BODOY,E.PARDON, JRNL AUTH 3 J.STEYAERT,O.LLORCA,M.OROZCO,T.CORDES,M.PALACIN JRNL TITL THE CONSERVED LYSINE RESIDUE IN TRANSMEMBRANE HELIX 5 IS JRNL TITL 2 PIVOTAL FOR THE CYTOPLASMIC GATING OF THE L-AMINO ACID JRNL TITL 3 TRANSPORTERS. JRNL REF PNAS NEXUS V. 4 AE584 2025 JRNL REFN ESSN 2752-6542 JRNL PMID 39822574 JRNL DOI 10.1093/PNASNEXUS/PGAE584 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, 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 : 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) : 2.900 REMARK 3 NUMBER OF PARTICLES : 324910 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 9H76 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1292142017. 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 : BASC-NB53 COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.90 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 38963 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 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) : 104.00 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 LYS A 2 REMARK 465 SER A 433 REMARK 465 PRO A 434 REMARK 465 GLU A 435 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLN B 3 REMARK 465 HIS B 120 REMARK 465 HIS B 121 REMARK 465 HIS B 122 REMARK 465 HIS B 123 REMARK 465 HIS B 124 REMARK 465 HIS B 125 REMARK 465 GLU B 126 REMARK 465 PRO B 127 REMARK 465 GLU B 128 REMARK 465 ALA B 129 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 OE2 GLU A 59 NH2 ARG A 369 2.19 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 ILE A 93 -61.76 -120.94 REMARK 500 LEU A 138 30.65 -96.19 REMARK 500 PHE A 179 -10.16 73.06 REMARK 500 PHE A 267 50.41 -119.73 REMARK 500 VAL A 386 -55.38 -120.45 REMARK 500 ALA B 93 -174.66 -172.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6F2W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BASC + NB74 REMARK 900 RELATED ID: 6F2G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BASC + NB74 REMARK 900 RELATED ID: EMD-51912 RELATED DB: EMDB REMARK 900 BACTERIAL LAT TRANSPORTER BASC IN COMPLEX WITH L-ALA AND NB53 DBREF 9H76 A 2 435 UNP A8UCQ5 A8UCQ5_9LACT 2 435 DBREF 9H76 B 1 129 PDB 9H76 9H76 1 129 SEQADV 9H76 MET A 1 UNP A8UCQ5 INITIATING METHIONINE SEQRES 1 A 435 MET LYS GLU VAL SER GLY ILE THR ALA LEU THR VAL VAL SEQRES 2 A 435 VAL GLY THR VAL ILE GLY ALA GLY ILE PHE PHE LYS PRO SEQRES 3 A 435 THR ALA VAL TYR GLY ALA ALA GLY ALA PRO GLY LEU GLY SEQRES 4 A 435 LEU LEU ALA TRP PHE VAL ALA GLY ILE ILE THR ILE ALA SEQRES 5 A 435 GLY GLY LEU THR VAL ALA GLU ILE GLY THR ILE TYR PRO SEQRES 6 A 435 GLN THR GLY GLY MET MET