HEADER MEMBRANE PROTEIN 01-AUG-22 8DWI TITLE MOLECULAR MECHANISM OF SIALIC ACID TRANSPORT MEDIATED BY SIALIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIALIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: H(+)/NITRATE COTRANSPORTER,H(+)/SIALIC ACID COTRANSPORTER, COMPND 5 AST,MEMBRANE GLYCOPROTEIN HP59,SOLUTE CARRIER FAMILY 17 MEMBER 5, COMPND 6 VESICULAR H(+)/ASPARTATE-GLUTAMATE COTRANSPORTER; COMPND 7 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: SLC17A5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SIALIC ACID TRANSPORT, SOLUTE CARRIER TRANSPORTER, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR W.HU,H.ZHENG REVDAT 3 22-FEB-23 8DWI 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQRES HELIX ATOM REVDAT 2 01-FEB-23 8DWI 1 JRNL REVDAT 1 25-JAN-23 8DWI 0 JRNL AUTH W.HU,C.CHI,K.SONG,H.ZHENG JRNL TITL THE MOLECULAR MECHANISM OF SIALIC ACID TRANSPORT MEDIATED BY JRNL TITL 2 SIALIN. JRNL REF SCI ADV V. 9 E8346 2023 JRNL REFN ESSN 2375-2548 JRNL PMID 36662855 JRNL DOI 10.1126/SCIADV.ADE8346 REMARK 2 REMARK 2 RESOLUTION. 3.40 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 394078 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 8DWI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267489. 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 : SIALIN COMPLEX WITH FAB 8B1 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 : 7.40 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 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 5720.00 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 ARG A 2 REMARK 465 SER A 3 REMARK 465 PRO A 4 REMARK 465 VAL A 5 REMARK 465 ARG A 6 REMARK 465 ASP A 7 REMARK 465 LEU A 8 REMARK 465 ALA A 9 REMARK 465 ARG A 10 REMARK 465 ASN A 11 REMARK 465 ASP A 12 REMARK 465 GLY A 13 REMARK 465 GLU A 14 REMARK 465 GLU A 15 REMARK 465 SER A 16 REMARK 465 THR A 17 REMARK 465 ASP A 18 REMARK 465 ARG A 19 REMARK 465 THR A 20 REMARK 465 PRO A 21 REMARK 465 LEU A 22 REMARK 465 LEU A 23 REMARK 465 PRO A 24 REMARK 465 GLY A 25 REMARK 465 ALA A 26 REMARK 465 PRO A 27 REMARK 465 ARG A 28 REMARK 465 ALA A 29 REMARK 465 GLU A 30 REMARK 465 ALA A 31 REMARK 465 ASP A 69 REMARK 465 SER A 70 REMARK 465 ASN A 71 REMARK 465 THR A 72 REMARK 465 THR A 73 REMARK 465 LEU A 74 REMARK 465 GLU A 75 REMARK 465 ASP A 76 REMARK 465 ASN A 77 REMARK 465 ARG A 78 REMARK 465 THR A 79 REMARK 465 SER A 80 REMARK 465 LYS A 81 REMARK 465 ALA A 82 REMARK 465 CYS A 83 REMARK 465 PRO A 84 REMARK 465 GLU A 85 REMARK 465 HIS A 86 REMARK 465 SER A 87 REMARK 465 ALA A 88 REMARK 465 PRO A 89 REMARK 465 ILE A 90 REMARK 465 LYS A 91 REMARK 465 VAL A 92 REMARK 465 HIS A 93 REMARK 465 HIS A 94 REMARK 465 ASN A 95 REMARK 465 GLN A 96 