HEADER TRANSPORT PROTEIN 17-JAN-22 7WN1 TITLE STRUCTURE OF PFNT1(Y190A) IN COMPLEX WITH NANOBODY 48 AND INOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: EQUILIBRATIVE NUCLEOSIDE/NUCLEOBASE TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEOSIDE TRANSPORTER 1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NANOBODY48; COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_COMMON: MALARIA PARASITE P. FALCIPARUM; SOURCE 4 ORGANISM_TAXID: 5833; SOURCE 5 GENE: NT1, ENT1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: IPLB-SF-21-AE(SF9); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 11 ORGANISM_TAXID: 30538; SOURCE 12 EXPRESSION_SYSTEM: BACILLUS SUBTILIS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 1423 KEYWDS MALARIA, EQUILIBRATIVE NUCLEOSIDE TRANSPORTER, INOSINE, TRANSPORT KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR C.WANG,D.DENG,R.B.REN,L.Y.YU REVDAT 2 16-AUG-23 7WN1 1 JRNL REVDAT 1 01-FEB-23 7WN1 0 JRNL AUTH C.WANG,L.YU,J.ZHANG,Y.ZHOU,B.SUN,Q.XIAO,M.ZHANG,H.LIU,J.LI, JRNL AUTH 2 J.LI,Y.LUO,J.XU,Z.LIAN,J.LIN,X.WANG,P.ZHANG,L.GUO,R.REN, JRNL AUTH 3 D.DENG JRNL TITL STRUCTURAL BASIS OF THE SUBSTRATE RECOGNITION AND INHIBITION JRNL TITL 2 MECHANISM OF PLASMODIUM FALCIPARUM NUCLEOSIDE TRANSPORTER JRNL TITL 3 PFENT1. JRNL REF NAT COMMUN V. 14 1727 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 36977719 JRNL DOI 10.1038/S41467-023-37411-1 REMARK 2 REMARK 2 RESOLUTION. 3.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.110 REMARK 3 NUMBER OF PARTICLES : 183797 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 7WN1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300026827. 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 : STRUCTURE OF PFNT1(Y190A) IN REMARK 245 COMPLEX WITH NANOBODY 48 AND REMARK 245 INOSINE; PFNT1; NANOBODY 48 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 : 6.00 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) : 1800.00 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) : 5630.00 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, C 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 SER A 2 REMARK 465 THR A 3 REMARK 465 GLY A 4 REMARK 465 LYS A 5 REMARK 465 GLU A 6 REMARK 465 SER A 7 REMARK 465 SER A 8 REMARK 465 LYS A 9 REMARK 465 ALA A 10 REMARK 465 TYR A 11 REMARK 465 ALA A 12 REMARK 465 ASP A 13 REMARK 465 ILE A 14 REMARK 465 GLU A 15 REMARK 465 SER A 16 REMARK 465 ARG A 17 REMARK 465 GLY A 18 REMARK 465 ASP A 19 REMARK 465 TYR A 20 REMARK 465 LYS A 21 REMARK 465 ASP A 22 REMARK 465 ASP A 23 REMARK 465 GLY A 24 REMARK 465 LYS A 25 REMARK 465 LYS A 26 REMARK 465 GLY A 27 REMARK 465 SER A 28 REMARK 465 THR A 