HEADER VIRAL PROTEIN 09-FEB-22 7WUS TITLE CRYOEM STRUCTURE OF A DIMER OF LOOSE SNS1 TETRAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: CORE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS 2; SOURCE 3 ORGANISM_TAXID: 11060; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS NS1 PROTEIN, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR B.SHU,S.M.LOK REVDAT 1 21-DEC-22 7WUS 0 JRNL AUTH B.SHU,J.S.G.OOI,A.W.K.TAN,T.S.NG,W.DEJNIRATTISAI, JRNL AUTH 2 J.MONGKOLSAPAYA,G.FIBRIANSAH,J.SHI,V.A.KOSTYUCHENKO, JRNL AUTH 3 G.R.SCREATON,S.M.LOK JRNL TITL CRYOEM STRUCTURES OF THE MULTIMERIC SECRETED NS1, A MAJOR JRNL TITL 2 FACTOR FOR DENGUE HEMORRHAGIC FEVER. JRNL REF NAT COMMUN V. 13 6756 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36347841 JRNL DOI 10.1038/S41467-022-34415-1 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERA, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 5GS6 REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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 : 181587 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 7WUS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1300027540. 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 : DENGUE NS1 DIMER OF LOOSE REMARK 245 TETRAMER REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.20 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 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) : 800.00 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) : 8150.00 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, 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 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 ASP A 23 -153.63 -80.21 REMARK 500 ASN A 24 32.44 80.36 REMARK 500 THR A 27 -10.57 72.96 REMARK 500 TRP A 28 173.85 177.98 REMARK 500 THR A 29 73.68 -101.62 REMARK 500 GLN A 31 70.13 58.14 REMARK 500 GLU A 37 -166.03 -78.55 REMARK 500 GLN A 107 67.96 36.35 REMARK 500 TYR A 158 -9.85 71.10 REMARK 500 THR A 164 -70.53 -64.78 REMARK 500 THR A 165 141.98 -172.15 REMARK 500 ASP A 190 -10.75 61.23 REMARK 500 ASN A 191 -25.04 -140.82 REMARK 500 PHE A 247 37.03 -99.57 REMARK 500 ASP B 23 -153.65 -80.12 REMARK 500 ASN B 24 32.51 80.35 REMARK 500 THR B 27 -10.60 72.96 REMARK 500 TRP B 28 173.85 178.00 REMARK 500 THR B 29 73.59 -101.55 REMARK 500 GLN B 31 70.13 58.12 REMARK 500 GLU B 37 -166.02 -78.52 REMARK 500 GLN B 107 67.98 36.32 REMARK 500 TYR B 158 -9.94 71.18 REMARK 500 THR B 164 -70.53 -64.79 REMARK 500 THR B 165 141.99 -172.11 REMARK 500 ASP B 190 -10.76 61.26 REMARK 500 ASN B 191 -25.06 -140.83 REMARK 500 PHE B 247 37.02 -99.