HEADER TRANSPORT PROTEIN 10-JUL-23 8K1B TITLE SID1 TRANSMEMBRANE FAMILY MEMBER 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SID1 TRANSMEMBRANE FAMILY MEMBER 1; COMPND 3 CHAIN: A, B; 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: SIDT1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.GUO,C.QI,Y.LU,H.YANG,Y.ZHU,F.SUN,X.JI REVDAT 1 10-JUL-24 8K1B 0 JRNL AUTH L.ZHENG,T.YANG,H.GUO,C.QI,Y.LU,H.XIAO,Y.GAO,Y.LIU,Y.YANG, JRNL AUTH 2 M.ZHOU,H.C.NGUYEN,Y.ZHU,F.SUN,C.Y.ZHANG,X.JI JRNL TITL CRYO-EM STRUCTURES OF HUMAN SID-1 TRANSMEMBRANE FAMILY JRNL TITL 2 PROTEINS AND IMPLICATIONS FOR THEIR LOW-PH-DEPENDENT RNA JRNL TITL 3 TRANSPORT ACTIVITY. JRNL REF CELL RES. V. 34 80 2024 JRNL REFN ISSN 1001-0602 JRNL PMID 37932445 JRNL DOI 10.1038/S41422-023-00893-1 REMARK 2 REMARK 2 RESOLUTION. 3.47 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) : 3.470 REMARK 3 NUMBER OF PARTICLES : 94868 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 8K1B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 19-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039325. 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 : HUMAN SID1 TRANSMEMBRANE FAMILY REMARK 245 MEMBER 1 (SIDT1) HOMODIMER, ECD REMARK 245 FOCUSED REFINEMENT 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 REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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 : SPOT SCAN 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 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 ARG A 118 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 118 CG CD NE CZ NH1 NH2 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 GLN A 99 -168.41 -101.93 REMARK 500 GLU A 137 97.86 -68.98 REMARK 500 GLN A 185 73.55 -115.32 REMARK 500 GLU B 137 97.82 -68.97 REMARK 500 GLN B 185 73.50 -115.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-36791 RELATED DB: EMDB REMARK 900 TO BE PUBLISHED DBREF 8K1B A 47 300 UNP Q9NXL6 SIDT1_HUMAN 47 300 DBREF 8K1B B 47 300 UNP Q9NXL6 SIDT1_HUMAN 47 300 SEQRES 1 A 254 ASP PHE ASP HIS VAL TYR SER GLY VAL VAL ASN LEU SER SEQRES 2 A 254 THR GLU ASN ILE TYR SER PHE ASN TYR THR SER GLN PRO SEQRES 3 A 254 ASP GLN VAL THR ALA VAL ARG VAL TYR VAL ASN SER SER SEQRES 4 A 254 SER GLU ASN LEU ASN TYR PRO VAL LEU VAL VAL VAL ARG SEQRES 5 A 254 GLN GLN LYS GLU VAL LEU SER TRP GLN VAL PRO LEU LEU SEQRES 6 A 254 PHE GLN GLY LEU TYR GLN ARG SER TYR ASN TYR GLN GLU SEQRES 7 A 254 VAL SER ARG THR LEU CYS PRO SER GLU ALA THR ASN GLU SEQRES 8 A 254 THR GLY PRO LEU GLN GLN LEU ILE PHE VAL ASP VAL ALA SEQRES 9 A 254 SER