PDB Short entry for 5TCX HEADER CELL INVASION 16-SEP-16 5TCX TITLE CRYSTAL STRUCTURE OF HUMAN TETRASPANIN CD81 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD81 ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 26 KDA CELL SURFACE PROTEIN TAPA-1,TARGET OF THE COMPND 5 ANTIPROLIFERATIVE ANTIBODY 1,TETRASPANIN-28,TSPAN-28; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CD81, TAPA1, TSPAN28; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS TETRASPANIN, TRANSMEMBRANE, CHOLESTEROL, CELL INVASION EXPDTA X-RAY DIFFRACTION AUTHOR B.ZIMMERMAN,B.J.MCMILLAN,T.C.M.SEEGAR,A.C.KRUSE,S.C.BLACKLOW REVDAT 4 04-DEC-19 5TCX 1 REMARK REVDAT 3 27-SEP-17 5TCX 1 REMARK REVDAT 2 21-DEC-16 5TCX 1 JRNL REVDAT 1 09-NOV-16 5TCX 0 JRNL AUTH B.ZIMMERMAN,B.KELLY,B.J.MCMILLAN,T.C.SEEGAR,R.O.DROR, JRNL AUTH 2 A.C.KRUSE,S.C.BLACKLOW JRNL TITL CRYSTAL STRUCTURE OF A FULL-LENGTH HUMAN TETRASPANIN REVEALS JRNL TITL 2 A CHOLESTEROL-BINDING POCKET. JRNL REF CELL V. 167 1041 2016 JRNL REFN ISSN 1097-4172 JRNL PMID 27881302 JRNL DOI 10.1016/J.CELL.2016.09.056 REMARK 2 REMARK 2 RESOLUTION. 2.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 55.7 REMARK 3 NUMBER OF REFLECTIONS : 5006 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.270 REMARK 3 R VALUE (WORKING SET) : 0.267 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.650 REMARK 3 FREE R VALUE TEST SET COUNT : 533 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 36.7578 - 4.6879 0.96 1964 230 0.2542 0.2773 REMARK 3 2 4.6879 - 3.7221 0.65 1304 159 0.2628 0.2984 REMARK 3 3 3.7221 - 3.2519 0.40 795 100 0.3211 0.3528 REMARK 3 4 3.2519 - 2.9547 0.20 410 44 0.3636 0.3621 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.530 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 : 0.002 1664 REMARK 3 ANGLE : 0.589 2258 REMARK 3 CHIRALITY : 0.034 274 REMARK 3 PLANARITY : 0.001 269 REMARK 3 DIHEDRAL : 9.466 962 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 5TCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000217111. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 7.6-8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5006 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950 REMARK 200 RESOLUTION RANGE LOW (A) : 36.755 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.18000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.300 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: 1G8Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25-35% PEG300, AMMONIUM CITRATE REMARK 280 DIBASIC, TRIS, PH 8.0, LIPIDIC CUBIC PHASE, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 50.71500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.75500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.71500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.75500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ARG A 1 REMARK 465 GLY A 2 REMARK 465 VAL A 3 REMARK 465 GLU A 4 REMARK 465 GLY A 5 REMARK 465 ASP A 38 REMARK 465 PRO A 39 REMARK 465 GLN A 40 REMARK 465 THR A 41 REMARK 465 THR A 42 REMARK 465 ASN A 43 REMARK 465 LEU A 44 REMARK 465 LEU A 45 REMARK 465 TYR A 46 REMARK 465 LEU A 47 REMARK 465 GLU A 48 REMARK 465 LEU A 49 REMARK 465 GLY A 50 REMARK 465 ASP A 51 REMARK 465 LYS A 52 REMARK 465 PRO A 53 REMARK 465 ALA A 54 REMARK 465 GLU A 86 REMARK 465 SER A 87 REMARK 465 SER A 233 REMARK 465 SER A 234 REMARK 465 VAL A 235 REMARK 465 TYR A 236 REMARK 465 VAL A 237 REMARK 465 PRO A 238 REMARK 465 HIS A 239 REMARK 465 HIS A 240 REMARK 465 HIS A 241 REMARK 465 HIS A 242 REMARK 465 HIS A 243 REMARK 465 HIS A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 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 36 CZ NH1 NH2 REMARK 470 ILE A 230 CG1 CG2 CD1 REMARK 470 ASN A 232 CG OD1 ND2 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 LEU A 170 -81.58 -82.98 REMARK 500 SER A 177 -133.89 51.85 REMARK 500 SER A 199 -78.56 -88.