HEADER MEMBRANE PROTEIN 09-APR-24 9EYD TITLE STRUCTURAL BASIS OF SPECIFIC LYSINE TRANSPORT BY PSEUDOMONAS TITLE 2 AERUGINOSA PERMEASE LYSP COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC PERMEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: K1001 IS A SUBSTRATE; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NANOBODY CA5755; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: NANOBODY CA5755 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 GENE: LYSP, PA4628; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C43; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 10 ORGANISM_TAXID: 9844; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COMPLEX, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR E.NJI,R.MATSUOKA REVDAT 4 17-DEC-25 9EYD 1 JRNL REVDAT 3 03-DEC-25 9EYD 1 TITLE REVDAT 2 26-NOV-25 9EYD 1 JRNL REVDAT 1 29-OCT-25 9EYD 0 JRNL AUTH D.BICER,R.MATSUOKA,A.F.A.MOUMBOCK,P.SUKUMAR,A.SUADES, JRNL AUTH 2 H.CHERUVARA,A.QUIGLEY,D.DREW,E.PARDON,J.STEYAERT, JRNL AUTH 3 P.J.F.HENDERSON,M.CAFFREY,J.J.GRIESE,E.NJI JRNL TITL STRUCTURAL BASIS OF SPECIFIC LYSINE TRANSPORT BY PSEUDOMONAS JRNL TITL 2 AERUGINOSA PERMEASE LYSP. JRNL REF NAT COMMUN 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 41345107 JRNL DOI 10.1038/S41467-025-66618-7 REMARK 2 REMARK 2 RESOLUTION. 3.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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) : 3.680 REMARK 3 NUMBER OF PARTICLES : 78459 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 9EYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-APR-24. REMARK 100 THE DEPOSITION ID IS D_1292137743. 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 : PALYSP-NBCA5755 COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 QUANTUM (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 8000.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 GLN B 1 REMARK 465 VAL B 2 REMARK 465 HIS B 123 REMARK 465 HIS B 124 REMARK 465 HIS B 125 REMARK 465 HIS B 126 REMARK 465 HIS B 127 REMARK 465 HIS B 128 REMARK 465 GLU B 129 REMARK 465 PRO B 130 REMARK 465 GLU B 131 REMARK 465 ALA B 132 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 ARG A 14 53.15 -91.62 REMARK 500 VAL A 36 -51.42 -121.52 REMARK 500 SER A 80 -159.73 58.98 REMARK 500 VAL A 89 -63.18 -120.80 REMARK 500 PHE A 122 -9.61 74.23 REMARK 500 PHE A 335 -21.41 -142.15 REMARK 500 ALA A 356 1.73 -66.09 REMARK 500 PRO A 417 36.21 -89.88 REMARK 500 ASP A 445 -155.45 52.45 REMARK 500 ARG B 26 -108.33 61.