MET ALA PRO LEU GLY ALA GLN TYR LYS LEU LEU VAL SEQRES 10 A 254 THR LYS LEU LYS HIS PHE GLN LEU ARG THR ASN VAL ALA SEQRES 11 A 254 PHE HIS PHE THR ALA SER PRO SER GLN PRO GLN TYR PHE SEQRES 12 A 254 LEU TYR LYS PHE PRO LYS ASP VAL ASP SER VAL ILE ILE SEQRES 13 A 254 LYS VAL VAL SER GLU MET ALA TYR PRO CYS SER VAL VAL SEQRES 14 A 254 SER VAL GLN ASN ILE MET CYS PRO VAL TYR ASP LEU ASP SEQRES 15 A 254 HIS ASN VAL GLU PHE ASN GLY VAL TYR GLN SER MET THR SEQRES 16 A 254 LYS LYS ALA ALA ILE THR LEU GLN LYS LYS ASP PHE PRO SEQRES 17 A 254 GLY GLU GLN PHE PHE VAL VAL PHE VAL ILE LYS PRO GLU SEQRES 18 A 254 ASP TYR ALA CYS GLY GLY SER PHE PHE ILE GLN GLU LYS SEQRES 19 A 254 GLU ASN GLN THR TRP ASN LEU GLN ARG LYS LYS ASN LEU SEQRES 20 A 254 GLU VAL THR ILE VAL PRO SER SEQRES 1 B 254 ASP PHE ASP HIS VAL TYR SER GLY VAL VAL ASN LEU SER SEQRES 2 B 254 THR GLU ASN ILE TYR SER PHE ASN TYR THR SER GLN PRO SEQRES 3 B 254 ASP GLN VAL THR ALA VAL ARG VAL TYR VAL ASN SER SER SEQRES 4 B 254 SER GLU ASN LEU ASN TYR PRO VAL LEU VAL VAL VAL ARG SEQRES 5 B 254 GLN GLN LYS GLU VAL LEU SER TRP GLN VAL PRO LEU LEU SEQRES 6 B 254 PHE GLN GLY LEU TYR GLN ARG SER TYR ASN TYR GLN GLU SEQRES 7 B 254 VAL SER ARG THR LEU CYS PRO SER GLU ALA THR ASN GLU SEQRES 8 B 254 THR GLY PRO LEU GLN GLN LEU ILE PHE VAL ASP VAL ALA SEQRES 9 B 254 SER MET ALA PRO LEU GLY ALA GLN TYR LYS LEU LEU VAL SEQRES 10 B 254 THR LYS LEU LYS HIS PHE GLN LEU ARG THR ASN VAL ALA SEQRES 11 B 254 PHE HIS PHE THR ALA SER PRO SER GLN PRO GLN TYR PHE SEQRES 12 B 254 LEU TYR LYS PHE PRO LYS ASP VAL ASP SER VAL ILE ILE SEQRES 13 B 254 LYS VAL VAL SER GLU MET ALA TYR PRO CYS SER VAL VAL SEQRES 14 B 254 SER VAL GLN ASN ILE MET CYS PRO VAL TYR ASP LEU ASP SEQRES 15 B 254 HIS ASN VAL GLU PHE ASN GLY VAL TYR GLN SER MET THR SEQRES 16 B 254 LYS LYS ALA ALA ILE THR LEU GLN LYS LYS ASP PHE PRO SEQRES 17 B 254 GLY GLU GLN PHE PHE VAL VAL PHE VAL ILE LYS PRO GLU SEQRES 18 B 254 ASP TYR ALA CYS GLY GLY SER PHE PHE ILE GLN GLU LYS SEQRES 19 B 254 GLU ASN GLN THR TRP ASN LEU GLN ARG LYS LYS ASN LEU SEQRES 20 B 254 GLU VAL THR ILE VAL PRO SER HET NAG A 401 14 HET NAG A 402 14 HET NAG A 403 14 HET NAG B 401 14 HET NAG B 402 14 HET NAG B 403 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 NAG 6(C8 H15 N O6) HELIX 1 AA1 LEU A 115 GLN A 117 5 3 HELIX 2 AA2 LYS A 251 PHE A 253 5 3 HELIX 3 AA3 LEU B 115 GLN B 117 5 3 HELIX 4 AA4 LYS B 251 PHE B 253 5 3 SHEET 1 AA1 4 HIS A 50 VAL A 56 0 SHEET 2 AA1 4 ALA A 157 LYS A 165 -1 O LEU A 161 N TYR A 52 SHEET 3 AA1 4 VAL A 78 ASN A 83 -1 N TYR A 81 O LEU A 162 SHEET 4 AA1 4 GLU A 124 