HEADER MEMBRANE PROTEIN 07-SEP-23 8U3D TITLE STRUCTURE OF APO SIALIN AT PH7.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIALIN; COMPND 3 CHAIN: A; COMPND 4 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: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS TRANSPORTER, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR P.SCHMIEGE,X.LI REVDAT 1 29-MAY-24 8U3D 0 JRNL AUTH P.SCHMIEGE,X.LI JRNL TITL STRUCTURE OF APO SIALIN AT PH7.5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX, ISOLDE 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) : 2.830 REMARK 3 NUMBER OF PARTICLES : 200101 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 8U3D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1000275992. 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 APO SIALIN AT REMARK 245 PH7.5 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 6000.00 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 -7 REMARK 465 ASP A -6 REMARK 465 TYR A -5 REMARK 465 LYS A -4 REMARK 465 ASP A -3 REMARK 465 ASP A -2 REMARK 465 ASP A -1 REMARK 465 ASP A 0 REMARK 465 LYS 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 ALA A 32 REMARK 465 PRO A 33 REMARK 465 VAL A 34 REMARK 465 CYS A 35 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 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 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 SER A 359 -1.94 68.26 REMARK 500 THR A 360 -9.10 69.82 REMARK 500 CYS A 387 -0.09 73.79 REMARK 500 ALA A 418 76.94 -164.94 REMARK 500 SER A 420 -7.20 71.77 REMARK 500 ASP A 450 -77.41 -116.77 REMARK 500 ASN A 451 -63.38 -134.78 REMARK 500 THR A 452 77.17 43.63 REMARK 500 VAL A 453 -32.14 -38.24 REMARK 500 TRP A 485 0.60 -66.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-41858 RELATED DB: EMDB REMARK 900 STRUCTURE OF APO SIALIN AT PH7.5 DBREF 8U3D A 2 495 UNP Q9NRA2 S17A5_HUMAN 2 495 SEQADV 8U3D MET A -7 UNP Q9NRA2 INITIATING METHIONINE SEQADV 8U3D ASP A -6 UNP Q9NRA2 EXPRESSION TAG SEQADV 8U3D TYR A -5 UNP Q9NRA2 EXPRESSION TAG SEQADV 8U3D LYS A -4 UNP Q9NRA2 EXPRESSION TAG SEQADV 8U3D ASP A -3 UNP Q9NRA2 EXPRESSION TAG SEQADV 8U3D ASP A -2 UNP Q9NRA2 EXPRESSION TAG SEQADV 8U3D ASP A -1 UNP Q9NRA2 EXPRESSION TAG SEQADV 8U3D ASP A 0 UNP Q9NRA2 EXPRESSION TAG SEQADV 8U3D LYS A 1 UNP Q9NRA2 EXPRESSION TAG SEQRES 1 A 503 MET ASP TYR LYS ASP ASP ASP ASP LYS ARG SER PRO VAL SEQRES 2 A 503 ARG ASP LEU ALA ARG ASN ASP GLY GLU GLU SER THR ASP SEQRES 3 A 503 ARG THR PRO LEU LEU PRO GLY ALA PRO ARG ALA GLU ALA SEQRES 4 A 503 ALA PRO VAL CYS CYS SER ALA ARG TYR ASN LEU ALA ILE SEQRES 5 A 503 LEU ALA PHE PHE GLY PHE PHE ILE VAL TYR ALA LEU ARG SEQRES 6 A 503 VAL ASN LEU SER VAL ALA LEU VAL ASP MET VAL ASP SER SEQRES 7 A 503 ASN THR THR LEU GLU ASP ASN ARG THR SER LYS ALA CYS SEQRES 8 A 503 PRO GLU HIS SER ALA PRO ILE LYS VAL HIS HIS ASN GLN SEQRES 9 A 503 THR GLY LYS LYS TYR GLN TRP ASP ALA GLU THR GLN