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32840 RELATED DB: EMDB REMARK 900 NS1 DIMER OF LOOSE TETRAMER DBREF 7WUS A 1 341 UNP D3XNS4 D3XNS4_9FLAV 776 1116 DBREF 7WUS B 1 341 UNP D3XNS4 D3XNS4_9FLAV 776 1116 SEQRES 1 A 341 ASP SER GLY CYS VAL VAL SER TRP LYS ASN LYS GLU LEU SEQRES 2 A 341 LYS CYS GLY SER GLY ILE PHE ILE THR ASP ASN VAL HIS SEQRES 3 A 341 THR TRP THR GLU GLN TYR LYS PHE GLN PRO GLU SER PRO SEQRES 4 A 341 SER LYS LEU ALA SER ALA ILE GLN LYS ALA HIS GLU GLU SEQRES 5 A 341 GLY ILE CYS GLY ILE ARG SER VAL THR ARG LEU GLU ASN SEQRES 6 A 341 LEU MET TRP LYS GLN ILE THR PRO GLU LEU ASN HIS ILE SEQRES 7 A 341 LEU THR GLU ASN GLU VAL LYS LEU THR ILE MET THR GLY SEQRES 8 A 341 ASP ILE LYS GLY ILE MET GLN ALA GLY LYS ARG SER LEU SEQRES 9 A 341 ARG PRO GLN PRO THR GLU LEU LYS TYR SER TRP LYS ALA SEQRES 10 A 341 TRP GLY LYS ALA LYS MET LEU SER THR GLU LEU HIS ASN SEQRES 11 A 341 HIS THR PHE LEU ILE ASP GLY PRO GLU THR ALA GLU CYS SEQRES 12 A 341 PRO ASN THR ASN ARG ALA TRP ASN SER LEU GLU VAL GLU SEQRES 13 A 341 ASP TYR GLY PHE GLY VAL PHE THR THR ASN ILE TRP LEU SEQRES 14 A 341 LYS LEU LYS GLU ARG GLN ASP VAL PHE CYS ASP SER LYS SEQRES 15 A 341 LEU MET SER ALA ALA ILE LYS ASP ASN ARG ALA VAL HIS SEQRES 16 A 341 ALA ASP MET GLY TYR TRP ILE GLU SER ALA LEU ASN ASP SEQRES 17 A 341 THR TRP LYS ILE GLU LYS ALA SER PHE ILE GLU VAL LYS SEQRES 18 A 341 SER CYS HIS TRP PRO LYS SER HIS THR LEU TRP SER ASN SEQRES 19 A 341 GLY VAL LEU GLU SER GLU MET ILE ILE PRO LYS ASN PHE SEQRES 20 A 341 ALA GLY PRO VAL SER GLN HIS ASN TYR ARG PRO GLY TYR SEQRES 21 A 341 HIS THR GLN THR ALA GLY PRO TRP HIS LEU GLY ARG LEU SEQRES 22 A 341 GLU MET ASP PHE ASP PHE CYS GLU GLY THR THR VAL VAL SEQRES 23 A 341 VAL THR GLU ASP CYS GLY ASN ARG GLY PRO SER LEU ARG SEQRES 24 A 341 THR THR THR ALA SER GLY LYS LEU ILE THR GLU TRP CYS SEQRES 25 A 341 CYS ARG SER CYS THR LEU PRO PRO LEU ARG TYR ARG GLY SEQRES 26 A 341 GLU ASP GLY CYS TRP TYR GLY MET GLU ILE ARG PRO LEU SEQRES 27 A 341 LYS GLU LYS SEQRES 1 B 341 ASP SER GLY CYS VAL VAL SER TRP LYS ASN LYS GLU LEU SEQRES 2 B 341 LYS CYS GLY SER GLY ILE PHE ILE THR ASP ASN VAL HIS SEQRES 3 B 341 THR TRP THR GLU GLN TYR LYS PHE GLN PRO GLU SER PRO SEQRES 4 B 341 SER LYS LEU ALA SER ALA ILE GLN LYS ALA HIS GLU GLU SEQRES 5 B 341 GLY ILE CYS GLY ILE ARG SER VAL THR ARG LEU GLU ASN SEQRES 6 B 341 LEU MET TRP LYS GLN ILE THR PRO GLU LEU ASN HIS ILE SEQRES 7 B 341 LEU THR GLU