HEADER TRANSPORT PROTEIN 14-DEC-22 8HQW TITLE THE COMPLEX STRUCTURE OF COPI CARGO SORTING MODULE WITH MHV SPIKE HXX TITLE 2 SORTING MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: COATOMER SUBUNIT BETA',MHV SPIKE HXX SORTING MOTIF; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN YJM789), SOURCE 3 MURINE HEPATITIS VIRUS; SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 307796, 11138; SOURCE 6 GENE: SEC27, SCY_1929; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MHV, SPIKE, COPI VESICLE, HXX MOTIF, RETENTION SIGNAL, FUSION KEYWDS 2 PROTEIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.F.MA,Y.N.NAN,M.R.YANG,Y.Q.LI REVDAT 1 20-DEC-23 8HQW 0 JRNL AUTH Y.Q.LI,M.R.YANG,Y.N.NAN,J.M.WANG,J.J.GUO,P.F.HE,W.X.DAI, JRNL AUTH 2 S.Q.ZHOU,S.J.WANG,Y.ZHANG,W.F.MA JRNL TITL TIGHTER ER RETENTION OF SARS-COV-2 OMICRON SPIKE CAUSED BY A JRNL TITL 2 CONSTELLATION OF FOLDING DISRUPTIVE MUTATIONS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16.3349 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 54115 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.710 REMARK 3 FREE R VALUE TEST SET COUNT : 2010 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 25.3790 - 3.3838 1.00 4129 161 0.1533 0.1664 REMARK 3 2 3.3838 - 2.6868 1.00 3936 151 0.1629 0.1750 REMARK 3 3 2.6868 - 2.3475 0.99 3904 153 0.1585 0.1916 REMARK 3 4 2.3475 - 2.1330 0.99 3848 148 0.1432 0.1946 REMARK 3 5 2.1330 - 1.9801 0.99 3862 149 0.1343 0.1802 REMARK 3 6 1.9801 - 1.8634 0.99 3793 150 0.1411 0.2432 REMARK 3 7 1.8634 - 1.7701 0.97 3766 147 0.1439 0.2197 REMARK 3 8 1.7701 - 1.6931 0.98 3771 135 0.1559 0.2147 REMARK 3 9 1.6931 - 1.6279 0.98 3745 146 0.1551 0.2284 REMARK 3 10 1.6279 - 1.5718 0.97 3738 143 0.1622 0.2249 REMARK 3 11 1.5718 - 1.5226 0.95 3651 150 0.1818 0.2629 REMARK 3 12 1.5226 - 1.4791 0.94 3611 126 0.1995 0.2349 REMARK 3 13 1.4791 - 1.4402 0.88 3371 131 0.2291 0.2883 REMARK 3 14 1.4402 - 1.4050 0.78 2980 120 0.2474 0.3005 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2539 REMARK 3 ANGLE : 0.979 3466 REMARK 3 CHIRALITY : 0.098 385 REMARK 3 PLANARITY : 0.007 440 REMARK 3 DIHEDRAL : 16.922 888 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8HQW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 20-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300034159. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54115 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M CACL2, 0.1 M TRIS-HCL, PH 8.5, REMARK 280 EVAPORATION, TEMPERATURE 281.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 21.34450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.84550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.95050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.84550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.34450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.95050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 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 LYS A 7 CG CD CE NZ REMARK 470 ARG A 78 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 140 CG CD OE1 OE2 REMARK 470 ARG A 185 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 191 CG OD1 OD2 REMARK 470 GLU A 271 CG CD OE1 OE2 REMARK 470 PRO A 280 CG CD REMARK 470 THR A 281 OG1 CG2 REMARK 470 ARG A 283 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 284 CG CD CE NZ REMARK 470 ILE A 306 CG1 CG2 CD1 REMARK 470 SER A 307 OG 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 ILE A 64 76.56 -118.03 REMARK 500 PHE A 77 2.61 84.73 REMARK 500 PRO A 97 32.57 -82.30 REMARK 500 LEU A 119 2.51 85.16 REMARK 500 ASP A 152 80.99 -159.24 REMARK 500 LEU A 208 5.15 82.04 REMARK 500 GLU A 271 -144.20 