ILE TYR LEU GLU LYS VAL TYR SEQRES 7 A 435 GLY ARG TRP LEU GLY PHE LEU VAL GLY TRP ALA GLN MET SEQRES 8 A 435 VAL ILE TYR TYR PRO ALA ASN ILE ALA ALA LEU ALA ILE SEQRES 9 A 435 ILE PHE ALA THR GLN PHE VAL ASN LEU PHE ALA LEU SER SEQRES 10 A 435 ASP SER THR ILE VAL PRO THR ALA ILE LEU THR SER ILE SEQRES 11 A 435 PHE LEU MET GLY VAL ASN PHE LEU GLY THR LYS TYR SER SEQRES 12 A 435 GLY TRP ILE GLN THR LEU ALA THR ILE LEU LYS LEU ILE SEQRES 13 A 435 PRO LEU VAL VAL ILE ILE VAL ALA GLY LEU LEU TYR PRO SEQRES 14 A 435 GLY GLY GLY VAL ILE ARG LEU VAL PRO PHE SER VAL GLU SEQRES 15 A 435 THR HIS PRO VAL LEU THR SER PHE GLY SER ALA LEU ILE SEQRES 16 A 435 ALA THR LEU PHE ALA TYR ASP GLY TRP ILE ASN VAL GLY SEQRES 17 A 435 THR LEU ALA GLY GLU MET LYS ASN PRO GLY LYS MET LEU SEQRES 18 A 435 PRO LYS VAL ILE ILE GLY GLY LEU SER ILE VAL MET ALA SEQRES 19 A 435 VAL TYR LEU LEU THR ASN ILE ALA TYR LEU PHE VAL LEU SEQRES 20 A 435 ASP SER SER GLN LEU ALA GLY THR ASP THR PRO ALA ALA SEQRES 21 A 435 LEU VAL ALA SER HIS LEU PHE GLU GLY ILE GLY SER LYS SEQRES 22 A 435 LEU VAL THR ILE GLY ILE LEU ILE SER VAL PHE GLY GLY SEQRES 23 A 435 ILE ASN GLY TYR ILE ILE SER GLY LEU ARG VAL PRO TYR SEQRES 24 A 435 ALA LEU ALA THR GLN LYS MET LEU PRO PHE SER ASP TRP SEQRES 25 A 435 PHE ALA ARG ILE ASN PRO LYS THR ASN LEU PRO ILE ASN SEQRES 26 A 435 GLY GLY LEU VAL MET LEU GLY ILE ALA ILE VAL MET ILE SEQRES 27 A 435 LEU THR GLY GLN PHE ASN GLN LEU THR ASP LEU ILE VAL SEQRES 28 A 435 PHE VAL ILE TRP PHE PHE ILE THR LEU THR PHE ILE ALA SEQRES 29 A 435 VAL ILE ILE LEU ARG LYS THR GLN PRO ASP ILE GLU ARG SEQRES 30 A 435 PRO TYR ARG VAL PRO PHE TYR PRO VAL ILE PRO LEU ILE SEQRES 31 A 435 ALA ILE ILE GLY GLY LEU TYR ILE ILE PHE ASN THR LEU SEQRES 32 A 435 ILE VAL GLN PRO LYS ASN ALA PHE ILE GLY ILE LEU LEU SEQRES 33 A 435 THR LEU ILE GLY ILE PRO ILE TYR PHE TYR CYS LYS LYS SEQRES 34 A 435 LYS TYR GLY SER PRO GLU SEQRES 1 B 129 MET ALA GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU SEQRES 2 B 129 VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SEQRES 3 B 129 SER GLY ILE ALA PHE SER ARG MET SER MET ALA TRP TYR SEQRES 4 B 129 ARG GLN ASP PRO GLY LYS GLN ARG ALA LEU VAL ALA ARG SEQRES 5 B 129 ILE THR ASN ASP GLY SER THR TYR TYR ASP ASP SER VAL SEQRES 6 B 129 LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SEQRES 7 B 129 THR VAL HIS LEU GLN MET ASN SER LEU LYS PRO GLU ASP SEQRES 8 B 129 THR ALA VAL TYR TYR CYS ASN ALA GLN LEU VAL ALA TRP SEQRES 9 B 129 SER GLU ASN TYR TRP GLY GLN GLY THR GLN VAL THR VAL SEQRES 10 B 129 SER SER HIS HIS HIS HIS HIS HIS GLU PRO