GLY SEQRES 10 A 503 TRP ILE LEU GLY SER PHE PHE TYR GLY TYR ILE ILE THR SEQRES 11 A 503 GLN ILE PRO GLY GLY TYR VAL ALA SER LYS ILE GLY GLY SEQRES 12 A 503 LYS MET LEU LEU GLY PHE GLY ILE LEU GLY THR ALA VAL SEQRES 13 A 503 LEU THR LEU PHE THR PRO ILE ALA ALA ASP LEU GLY VAL SEQRES 14 A 503 GLY PRO LEU ILE VAL LEU ARG ALA LEU GLU GLY LEU GLY SEQRES 15 A 503 GLU GLY VAL THR PHE PRO ALA MET HIS ALA MET TRP SER SEQRES 16 A 503 SER TRP ALA PRO PRO LEU GLU ARG SER LYS LEU LEU SER SEQRES 17 A 503 ILE SER TYR ALA GLY ALA GLN LEU GLY THR VAL ILE SER SEQRES 18 A 503 LEU PRO LEU SER GLY ILE ILE CYS TYR TYR MET ASN TRP SEQRES 19 A 503 THR TYR VAL PHE TYR PHE PHE GLY THR ILE GLY ILE PHE SEQRES 20 A 503 TRP PHE LEU LEU TRP ILE TRP LEU VAL SER ASP THR PRO SEQRES 21 A 503 GLN LYS HIS LYS ARG ILE SER HIS TYR GLU LYS GLU TYR SEQRES 22 A 503 ILE LEU SER SER LEU ARG ASN GLN LEU SER SER GLN LYS SEQRES 23 A 503 SER VAL PRO TRP VAL PRO ILE LEU LYS SER LEU PRO LEU SEQRES 24 A 503 TRP ALA ILE VAL VAL ALA HIS PHE SER TYR ASN TRP THR SEQRES 25 A 503 PHE TYR THR LEU LEU THR LEU LEU PRO THR TYR MET LYS SEQRES 26 A 503 GLU ILE LEU ARG PHE ASN VAL GLN GLU ASN GLY PHE LEU SEQRES 27 A 503 SER SER LEU PRO TYR LEU GLY SER TRP LEU CYS MET ILE SEQRES 28 A 503 LEU SER GLY GLN ALA ALA ASP ASN LEU ARG ALA LYS TRP SEQRES 29 A 503 ASN PHE SER THR LEU CYS VAL ARG ARG ILE PHE SER LEU SEQRES 30 A 503 ILE GLY MET ILE GLY PRO ALA VAL PHE LEU VAL ALA ALA SEQRES 31 A 503 GLY PHE ILE GLY CYS ASP TYR SER LEU ALA VAL ALA PHE SEQRES 32 A 503 LEU THR ILE SER THR THR LEU GLY GLY PHE CYS SER SER SEQRES 33 A 503 GLY PHE SER ILE ASN HIS LEU ASP ILE ALA PRO SER TYR SEQRES 34 A 503 ALA GLY ILE LEU LEU GLY ILE THR ASN THR PHE ALA THR SEQRES 35 A 503 ILE PRO GLY MET VAL GLY PRO VAL ILE ALA LYS SER LEU SEQRES 36 A 503 THR PRO ASP ASN THR VAL GLY GLU TRP GLN THR VAL PHE SEQRES 37 A 503 TYR ILE ALA ALA ALA ILE ASN VAL PHE GLY ALA ILE PHE SEQRES 38 A 503 PHE THR LEU PHE ALA LYS GLY GLU VAL GLN ASN TRP ALA SEQRES 39 A 503 LEU ASN ASP HIS HIS GLY HIS ARG HIS HELIX 1 AA1 SER A 37 VAL A 68 1 32 HELIX 2 AA2 ASP A 104 ILE A 120 1 17 HELIX 3 AA3 GLN A 123 GLY A 134 1 12 HELIX 4 AA4 GLY A 134 LEU A 151 1 18 HELIX 5 AA5 PHE A 152 GLY A 160 1 9 HELIX 6 AA6 GLY A 160 VAL A 177 1 18 HELIX 7 AA7 VAL A 177 ALA A 190 1 14 HELIX 8 AA8 PRO A 191 LEU A 193 5 3 HELIX 9 AA9 GLU A 194 MET A 224 1 31 HELIX 10 AB1 TRP A 226 VAL A 248 1 23 HELIX 11 AB2 SER A 259 ARG A 271 1 13 HELIX 12 AB3 SER A 288 ILE A 319 1 32 HELIX 13 AB4 ASN A 323 TRP A 356 1 34 HELIX 14 AB5 LEU A 361 ILE A 385 1 25 HELIX 15 AB6 ASP A 388 GLY A 403 1 16 HELIX 16 AB7 GLY A 404 SER A 408 5 5 HELIX 17 AB8 GLY A 409 ILE A 412 5 4 HELIX 18 AB9 ASN A 413 ALA A 418 1 6 HELIX 19 AC1 TYR A 421 THR A 434 1 14 HELIX 20 AC2 THR A 434 THR A 448 1 15 HELIX 21 AC3 THR A 452 ALA A 478 1 27 HELIX 22 AC4 GLN A 483 LEU A 487 5 5 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