ASN GLU VAL LYS LEU THR ILE MET THR GLY SEQRES 8 B 341 ASP ILE LYS GLY ILE MET GLN ALA GLY LYS ARG SER LEU SEQRES 9 B 341 ARG PRO GLN PRO THR GLU LEU LYS TYR SER TRP LYS ALA SEQRES 10 B 341 TRP GLY LYS ALA LYS MET LEU SER THR GLU LEU HIS ASN SEQRES 11 B 341 HIS THR PHE LEU ILE ASP GLY PRO GLU THR ALA GLU CYS SEQRES 12 B 341 PRO ASN THR ASN ARG ALA TRP ASN SER LEU GLU VAL GLU SEQRES 13 B 341 ASP TYR GLY PHE GLY VAL PHE THR THR ASN ILE TRP LEU SEQRES 14 B 341 LYS LEU LYS GLU ARG GLN ASP VAL PHE CYS ASP SER LYS SEQRES 15 B 341 LEU MET SER ALA ALA ILE LYS ASP ASN ARG ALA VAL HIS SEQRES 16 B 341 ALA ASP MET GLY TYR TRP ILE GLU SER ALA LEU ASN ASP SEQRES 17 B 341 THR TRP LYS ILE GLU LYS ALA SER PHE ILE GLU VAL LYS SEQRES 18 B 341 SER CYS HIS TRP PRO LYS SER HIS THR LEU TRP SER ASN SEQRES 19 B 341 GLY VAL LEU GLU SER GLU MET ILE ILE PRO LYS ASN PHE SEQRES 20 B 341 ALA GLY PRO VAL SER GLN HIS ASN TYR ARG PRO GLY TYR SEQRES 21 B 341 HIS THR GLN THR ALA GLY PRO TRP HIS LEU GLY ARG LEU SEQRES 22 B 341 GLU MET ASP PHE ASP PHE CYS GLU GLY THR THR VAL VAL SEQRES 23 B 341 VAL THR GLU ASP CYS GLY ASN ARG GLY PRO SER LEU ARG SEQRES 24 B 341 THR THR THR ALA SER GLY LYS LEU ILE THR GLU TRP CYS SEQRES 25 B 341 CYS ARG SER CYS THR LEU PRO PRO LEU ARG TYR ARG GLY SEQRES 26 B 341 GLU ASP GLY CYS TRP TYR GLY MET GLU ILE ARG PRO LEU SEQRES 27 B 341 LYS GLU LYS HELIX 1 AA1 SER A 38 HIS A 50 1 13 HELIX 2 AA2 GLU A 51 GLY A 53 5 3 HELIX 3 AA3 THR A 61 LYS A 69 1 9 HELIX 4 AA4 ILE A 71 ASN A 82 1 12 HELIX 5 AA5 PRO A 144 THR A 146 5 3 HELIX 6 AA6 PRO A 226 THR A 230 5 5 HELIX 7 AA7 PRO A 244 ALA A 248 5 5 HELIX 8 AA8 SER A 252 TYR A 256 5 5 HELIX 9 AA9 SER B 38 HIS B 50 1 13 HELIX 10 AB1 GLU B 51 GLY B 53 5 3 HELIX 11 AB2 THR B 61 LYS B 69 1 9 HELIX 12 AB3 ILE B 71 ASN B 82 1 12 HELIX 13 AB4 PRO B 144 THR B 146 5 3 HELIX 14 AB5 PRO B 226 THR B 230 5 5 HELIX 15 AB6 PRO B 244 ALA B 248 5 5 HELIX 16 AB7 SER B 252 TYR B 256 5 5 SHEET 1 AA1 4 GLU A 12 GLY A 16 0 SHEET 2 AA1 4 GLY A 3 SER A 7 -1 N SER A 7 O GLU A 12 SHEET 3 AA1 4 GLY B 3 SER B 7 -1 O CYS B 4 N CYS A 4 SHEET 4 AA1 4 GLU B 12 GLY B 16 -1 O GLU B 12 N SER B 7 SHEET 1 AA2 2 ILE A 19 ILE A 21 0 SHEET 2 AA2 2 ILE B 19 ILE B 21 -1 O ILE B 21 N ILE A 19 SHEET 1 AA3 3 PHE A 34 PRO A 36 0 SHEET 2 AA3 3 ILE A 167 LYS A 170 1 O LEU A 169 N GLN A 35 SHEET 3 AA3 3 GLU A 154 GLU A 156 -1 N GLU A 154 O LYS A 170 SHEET 1 AA4 4 THR A 87 MET A 89 0 SHEET 2 AA4 4 THR A 132 ILE A 135 1 O PHE A 133 N THR A 87 SHEET 3 AA4 4 GLY A 56 ILE A 57 1 N ILE A 57 O LEU A 134 