68.77 REMARK 500 LYS A 284 18.98 53.23 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HQW A 1 301 UNP A6ZU46 A6ZU46_YEAS7 1 301 DBREF 8HQW A 302 311 PDB 8HQW 8HQW 302 311 SEQRES 1 A 311 MET LYS LEU ASP ILE LYS LYS THR PHE SER ASN ARG SER SEQRES 2 A 311 ASP ARG VAL LYS GLY ILE ASP PHE HIS PRO THR GLU PRO SEQRES 3 A 311 TRP VAL LEU THR THR LEU TYR SER GLY ARG VAL GLU ILE SEQRES 4 A 311 TRP ASN TYR GLU THR GLN VAL GLU VAL ARG SER ILE GLN SEQRES 5 A 311 VAL THR GLU THR PRO VAL ARG ALA GLY LYS PHE ILE ALA SEQRES 6 A 311 ARG LYS ASN TRP ILE ILE VAL GLY SER ASP ASP PHE ARG SEQRES 7 A 311 ILE ARG VAL PHE ASN TYR ASN THR GLY GLU LYS VAL VAL SEQRES 8 A 311 ASP PHE GLU ALA HIS PRO ASP TYR ILE ARG SER ILE ALA SEQRES 9 A 311 VAL HIS PRO THR LYS PRO TYR VAL LEU SER GLY SER ASP SEQRES 10 A 311 ASP LEU THR VAL LYS LEU TRP ASN TRP GLU ASN ASN TRP SEQRES 11 A 311 ALA LEU GLU GLN THR PHE GLU GLY HIS GLU HIS PHE VAL SEQRES 12 A 311 MET CYS VAL ALA PHE ASN PRO LYS ASP PRO SER THR PHE SEQRES 13 A 311 ALA SER GLY CYS LEU ASP ARG THR VAL LYS VAL TRP SER SEQRES 14 A 311 LEU GLY GLN SER THR PRO ASN PHE THR LEU THR THR GLY SEQRES 15 A 311 GLN GLU ARG GLY VAL ASN TYR VAL ASP TYR TYR PRO LEU SEQRES 16 A 311 PRO ASP LYS PRO TYR MET ILE THR ALA SER ASP ASP LEU SEQRES 17 A 311 THR ILE LYS ILE TRP ASP TYR GLN THR LYS SER CYS VAL SEQRES 18 A 311 ALA THR LEU GLU GLY HIS MET SER ASN VAL SER PHE ALA SEQRES 19 A 311 VAL PHE HIS PRO THR LEU PRO ILE ILE ILE SER GLY SER SEQRES 20 A 311 GLU ASP GLY THR LEU LYS ILE TRP ASN SER SER THR TYR SEQRES 21 A 311 LYS VAL GLU LYS THR LEU ASN VAL GLY LEU GLU ARG SER SEQRES 22 A 311 TRP CYS ILE ALA THR HIS PRO THR GLY ARG LYS ASN TYR SEQRES 23 A 311 ILE ALA SER GLY PHE ASP ASN GLY PHE THR VAL LEU SER SEQRES 24 A 311 LEU GLY VAL ILE HIS ASN ILE SER SER HIS GLU ASP FORMUL 2 HOH *308(H2 O) HELIX 1 AA1 ALA A 65 LYS A 67 5 3 HELIX 2 AA2 GLU A 127 ASN A 129 5 3 HELIX 3 AA3 GLY A 282 ASN A 285 5 4 SHEET 1 AA1 4 LYS A 6 ARG A 12 0 SHEET 2 AA1 4 GLY A 294 SER A 299 -1 O VAL A 297 N PHE A 9 SHEET 3 AA1 4 ILE A 287 PHE A 291 -1 N PHE A 291 O GLY A 294 SHEET 4 AA1 4 SER A 273 THR A 278 -1 N TRP A 274 O GLY A 290 SHEET 1 AA2 4 VAL A 16 PHE A 21 0 SHEET 2 AA2 4 TRP A 27 LEU A 32 -1 O LEU A 29 N ASP A 20 SHEET 3 AA2 4 ARG A 36 ASN A 41 -1 O GLU A 38 N THR A 30 SHEET 4 AA2 4 VAL A 46 GLN A 52 -1 O VAL A 46 N ASN A 41 SHEET 1 AA3 4 VAL A 58 ILE A 64 0 SHEET 2 AA3 4 TRP A 69 SER A 74 -1 O TRP A 69 N ILE A 64 SHEET 3 AA3 4 ARG A 78 ASN A 83 -1 O ARG A 80 N VAL A 72 SHEET 4 AA3 4 LYS A 89 GLU A 94 -1 O PHE A 93 N ILE A 79 SHEET 1 AA4 4 ILE A 100 VAL A 105 0 SHEET 2 AA4 4 TYR A 111 SER A 116 -1 O LEU A 113 N ALA A 104 SHEET 3 AA4 4 VAL A 121 ASN A 125 -1 O TRP A 124 N VAL A 112 SHEET 4 AA4 4 LEU A 132 PHE A 136 -1 O PHE A 136 N VAL A 121 SHEET 1 AA5 4 VAL A 143 PHE A 148 0 SHEET 2 AA5 4 THR A 155 CYS A 160 -1 O ALA A 157 N ALA A 147 SHEET 3 AA5 4 THR A 164 SER A 169 -1 O TRP A 168 N PHE A 156 SHEET 4 AA5 4 PHE A 177 THR A 180 -1 O LEU A 179 N VAL A 165 SHEET 1 AA6 4 VAL A 187 TYR A 192 0 SHEET 2 AA6 4 TYR A 200 SER A 205 -1 O ALA A 204 N ASN A 188 SHEET 3 AA6 4 THR A 209 ASP A 214 -1 O TRP A 213 N MET A 201 SHEET 4 AA6 4 SER A 219 GLU A 225 -1 O LEU A 224 N ILE A 210 SHEET 1 AA7 4 VAL A 231 PHE A 236 0 SHEET 2 AA7 4 ILE A 242 SER A 247 -1 O ILE A 244 N VAL A 235 SHEET 3 AA7 4 LEU A 252 ASN A 256 -1 O TRP A 255 N ILE A 243 SHEET 4 AA7 4 VAL A 262 LEU A 266 -1 O GLU A 263 N ILE A 254 CRYST1 42.689 79.901 83.691 90.00 90.00 90.00 P 21 21 21 4 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 0.023425 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012515 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011949 0.00000