GLU ALA HET ALA A 501 6 HETNAM ALA ALANINE FORMUL 3 ALA C3 H7 N O2 HELIX 1 AA1 SER A 5 ILE A 18 1 14 HELIX 2 AA2 ALA A 20 LYS A 25 1 6 HELIX 3 AA3 LYS A 25 ALA A 33 1 9 HELIX 4 AA4 ALA A 35 TYR A 64 1 30 HELIX 5 AA5 GLY A 69 TYR A 78 1 10 HELIX 6 AA6 GLY A 79 ILE A 93 1 15 HELIX 7 AA7 ILE A 93 ALA A 115 1 23 HELIX 8 AA8 SER A 117 SER A 119 5 3 HELIX 9 AA9 THR A 120 PHE A 137 1 18 HELIX 10 AB1 GLY A 139 LYS A 154 1 16 HELIX 11 AB2 LYS A 154 LEU A 167 1 14 HELIX 12 AB3 GLY A 172 VAL A 177 5 6 HELIX 13 AB4 PRO A 185 TYR A 201 1 17 HELIX 14 AB5 ASP A 202 TRP A 204 5 3 HELIX 15 AB6 ILE A 205 MET A 214 1 10 HELIX 16 AB7 LYS A 219 LEU A 247 1 29 HELIX 17 AB8 ASP A 248 GLY A 254 1 7 HELIX 18 AB9 THR A 257 PHE A 267 1 11 HELIX 19 AC1 GLY A 269 GLN A 304 1 36 HELIX 20 AC2 PHE A 309 ARG A 315 1 7 HELIX 21 AC3 ILE A 324 THR A 340 1 17 HELIX 22 AC4 GLN A 342 GLN A 372 1 31 HELIX 23 AC5 VAL A 386 GLN A 406 1 21 HELIX 24 AC6 GLN A 406 TYR A 431 1 26 HELIX 25 AC7 ALA B 30 MET B 34 5 5 HELIX 26 AC8 LYS B 88 THR B 92 5 5 SHEET 1 AA1 4 GLN B 5 GLU B 8 0 SHEET 2 AA1 4 CYS B 24 SER B 27 -1 O ALA B 25 N VAL B 7 SHEET 3 AA1 4 THR B 79 MET B 84 -1 O VAL B 80 N CYS B 24 SHEET 4 AA1 4 LEU B 20 ARG B 21 -1 N LEU B 20 O MET B 84 SHEET 1 AA2 4 GLN B 5 GLU B 8 0 SHEET 2 AA2 4 CYS B 24 SER B 27 -1 O ALA B 25 N VAL B 7 SHEET 3 AA2 4 THR B 79 MET B 84 -1 O VAL B 80 N CYS B 24 SHEET 4 AA2 4 PHE B 69 ASP B 74 -1 N SER B 72 O HIS B 81 SHEET 1 AA3 6 LEU B 13 VAL B 14 0 SHEET 2 AA3 6 THR B 113 VAL B 117 1 O THR B 116 N VAL B 14 SHEET 3 AA3 6 ALA B 93 GLN B 100 -1 N TYR B 95 O THR B 113 SHEET 4 AA3 6 SER B 35 GLN B 41 -1 N ALA B 37 O ASN B 98 SHEET 5 AA3 6 ALA B 48 ILE B 53 -1 O ALA B 48 N ARG B 40 SHEET 6 AA3 6 THR B 59 TYR B 61 -1 O TYR B 60 N ARG B 52 SHEET 1 AA4 4 LEU B 13 VAL B 14 0 SHEET 2 AA4 4 THR B 113 VAL B 117 1 O THR B 116 N VAL B 14 SHEET 3 AA4 4 ALA B 93 GLN B 100 -1 N TYR B 95 O THR B 113 SHEET 4 AA4 4 TYR B 108 TRP B 109 -1 O TYR B 108 N ALA B 99 SSBOND 1 CYS B 24 CYS B 97 1555 1555 2.03 CISPEP 1 VAL A 177 PRO A 178 0 2.87 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 TER 3264 GLY A 432 TER 4153 SER B 119 HETATM 4154 N ALA A 501 131.757 125.977 135.477 0.00 90.83 N HETATM 4155 CA ALA A 501 132.863 126.468 134.632 0.00 90.82 C HETATM 4156 C ALA A 501 134.085 125.573 134.661 0.00 89.58 C HETATM 4157 O ALA A 501 135.045 125.837 133.951 0.00 88.90 O HETATM 4158 CB ALA A 501 133.248 127.864 135.057 0.00 90.78 C HETATM 4159 OXT ALA A 501 134.079 124.554 135.395 0.00 89.34 O CONECT 3404 3981 CONECT 3981 3404 MASTER 160 0 1 26 18 0 0 6 4157 2 2 44 END