SHEET 4 AA4 4 ARG A 148 ALA A 149 1 O ALA A 149 N GLY A 56 SHEET 1 AA510 LEU A 273 MET A 275 0 SHEET 2 AA510 TRP A 210 PHE A 217 -1 N ALA A 215 O MET A 275 SHEET 3 AA510 TRP A 201 LEU A 206 -1 N GLU A 203 O LYS A 214 SHEET 4 AA510 ARG A 192 ALA A 196 -1 N HIS A 195 O ILE A 202 SHEET 5 AA510 SER A 185 LYS A 189 -1 N SER A 185 O ALA A 196 SHEET 6 AA510 SER B 185 LYS B 189 -1 O ILE B 188 N ALA A 186 SHEET 7 AA510 ARG B 192 ALA B 196 -1 O ALA B 196 N SER B 185 SHEET 8 AA510 TRP B 201 LEU B 206 -1 O ILE B 202 N HIS B 195 SHEET 9 AA510 TRP B 210 PHE B 217 -1 O LYS B 214 N GLU B 203 SHEET 10 AA510 LEU B 273 MET B 275 -1 O MET B 275 N ALA B 215 SHEET 1 AA6 3 THR A 284 VAL A 287 0 SHEET 2 AA6 3 GLU A 310 CYS A 313 1 O TRP A 311 N VAL A 286 SHEET 3 AA6 3 ILE A 335 PRO A 337 -1 O ARG A 336 N CYS A 312 SHEET 1 AA7 2 ARG A 322 ARG A 324 0 SHEET 2 AA7 2 CYS A 329 TYR A 331 -1 O TRP A 330 N TYR A 323 SHEET 1 AA8 3 PHE B 34 PRO B 36 0 SHEET 2 AA8 3 ILE B 167 LYS B 170 1 O LEU B 169 N GLN B 35 SHEET 3 AA8 3 GLU B 154 GLU B 156 -1 N GLU B 154 O LYS B 170 SHEET 1 AA9 4 THR B 87 MET B 89 0 SHEET 2 AA9 4 THR B 132 ILE B 135 1 O PHE B 133 N THR B 87 SHEET 3 AA9 4 GLY B 56 ILE B 57 1 N ILE B 57 O LEU B 134 SHEET 4 AA9 4 ARG B 148 ALA B 149 1 O ALA B 149 N GLY B 56 SHEET 1 AB1 3 THR B 284 VAL B 287 0 SHEET 2 AB1 3 GLU B 310 CYS B 313 1 O TRP B 311 N VAL B 286 SHEET 3 AB1 3 ILE B 335 PRO B 337 -1 O ARG B 336 N CYS B 312 SHEET 1 AB2 2 ARG B 322 ARG B 324 0 SHEET 2 AB2 2 CYS B 329 TYR B 331 -1 O TRP B 330 N TYR B 323 SSBOND 1 CYS A 4 CYS A 15 1555 1555 2.03 SSBOND 2 CYS A 55 CYS A 143 1555 1555 2.03 SSBOND 3 CYS A 179 CYS A 223 1555 1555 2.03 SSBOND 4 CYS A 280 CYS A 329 1555 1555 2.03 SSBOND 5 CYS A 291 CYS A 312 1555 1555 2.03 SSBOND 6 CYS A 313 CYS A 316 1555 1555 2.03 SSBOND 7 CYS B 4 CYS B 15 1555 1555 2.03 SSBOND 8 CYS B 55 CYS B 143 1555 1555 2.03 SSBOND 9 CYS B 179 CYS B 223 1555 1555 2.03 SSBOND 10 CYS B 280 CYS B 329 1555 1555 2.03 SSBOND 11 CYS B 291 CYS B 312 1555 1555 2.03 SSBOND 12 CYS B 313 CYS B 316 1555 1555 2.03 CISPEP 1 TYR A 32 LYS A 33 0 -3.56 CISPEP 2 GLY A 95 ILE A 96 0 0.96 CISPEP 3 PRO A 106 GLN A 107 0 3.00 CISPEP 4 GLY A 161 VAL A 162 0 6.90 CISPEP 5 VAL A 162 PHE A 163 0 1.67 CISPEP 6 LEU A 318 PRO A 319 0 -3.95 CISPEP 7 TYR B 32 LYS B 33 0 -3.67 CISPEP 8 GLY B 95 ILE B 96 0 0.98 CISPEP 9 PRO B 106 GLN B 107 0 3.06 CISPEP 10 GLY B 161 VAL B 162 0 6.98 CISPEP 11 VAL B 162 PHE B 163 0 1.64 CISPEP 12 LEU B 318 PRO B 319 0 -3.89 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