REMARK 465 THR A 97 REMARK 465 GLY A 98 REMARK 465 LYS A 99 REMARK 465 LYS A 100 REMARK 465 TYR A 101 REMARK 465 ASP A 489 REMARK 465 HIS A 490 REMARK 465 HIS A 491 REMARK 465 GLY A 492 REMARK 465 HIS A 493 REMARK 465 ARG A 494 REMARK 465 HIS A 495 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL A 34 CG1 CG2 REMARK 470 CYS A 35 SG REMARK 470 VAL A 65 CG1 CG2 REMARK 470 ASP A 66 CG OD1 OD2 REMARK 470 MET A 67 CG SD CE REMARK 470 VAL A 68 CG1 CG2 REMARK 470 ASP A 158 CG OD1 OD2 REMARK 470 VAL A 161 CG1 CG2 REMARK 470 TYR A 222 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 242 CG CD1 CD2 REMARK 470 LEU A 243 CG CD1 CD2 REMARK 470 LYS A 263 CG CD CE NZ REMARK 470 TYR A 265 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 267 CG CD1 CD2 REMARK 470 LEU A 270 CG CD1 CD2 REMARK 470 ARG A 271 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 272 CG OD1 ND2 REMARK 470 GLN A 273 CG CD OE1 NE2 REMARK 470 LEU A 274 CG CD1 CD2 REMARK 470 SER A 275 OG REMARK 470 SER A 276 OG REMARK 470 GLN A 277 CG CD OE1 NE2 REMARK 470 LYS A 278 CG CD CE NZ REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 GLU A 318 CG CD OE1 OE2 REMARK 470 ASN A 323 CG OD1 ND2 REMARK 470 GLU A 326 CG CD OE1 OE2 REMARK 470 LEU A 330 CG CD1 CD2 REMARK 470 GLN A 347 CG CD OE1 NE2 REMARK 470 ASP A 350 CG OD1 OD2 REMARK 470 ASN A 351 CG OD1 ND2 REMARK 470 ASN A 357 CG OD1 ND2 REMARK 470 ASP A 388 CG OD1 OD2 REMARK 470 GLU A 455 CG CD OE1 OE2 REMARK 470 GLU A 481 CG CD OE1 OE2 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 ALA A 38 -122.81 63.28 REMARK 500 THR A 107 49.70 36.65 REMARK 500 ARG A 257 -5.50 73.82 REMARK 500 SER A 259 -167.51 58.35 REMARK 500 TYR A 261 -162.92 60.48 REMARK 500 VAL A 280 69.88 37.23 REMARK 500 PHE A 384 -5.84 71.44 REMARK 500 ALA A 418 84.37 -154.94 REMARK 500 TYR A 421 32.61 -98.22 REMARK 500 GLU A 481 -147.42 56.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-27755 RELATED DB: EMDB REMARK 900 MOLECULAR MECHANISM OF SIALIC ACID TRANSPORT MEDIATED BY SIALIN DBREF 8DWI A 1 495 UNP Q9NRA2 S17A5_HUMAN 1 495 SEQRES 1 A 495 MET ARG SER PRO VAL ARG ASP LEU ALA ARG ASN ASP GLY SEQRES 2 A 495 GLU GLU SER THR ASP ARG THR PRO LEU LEU PRO GLY ALA SEQRES 3 A 495 PRO ARG ALA GLU ALA ALA PRO VAL CYS CYS SER ALA ARG SEQRES 4 A 495 TYR ASN LEU ALA ILE LEU ALA PHE PHE GLY PHE PHE ILE SEQRES 5 A 495 VAL TYR ALA LEU ARG VAL ASN LEU SER VAL ALA LEU VAL SEQRES 6 A 495 ASP MET VAL ASP SER ASN THR THR LEU GLU ASP ASN ARG SEQRES 7 A 495 THR SER LYS ALA CYS PRO GLU HIS SER ALA PRO ILE LYS SEQRES 8 A 495 VAL HIS HIS ASN GLN THR GLY LYS LYS TYR GLN TRP ASP SEQRES 9 A 495 ALA GLU THR GLN GLY TRP ILE LEU GLY SER PHE PHE TYR SEQRES 10 A 495 GLY TYR ILE ILE THR GLN ILE PRO