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-50053 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF A LYSINE-SPECIFIC PERMEASE FROM PSEUDOMONAS REMARK 900 AERUGINOSA. DBREF 9EYD A 13 487 UNP Q9HVG3 Q9HVG3_PSEAE 13 487 DBREF 9EYD B 1 132 PDB 9EYD 9EYD 1 132 SEQRES 1 A 475 ARG ARG VAL LEU LYS PRO ARG HIS LEU ASN MET ILE ALA SEQRES 2 A 475 ILE GLY GLY SER ILE GLY THR GLY LEU PHE VAL ALA SER SEQRES 3 A 475 GLY ALA THR VAL ALA THR ALA GLY PRO GLY GLY ALA LEU SEQRES 4 A 475 LEU SER TYR ALA LEU ILE GLY LEU MET VAL TYR PHE LEU SEQRES 5 A 475 MET THR SER LEU GLY GLU MET ALA ALA TYR MET PRO VAL SEQRES 6 A 475 SER GLY SER PHE CYS THR TYR GLY SER ARG PHE VAL GLU SEQRES 7 A 475 ASP GLY PHE GLY PHE ALA LEU GLY TRP ASN TYR TRP TYR SEQRES 8 A 475 ASN TRP ALA VAL THR ILE ALA ALA GLU LEU VAL ALA ALA SEQRES 9 A 475 GLN LEU VAL MET SER PHE TRP PHE PRO GLU VAL PRO GLY SEQRES 10 A 475 ILE TYR TRP SER ALA ILE PHE LEU GLY ILE MET PHE GLY SEQRES 11 A 475 LEU ASN VAL ILE SER ALA ARG GLY PHE GLY GLU SER GLU SEQRES 12 A 475 PHE TRP PHE ALA LEU ILE LYS VAL VAL THR VAL VAL ILE SEQRES 13 A 475 PHE ILE GLY VAL GLY LEU ALA THR ILE PHE GLY ILE MET SEQRES 14 A 475 HIS GLY VAL GLU SER PRO GLY PHE SER ASN PHE THR MET SEQRES 15 A 475 GLY ASP ALA PRO PHE VAL GLY GLY PHE GLN ALA MET VAL SEQRES 16 A 475 GLY VAL ALA MET ILE ALA GLY PHE SER PHE GLN GLY THR SEQRES 17 A 475 GLU LEU ILE GLY ILE ALA ALA GLY GLU SER GLU ASN PRO SEQRES 18 A 475 ARG LYS ASN ILE PRO ILE ALA ILE ARG GLN VAL PHE TRP SEQRES 19 A 475 ARG ILE LEU MET PHE TYR ILE LEU ALA ILE PHE VAL ILE SEQRES 20 A 475 GLY MET LEU ILE PRO TYR THR ASP PRO ASN LEU LEU LYS SEQRES 21 A 475 ASN ASP ALA SER ASP ILE SER VAL SER PRO PHE THR LEU SEQRES 22 A 475 LEU PHE GLU ARG ALA GLY PHE ALA ALA ALA ALA GLY VAL SEQRES 23 A 475 MET ASN ALA VAL ILE LEU SER ALA ILE LEU SER ALA GLY SEQRES 24 A 475 ASN SER GLY MET TYR ALA SER THR ARG MET LEU TYR ASN SEQRES 25 A 475 LEU ALA LEU GLU GLY LYS ALA PRO ARG LEU PHE SER ARG SEQRES 26 A 475 VAL SER ARG SER GLY VAL PRO ARG ASN ALA LEU TYR ALA SEQRES 27 A 475 THR THR LEU VAL GLY ALA LEU CYS PHE LEU THR SER ALA SEQRES 28 A 475 PHE GLY ASP SER THR VAL TYR THR TRP LEU LEU ASN THR SEQRES 29 A 475 SER GLY MET CYS GLY PHE ILE ALA TRP LEU GLY ILE ALA SEQRES 30 A 475 ILE SER HIS TYR ARG PHE ARG LYS GLY TYR LEU ALA GLN SEQRES 31 A 475 GLY GLY ARG LEU GLU ASP LEU PRO TYR ARG ALA LYS LEU SEQRES 32 A 475 PHE PRO PHE GLY PRO LEU PHE ALA PHE ALA LEU CYS MET SEQRES 33 A 475 VAL ILE THR LEU GLY GLN ASN TYR GLN ALA LEU VAL GLY SEQRES 34 A 475 GLU ARG ILE ASP TRP ILE GLY LEU LEU ALA THR TYR ILE SEQRES 35 A 475 SER LEU PRO LEU PHE LEU ALA ILE TRP LEU GLY TYR ARG SEQRES 36 A 475 TRP LYS LYS ARG ALA ARG PHE VAL ARG TYR HIS GLU MET SEQRES 37 A 475 ASP VAL SER PRO THR ASN THR SEQRES 1 B 132 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 132 GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY ARG SEQRES 3 B 132 THR PHE SER ILE TYR GLY MET ALA TRP VAL ARG