29 REMARK 465 LYS A 215 REMARK 465 ASN A 216 REMARK 465 ASN A 217 REMARK 465 LYS A 218 REMARK 465 LYS A 219 REMARK 465 ASP A 220 REMARK 465 GLU A 221 REMARK 465 GLU A 222 REMARK 465 ASN A 223 REMARK 465 LYS A 224 REMARK 465 GLU A 225 REMARK 465 ASN A 226 REMARK 465 ASN A 227 REMARK 465 ASP A 414 REMARK 465 LEU A 415 REMARK 465 PRO A 416 REMARK 465 PRO A 417 REMARK 465 ILE A 418 REMARK 465 ASP A 419 REMARK 465 VAL A 420 REMARK 465 THR A 421 REMARK 465 GLN A 422 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 112 -168.36 -79.98 REMARK 500 ASP A 147 62.45 38.52 REMARK 500 LEU A 296 58.68 -95.46 REMARK 500 PHE C 27 59.29 36.31 REMARK 500 TYR C 102 70.69 46.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32619 RELATED DB: EMDB REMARK 900 STRUCTURE OF PFNT1(Y190A) IN COMPLEX WITH NANOBODY 48 AND INOSINE DBREF 7WN1 A 1 422 UNP Q9NIH7 Q9NIH7_PLAFA 1 422 DBREF 7WN1 C 1 122 PDB 7WN1 7WN1 1 122 SEQADV 7WN1 ALA A 190 UNP Q9NIH7 TYR 190 ENGINEERED MUTATION SEQRES 1 A 422 MET SER THR GLY LYS GLU SER SER LYS ALA TYR ALA ASP SEQRES 2 A 422 ILE GLU SER ARG GLY ASP TYR LYS ASP ASP GLY LYS LYS SEQRES 3 A 422 GLY SER THR LEU SER SER LYS GLN HIS PHE MET LEU SER SEQRES 4 A 422 LEU THR PHE ILE LEU ILE GLY LEU SER SER LEU ASN VAL SEQRES 5 A 422 TRP ASN THR ALA LEU GLY LEU ASN ILE ASN PHE LYS TYR SEQRES 6 A 422 ASN THR PHE GLN ILE THR GLY LEU VAL CYS SER SER ILE SEQRES 7 A 422 VAL ALA LEU PHE VAL GLU ILE PRO LYS ILE MET LEU PRO SEQRES 8 A 422 PHE LEU LEU GLY GLY LEU SER ILE LEU CYS ALA GLY PHE SEQRES 9 A 422 GLN ILE SER HIS SER PHE PHE THR ASP THR GLN PHE ASP SEQRES 10 A 422 THR TYR CYS LEU VAL ALA PHE ILE VAL ILE GLY VAL VAL SEQRES 11 A 422 ALA GLY LEU ALA GLN THR ILE ALA PHE ASN ILE GLY SER SEQRES 12 A 422 THR MET GLU ASP ASN MET GLY GLY TYR MET SER ALA GLY SEQRES 13 A 422 ILE GLY ILE SER GLY VAL PHE ILE PHE VAL ILE ASN LEU SEQRES 14 A 422 LEU LEU ASP GLN PHE VAL SER PRO GLU LYS HIS TYR GLY SEQRES 15 A 422 VAL ASN LYS ALA LYS LEU LEU ALA LEU TYR ILE ILE CYS SEQRES 16 A 422 GLU LEU CYS LEU ILE LEU ALA ILE VAL PHE CYS VAL CYS SEQRES 17 A 422 ASN LEU ASP LEU THR ASN LYS ASN ASN LYS LYS ASP GLU SEQRES 18 A 422 GLU ASN LYS GLU ASN ASN ALA THR LEU SER TYR MET GLU SEQRES 19 A 422 LEU PHE LYS ASP SER TYR LYS ALA ILE LEU THR MET PHE SEQRES 20 A 422 LEU VAL ASN TRP LEU THR LEU GLN LEU PHE PRO GLY VAL SEQRES 21 A 422 GLY HIS LYS LYS TRP GLN GLU SER HIS ASN ILE SER ASP SEQRES 22 A 422 TYR ASN VAL THR ILE ILE VAL GLY MET PHE GLN VAL PHE SEQRES 23 A 422 ASP PHE LEU SER ARG TYR PRO PRO ASN LEU THR HIS ILE SEQRES 24 A 422 LYS ILE PHE LYS ASN PHE THR PHE SER LEU ASN LYS LEU SEQRES 25 A 422 LEU VAL ALA ASN SER LEU ARG LEU LEU PHE ILE PRO TRP SEQRES 