GLY GLY TYR VAL ALA SEQRES 11 A 495 SER LYS ILE GLY GLY LYS MET LEU LEU GLY PHE GLY ILE SEQRES 12 A 495 LEU GLY THR ALA VAL LEU THR LEU PHE THR PRO ILE ALA SEQRES 13 A 495 ALA ASP LEU GLY VAL GLY PRO LEU ILE VAL LEU ARG ALA SEQRES 14 A 495 LEU GLU GLY LEU GLY GLU GLY VAL THR PHE PRO ALA MET SEQRES 15 A 495 HIS ALA MET TRP SER SER TRP ALA PRO PRO LEU GLU ARG SEQRES 16 A 495 SER LYS LEU LEU SER ILE SER TYR ALA GLY ALA GLN LEU SEQRES 17 A 495 GLY THR VAL ILE SER LEU PRO LEU SER GLY ILE ILE CYS SEQRES 18 A 495 TYR TYR MET ASN TRP THR TYR VAL PHE TYR PHE PHE GLY SEQRES 19 A 495 THR ILE GLY ILE PHE TRP PHE LEU LEU TRP ILE TRP LEU SEQRES 20 A 495 VAL SER ASP THR PRO GLN LYS HIS LYS ARG ILE SER HIS SEQRES 21 A 495 TYR GLU LYS GLU TYR ILE LEU SER SER LEU ARG ASN GLN SEQRES 22 A 495 LEU SER SER GLN LYS SER VAL PRO TRP VAL PRO ILE LEU SEQRES 23 A 495 LYS SER LEU PRO LEU TRP ALA ILE VAL VAL ALA HIS PHE SEQRES 24 A 495 SER TYR ASN TRP THR PHE TYR THR LEU LEU THR LEU LEU SEQRES 25 A 495 PRO THR TYR MET LYS GLU ILE LEU ARG PHE ASN VAL GLN SEQRES 26 A 495 GLU ASN GLY PHE LEU SER SER LEU PRO TYR LEU GLY SER SEQRES 27 A 495 TRP LEU CYS MET ILE LEU SER GLY GLN ALA ALA ASP ASN SEQRES 28 A 495 LEU ARG ALA LYS TRP ASN PHE SER THR LEU CYS VAL ARG SEQRES 29 A 495 ARG ILE PHE SER LEU ILE GLY MET ILE GLY PRO ALA VAL SEQRES 30 A 495 PHE LEU VAL ALA ALA GLY PHE ILE GLY CYS ASP TYR SER SEQRES 31 A 495 LEU ALA VAL ALA PHE LEU THR ILE SER THR THR LEU GLY SEQRES 32 A 495 GLY PHE CYS SER SER GLY PHE SER ILE ASN HIS LEU ASP SEQRES 33 A 495 ILE ALA PRO SER TYR ALA GLY ILE LEU LEU GLY ILE THR SEQRES 34 A 495 ASN THR PHE ALA THR ILE PRO GLY MET VAL GLY PRO VAL SEQRES 35 A 495 ILE ALA LYS SER LEU THR PRO ASP ASN THR VAL GLY GLU SEQRES 36 A 495 TRP GLN THR VAL PHE TYR ILE ALA ALA ALA ILE ASN VAL SEQRES 37 A 495 PHE GLY ALA ILE PHE PHE THR LEU PHE ALA LYS GLY GLU SEQRES 38 A 495 VAL GLN ASN TRP ALA LEU ASN ASP HIS HIS GLY HIS ARG SEQRES 39 A 495 HIS HELIX 1 1 ALA A 38 MET A 67 5 30 HELIX 2 2 GLY A 109 ILE A 133 1 25 HELIX 3 3 GLY A 135 LEU A 151 1 17 HELIX 4 4 THR A 153 LEU A 159 1 7 HELIX 5 5 VAL A 161 ARG A 168 1 8 HELIX 6 6 GLY A 176 TRP A 189 1 14 HELIX 7 7 ARG A 195 TYR A 223 1 29 HELIX 8 8 TRP A 226 LEU A 247 5 22 HELIX 9 9 GLU A 264 ASN A 272 1 9 HELIX 10 10 TRP A 282 LYS A 287 1 6 HELIX 11 11 LEU A 289 THR A 310 1 22 HELIX 12 12 LEU A 312 GLU A 318 1 7 HELIX 13 13 VAL A 324 ALA A 354 1 31 HELIX 14 14 THR A 360 ALA A 382 1 23 HELIX 15 15 TYR A 389 SER A 408 1 20 HELIX 16 16 SER A 411 ILE A 417 5 7 HELIX 17 17 ILE A 424 THR A 431 1 8 HELIX 18 18 ILE A 435 LYS A 445 1 11 HELIX 19 19 VAL A 453 PHE A 477 1 25 HELIX 20 20 ASN A 484 ALA A 486 5 3 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