HEADER CYTOSOLIC PROTEIN 27-JAN-21 7E0B TITLE THE CRYSTAL STRUCTURE OF SORTING NEXIN 27 AND PBM COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTING NEXIN-27; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PBM; COMPND 7 CHAIN: B; COMPND 8 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: SNX27, KIAA0488, MY014; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS SORTING NEXIN 27, CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.J.SHANG,J.X.QI REVDAT 3 29-NOV-23 7E0B 1 REMARK REVDAT 2 15-FEB-23 7E0B 1 JRNL REVDAT 1 02-FEB-22 7E0B 0 JRNL AUTH B.YANG,Y.JIA,Y.MENG,Y.XUE,K.LIU,Y.LI,S.LIU,X.LI,K.CUI, JRNL AUTH 2 L.SHANG,T.CHENG,Z.ZHANG,Y.HOU,X.YANG,H.YAN,L.DUAN,Z.TONG, JRNL AUTH 3 C.WU,Z.LIU,S.GAO,S.ZHUO,W.HUANG,G.F.GAO,J.QI,G.SHANG JRNL TITL SNX27 SUPPRESSES SARS-COV-2 INFECTION BY INHIBITING VIRAL JRNL TITL 2 LYSOSOME/LATE ENDOSOME ENTRY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 35022217 JRNL DOI 10.1073/PNAS.2117576119 REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 30746 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1507 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 20.8200 - 2.8700 1.00 2756 137 0.1676 0.1749 REMARK 3 2 2.8700 - 2.2800 1.00 2749 135 0.1875 0.1761 REMARK 3 3 2.2800 - 1.9900 1.00 2766 146 0.1735 0.1847 REMARK 3 4 1.9900 - 1.8100 1.00 2735 156 0.1831 0.2009 REMARK 3 5 1.8100 - 1.6800 1.00 2697 165 0.1861 0.1918 REMARK 3 6 1.6800 - 1.5800 1.00 2761 124 0.1873 0.1956 REMARK 3 7 1.5800 - 1.5000 1.00 2768 125 0.1916 0.2127 REMARK 3 8 1.5000 - 1.4300 0.98 2684 143 0.2138 0.2407 REMARK 3 9 1.4300 - 1.3800 0.97 2696 132 0.2487 0.2589 REMARK 3 10 1.3800 - 1.3300 0.93 2501 137 0.3202 0.3291 REMARK 3 11 1.3300 - 1.2900 0.76 2126 107 0.4146 0.4420 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) : 0.172 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.00 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 : 0.003 806 REMARK 3 ANGLE : 0.544 1091 REMARK 3 CHIRALITY : 0.464 126 REMARK 3 PLANARITY : 0.004 146 REMARK 3 DIHEDRAL : 22.898 308 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 16.2904 -3.5893 -5.1926 REMARK 3 T TENSOR REMARK 3 T11: 0.1711 T22: 0.1788 REMARK 3 T33: 0.1726 T12: 0.0001 REMARK 3 T13: -0.0044 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 2.0184 L22: 0.6863 REMARK 3 L33: 1.0377 L12: -0.2915 REMARK 3 L13: -0.7356 L23: -0.0089 REMARK 3 S TENSOR REMARK 3 S11: -0.0326 S12: 0.0200 S13: -0.0770 REMARK 3 S21: -0.0394 S22: -0.0161 S23: -0.0075 REMARK 3 S31: 0.0219 S32: -0.0096 S33: 0.0000 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 7E0B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020531. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30746 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 22.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 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: 4Z8J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM SULFATE, 20 % W/V PEG REMARK 280 3350., PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.27500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.56218 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.42333 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 44.27500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 25.56218 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.42333 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 44.27500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 25.56218 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 14.42333 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.12437 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 28.84667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 51.12437 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 28.84667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 51.12437 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 28.84667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL 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 GLU A 125 73.43 58.37 REMARK 500 LYS A 126 0.04 85.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 308 DISTANCE = 5.88 ANGSTROMS DBREF 7E0B A 40 135 UNP Q96L92 SNX27_HUMAN 40 135 DBREF 7E0B B 201 207 PDB 7E0B 7E0B 201 207 SEQRES 1 A 96 GLY PRO ARG VAL VAL ARG ILE VAL LYS SER GLU SER GLY SEQRES 2 A 96 TYR GLY PHE ASN VAL ARG GLY GLN VAL SER GLU GLY GLY SEQRES 3 A 96 GLN LEU ARG SER ILE ASN GLY GLU LEU TYR ALA PRO LEU SEQRES 4 A 96 GLN HIS VAL SER ALA VAL LEU PRO GLY GLY ALA ALA ASP SEQRES 5 A 96 ARG ALA GLY VAL ARG LYS GLY ASP ARG ILE LEU GLU VAL SEQRES 6 A 96 ASN HIS VAL ASN VAL GLU GLY ALA THR HIS LYS GLN VAL SEQRES 7 A 96 VAL ASP LEU ILE ARG ALA GLY GLU LYS GLU LEU ILE LEU SEQRES 8 A 96 THR VAL LEU SER VAL SEQRES 1 B 7 ASP ASP VAL GLN THR SER PHE FORMUL 3 HOH *122(H2 O) HELIX 1 AA1 GLY A 88 GLY A 94 1 7 HELIX 2 AA2 THR A 113 ALA A 123 1 11 SHEET 1 AA1 4 ARG A 42 VAL A 47 0 SHEET 2 AA1 4 GLU A 127 LEU A 133 -1 O LEU A 128 N ILE A 46 SHEET 3 AA1 4 ARG A 100 VAL A 104 -1 N LEU A 102 O THR A 131 SHEET 4 AA1 4 VAL A 107 ASN A 108 -1 O VAL A 107 N VAL A 104 SHEET 1 AA2 3 HIS A 80 VAL A 84 0 SHEET 2 AA2 3 PHE A 55 GLN A 60 -1 N ARG A 58 O HIS A 80 SHEET 3 AA2 3 ASP B 202 PHE B 207 -1 O PHE B 207 N PHE A 55 SHEET 1 AA3 2 ARG A 68 ILE A 70 0 SHEET 2 AA3 2 GLU A 73 TYR A 75 -1 O GLU A 73 N ILE A 70 CRYST1 88.550 88.550 43.270 90.00 90.00 120.00 H 3 9 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 0.011293 0.006520 0.000000 0.00000 SCALE2 0.000000 0.013040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023111 0.00000