26 A 422 PHE ILE LEU ASN ALA CYS VAL ASP HIS PRO PHE PHE LYS SEQRES 27 A 422 ASN ILE VAL GLN GLN CYS VAL CYS MET ALA MET LEU ALA SEQRES 28 A 422 PHE THR ASN GLY TRP PHE ASN THR VAL PRO PHE LEU VAL SEQRES 29 A 422 PHE VAL LYS GLU LEU LYS LYS ALA LYS LYS LYS LYS GLU SEQRES 30 A 422 ILE GLU ILE ILE SER THR PHE LEU VAL ILE ALA MET PHE SEQRES 31 A 422 VAL GLY LEU PHE CYS GLY ILE TRP THR THR TYR ILE TYR SEQRES 32 A 422 ASN LEU PHE ASN ILE VAL LEU PRO LYS PRO ASP LEU PRO SEQRES 33 A 422 PRO ILE ASP VAL THR GLN SEQRES 1 C 122 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 122 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 C 122 PHE THR GLY SER ILE ASN TYR MET GLY TRP TYR ARG GLN SEQRES 4 C 122 ALA PRO GLY LYS GLN ARG GLU LEU VAL ALA ARG PHE SER SEQRES 5 C 122 SER GLY GLY SER THR ASN TYR ALA ASP SER VAL LYS GLY SEQRES 6 C 122 ARG PHE THR ILE SER GLY ASP ASN ALA LYS ASN THR VAL SEQRES 7 C 122 TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 C 122 VAL TYR TYR CYS ASN ALA GLU THR ILE SER TYR VAL TYR SEQRES 9 C 122 THR VAL VAL PHE GLN ASP TYR TRP GLY GLN GLY THR GLN SEQRES 10 C 122 VAL THR VAL SER SER HET NOS A 501 19 HETNAM NOS INOSINE FORMUL 3 NOS C10 H12 N4 O5 HELIX 1 AA1 SER A 31 LEU A 59 1 29 HELIX 2 AA2 ASN A 62 VAL A 83 1 22 HELIX 3 AA3 PRO A 86 ILE A 88 5 3 HELIX 4 AA4 MET A 89 PHE A 111 1 23 HELIX 5 AA5 THR A 112 THR A 144 1 33 HELIX 6 AA6 MET A 149 VAL A 175 1 27 HELIX 7 AA7 ASN A 184 LEU A 210 1 27 HELIX 8 AA8 SER A 231 SER A 239 1 9 HELIX 9 AA9 SER A 239 PHE A 257 1 19 HELIX 10 AB1 HIS A 262 ASN A 270 1 9 HELIX 11 AB2 SER A 272 SER A 290 1 19 HELIX 12 AB3 ARG A 291 LEU A 296 1 6 HELIX 13 AB4 LEU A 309 ARG A 319 1 11 HELIX 14 AB5 LEU A 321 VAL A 332 1 12 HELIX 15 AB6 ASN A 339 LEU A 369 1 31 HELIX 16 AB7 LYS A 374 THR A 400 1 27 HELIX 17 AB8 TYR A 401 LEU A 405 5 5 HELIX 18 AB9 LYS C 86 THR C 90 5 5 SHEET 1 AA1 4 LEU C 4 SER C 7 0 SHEET 2 AA1 4 LEU C 18 ALA C 24 -1 O SER C 21 N SER C 7 SHEET 3 AA1 4 THR C 77 MET C 82 -1 O MET C 82 N LEU C 18 SHEET 4 AA1 4 PHE C 67 GLY C 71 -1 N SER C 70 O TYR C 79 SHEET 1 AA2 6 GLY C 10 VAL C 12 0 SHEET 2 AA2 6 THR C 116 VAL C 120 1 O THR C 119 N GLY C 10 SHEET 3 AA2 6 ALA C 91 ILE C 100 -1 N ALA C 91 O VAL C 118 SHEET 4 AA2 6 TYR C 33 GLN C 39 -1 N GLY C 35 O ASN C 96 SHEET 5 AA2 6 ARG C 45 SER C 52 -1 O ALA C 49 N TRP C 36 SHEET 6 AA2 6 THR C 57 TYR C 59 -1 O ASN C 58 N ARG C 50 SHEET 1 AA3 4 GLY C 10 VAL C 12 0 SHEET 2 AA3 4 THR C 116 VAL C 120 1 O THR C 119 N GLY C 10 SHEET 3 AA3 4 ALA C 91 ILE C 100 -1 N ALA C 91 O VAL C 118 SHEET 4 AA3 4 PHE C 108 TRP C 112 -1 O GLN C 109 N THR C 99 SSBOND 1 CYS C 22 CYS C 95 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