GLN ALA SEQRES 4 B 132 SER GLY LYS GLU ARG GLU PHE VAL ALA ALA MET PRO ARG SEQRES 5 B 132 GLY GLY GLY THR THR ASN TYR ALA ASP SER VAL LYS GLY SEQRES 6 B 132 ARG PHE SER ILE SER ARG ASP ASN ALA LYS ASN THR VAL SEQRES 7 B 132 ASP LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 B 132 VAL TYR TYR CYS VAL ALA ASP ARG GLY PHE THR LEU ARG SEQRES 9 B 132 LEU GLY ILE GLN HIS ASP TYR TRP GLY GLN GLY THR GLN SEQRES 10 B 132 VAL THR VAL SER SER HIS HIS HIS HIS HIS HIS GLU PRO SEQRES 11 B 132 GLU ALA HET LYS A 501 10 HETNAM LYS LYSINE FORMUL 3 LYS C6 H15 N2 O2 1+ HELIX 1 AA1 LYS A 17 ILE A 30 1 14 HELIX 2 AA2 VAL A 36 MET A 75 1 40 HELIX 3 AA3 GLY A 79 VAL A 89 1 11 HELIX 4 AA4 GLU A 90 MET A 120 1 31 HELIX 5 AA5 GLY A 129 SER A 147 1 19 HELIX 6 AA6 GLY A 150 GLY A 179 1 30 HELIX 7 AA7 GLY A 202 GLN A 218 1 17 HELIX 8 AA8 LEU A 222 GLY A 228 1 7 HELIX 9 AA9 ASN A 232 ILE A 263 1 32 HELIX 10 AB1 SER A 281 ARG A 289 1 9 HELIX 11 AB2 ALA A 295 GLU A 328 1 34 HELIX 12 AB3 ARG A 345 ALA A 356 1 12 HELIX 13 AB4 LEU A 357 PHE A 359 5 3 HELIX 14 AB5 LEU A 360 GLY A 365 1 6 HELIX 15 AB6 ASP A 366 GLY A 403 1 38 HELIX 16 AB7 ARG A 405 LEU A 409 5 5 HELIX 17 AB8 PRO A 417 GLY A 433 1 17 HELIX 18 AB9 TYR A 436 GLY A 441 1 6 HELIX 19 AC1 TRP A 446 TYR A 453 1 8 HELIX 20 AC2 ILE A 454 ARG A 471 1 18 HELIX 21 AC3 ASP B 61 LYS B 64 5 4 HELIX 22 AC4 LYS B 86 THR B 90 5 5 SHEET 1 AA1 4 LEU B 4 SER B 7 0 SHEET 2 AA1 4 LEU B 17 ALA B 23 -1 O ALA B 22 N GLN B 5 SHEET 3 AA1 4 THR B 77 MET B 82 -1 O MET B 82 N LEU B 17 SHEET 4 AA1 4 PHE B 67 ASP B 72 -1 N SER B 68 O GLN B 81 SHEET 1 AA2 6 LEU B 11 VAL B 12 0 SHEET 2 AA2 6 THR B 116 VAL B 120 1 O THR B 119 N VAL B 12 SHEET 3 AA2 6 ALA B 91 ASP B 98 -1 N ALA B 91 O VAL B 118 SHEET 4 AA2 6 GLY B 32 GLN B 38 -1 N GLN B 38 O VAL B 92 SHEET 5 AA2 6 GLU B 45 PRO B 51 -1 O MET B 50 N MET B 33 SHEET 6 AA2 6 ASN B 58 TYR B 59 -1 O ASN B 58 N ALA B 49 SSBOND 1 CYS B 21 CYS B 95 1555 1555 2.03 CISPEP 1 PHE A 416 PRO A 417 0 -1.27 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 3660 THR A 487 TER 4569 SER B 122 HETATM 4570 N LYS A 501 95.161 98.243 102.757 1.00 4.17 N HETATM 4571 CA LYS A 501 94.650 99.427 103.437 1.00 7.20 C HETATM 4572 C LYS A 501 95.251 100.698 102.849 1.00 0.00 C HETATM 4573 O LYS A 501 94.714 101.792 103.021 1.00 3.02 O HETATM 4574 CB LYS A 501 94.942 99.353 104.937 1.00 1.47 C HETATM 4575 CG LYS A 501 96.422 99.281 105.274 1.00 0.92 C HETATM 4576 CD LYS A 501 96.649 99.275 106.776 1.00 1.86 C HETATM 4577 CE LYS A 501 95.973 98.083 107.433 1.00 3.45 C HETATM 4578 NZ LYS A 501 96.210 98.054 108.903 1.00 3.97 N HETATM 4579 OXT LYS A 501 96.288 100.661 102.186 1.00 5.39 O CONECT 3790 4357 CONECT 4357 3790 MASTER 146 0 1 22 10 0 0 6 4577 2 2 48 END