THR A 128 -1 O VAL A 125 N VAL A 82 SHEET 1 AA2 4 ASN A 62 SER A 70 0 SHEET 2 AA2 4 LEU A 141 ALA A 150 -1 O ILE A 145 N PHE A 66 SHEET 3 AA2 4 VAL A 93 ARG A 98 -1 N ARG A 98 O PHE A 146 SHEET 4 AA2 4 VAL A 103 VAL A 108 -1 O LEU A 104 N VAL A 97 SHEET 1 AA3 3 LEU A 110 GLN A 113 0 SHEET 2 AA3 3 SER A 119 TYR A 122 -1 O TYR A 122 N LEU A 110 SHEET 3 AA3 3 ASN A 282 GLN A 283 1 O GLN A 283 N SER A 119 SHEET 1 AA4 4 PHE A 177 ALA A 181 0 SHEET 2 AA4 4 LYS A 291 PRO A 299 -1 O LYS A 291 N ALA A 181 SHEET 3 AA4 4 SER A 199 VAL A 205 -1 N LYS A 203 O THR A 296 SHEET 4 AA4 4 LYS A 243 GLN A 249 -1 O LEU A 248 N VAL A 200 SHEET 1 AA5 4 GLN A 187 LYS A 192 0 SHEET 2 AA5 4 GLN A 257 ILE A 264 -1 O VAL A 260 N PHE A 189 SHEET 3 AA5 4 SER A 213 ASN A 219 -1 N SER A 216 O VAL A 261 SHEET 4 AA5 4 VAL A 236 MET A 240 -1 O VAL A 236 N VAL A 217 SHEET 1 AA6 4 HIS B 50 VAL B 56 0 SHEET 2 AA6 4 ALA B 157 LYS B 165 -1 O LEU B 161 N TYR B 52 SHEET 3 AA6 4 VAL B 78 ASN B 83 -1 N TYR B 81 O LEU B 162 SHEET 4 AA6 4 GLU B 124 THR B 128 -1 O VAL B 125 N VAL B 82 SHEET 1 AA7 4 ASN B 62 SER B 70 0 SHEET 2 AA7 4 LEU B 141 ALA B 150 -1 O ILE B 145 N PHE B 66 SHEET 3 AA7 4 VAL B 93 ARG B 98 -1 N ARG B 98 O PHE B 146 SHEET 4 AA7 4 VAL B 103 VAL B 108 -1 O LEU B 104 N VAL B 97 SHEET 1 AA8 3 LEU B 110 GLN B 113 0 SHEET 2 AA8 3 SER B 119 TYR B 122 -1 O TYR B 122 N LEU B 110 SHEET 3 AA8 3 ASN B 282 GLN B 283 1 O GLN B 283 N SER B 119 SHEET 1 AA9 4 PHE B 177 ALA B 181 0 SHEET 2 AA9 4 LYS B 291 PRO B 299 -1 O LYS B 291 N ALA B 181 SHEET 3 AA9 4 SER B 199 VAL B 205 -1 N LYS B 203 O THR B 296 SHEET 4 AA9 4 LYS B 243 GLN B 249 -1 O LEU B 248 N VAL B 200 SHEET 1 AB1 4 GLN B 187 LYS B 192 0 SHEET 2 AB1 4 GLN B 257 ILE B 264 -1 O VAL B 260 N PHE B 189 SHEET 3 AB1 4 SER B 213 ASN B 219 -1 N SER B 216 O VAL B 261 SHEET 4 AB1 4 VAL B 236 MET B 240 -1 O VAL B 236 N VAL B 217 SSBOND 1 CYS A 130 CYS A 222 1555 1555 2.03 SSBOND 2 CYS A 212 CYS A 271 1555 1555 2.03 SSBOND 3 CYS B 130 CYS B 222 1555 1555 2.03 SSBOND 4 CYS B 212 CYS B 271 1555 1555 2.03 LINK ND2 ASN A 67 C1 NAG A 401 1555 1555 1.44 LINK ND2 ASN A 83 C1 NAG A 402 1555 1555 1.44 LINK ND2 ASN A 136 C1 NAG A 403 1555 1555 1.44 LINK ND2 ASN B 67 C1 NAG B 401 1555 1555 1.44 LINK ND2 ASN B 83 C1 NAG B 402 1555 1555 1.44 LINK ND2 ASN B 136 C1 NAG B 403 1555 1555 1.44 CISPEP 1 VAL A 108 PRO A 109 0 -1.00 CISPEP 2 TYR A 210 PRO A 211 0 4.41 CISPEP 3 CYS A 222 PRO A 223 0 16.15 CISPEP 4 VAL B 108 PRO B 109 0 -1.00 CISPEP 5 TYR B 210 PRO B 211 0 4.42 CISPEP 6 CYS B 222 PRO B 223 0 16.12 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