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CLR A 301 DBREF 5TCX A 2 236 UNP P60033 CD81_HUMAN 2 236 SEQADV 5TCX ARG A 1 UNP P60033 EXPRESSION TAG SEQADV 5TCX SER A 6 UNP P60033 CYS 6 ENGINEERED MUTATION SEQADV 5TCX SER A 9 UNP P60033 CYS 9 ENGINEERED MUTATION SEQADV 5TCX SER A 227 UNP P60033 CYS 227 ENGINEERED MUTATION SEQADV 5TCX SER A 228 UNP P60033 CYS 228 ENGINEERED MUTATION SEQADV 5TCX VAL A 237 UNP P60033 EXPRESSION TAG SEQADV 5TCX PRO A 238 UNP P60033 EXPRESSION TAG SEQADV 5TCX HIS A 239 UNP P60033 EXPRESSION TAG SEQADV 5TCX HIS A 240 UNP P60033 EXPRESSION TAG SEQADV 5TCX HIS A 241 UNP P60033 EXPRESSION TAG SEQADV 5TCX HIS A 242 UNP P60033 EXPRESSION TAG SEQADV 5TCX HIS A 243 UNP P60033 EXPRESSION TAG SEQADV 5TCX HIS A 244 UNP P60033 EXPRESSION TAG SEQADV 5TCX HIS A 245 UNP P60033 EXPRESSION TAG SEQADV 5TCX HIS A 246 UNP P60033 EXPRESSION TAG SEQRES 1 A 246 ARG GLY VAL GLU GLY SER THR LYS SER ILE LYS TYR LEU SEQRES 2 A 246 LEU PHE VAL PHE ASN PHE VAL PHE TRP LEU ALA GLY GLY SEQRES 3 A 246 VAL ILE LEU GLY VAL ALA LEU TRP LEU ARG HIS ASP PRO SEQRES 4 A 246 GLN THR THR ASN LEU LEU TYR LEU GLU LEU GLY ASP LYS SEQRES 5 A 246 PRO ALA PRO ASN THR PHE TYR VAL GLY ILE TYR ILE LEU SEQRES 6 A 246 ILE ALA VAL GLY ALA VAL MET MET PHE VAL GLY PHE LEU SEQRES 7 A 246 GLY YCM TYR GLY ALA ILE GLN GLU SER GLN YCM LEU LEU SEQRES 8 A 246 GLY THR PHE PHE THR CYS LEU VAL ILE LEU PHE ALA CYS SEQRES 9 A 246 GLU VAL ALA ALA GLY ILE TRP GLY PHE VAL ASN LYS ASP SEQRES 10 A 246 GLN ILE ALA LYS ASP VAL LYS GLN PHE TYR ASP GLN ALA SEQRES 11 A 246 LEU GLN GLN ALA VAL VAL ASP ASP ASP ALA ASN ASN ALA SEQRES 12 A 246 LYS ALA VAL VAL LYS THR PHE HIS GLU THR LEU ASP CYS SEQRES 13 A 246 CYS GLY SER SER THR LEU THR ALA LEU THR THR SER VAL SEQRES 14 A 246 LEU LYS ASN ASN LEU CYS PRO SER GLY SER ASN ILE ILE SEQRES 15 A 246 SER ASN LEU PHE LYS GLU ASP CYS HIS GLN LYS ILE ASP SEQRES 16 A 246 ASP LEU PHE SER GLY LYS LEU TYR LEU ILE GLY ILE ALA SEQRES 17 A 246 ALA ILE VAL VAL ALA VAL ILE MET ILE PHE GLU MET ILE SEQRES 18 A 246 LEU SER MET VAL LEU SER SER GLY ILE ARG ASN SER SER SEQRES 19 A 246 VAL TYR VAL PRO HIS HIS HIS HIS HIS HIS HIS HIS MODRES 5TCX YCM A 80 CYS MODIFIED RESIDUE MODRES 5TCX YCM A 89 CYS MODIFIED RESIDUE HET YCM A 80 10 HET YCM A 89 10 HET CLR A 301 28 HETNAM YCM S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HETNAM CLR CHOLESTEROL HETSYN YCM CYSTEINE-S-ACETAMIDE FORMUL 1 YCM 2(C5 H10 N2 O3 S) FORMUL 2 CLR C27 H46 O FORMUL 3 HOH *3(H2 O) HELIX 1 AA1 SER A 9 HIS A 37 1 29 HELIX 2 AA2 ASN A 56 TYR A 81 1 26 HELIX 3 AA3 GLY A 82 GLN A 85 5 4 HELIX 4 AA4 YCM A 89 ASN A 115 1 27 HELIX 5 AA5 ASN A 115 ASP A 137 1 23 HELIX 6 AA6 ALA A 140 ASP A 155 1 16 HELIX 7 AA7 SER A 160 LEU A 170 1 11 HELIX 8 AA8 ILE A 181 LYS A 187 1 7 HELIX 9 AA9 ASP A 189 SER A 199 1 11 HELIX 10 AB1 LYS A 201 ARG A 231 1 31 SSBOND 1 CYS A 156 CYS A 190 1555 1555 2.03 SSBOND 2 CYS A 157 CYS A 175 1555 1555 2.03 LINK C GLY A 79 N YCM A 80 1555 1555 1.33 LINK C YCM A 80 N TYR A 81 1555 1555 1.33 LINK C GLN A 88 N YCM A 89 1555 1555 1.33 LINK C YCM A 89 N LEU A 90 1555 1555 1.33 SITE 1 AC1 10 ASN A 18 PHE A 21 VAL A 68 VAL A 71 SITE 2 AC1 10 MET A 72 VAL A 75 YCM A 89 LEU A 101 SITE 3 AC1 10 MET A 216 GLU A 219 CRYST1 101.430 73.510 70.350 90.00 125.11 90.00 C 1 2 1 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 0.009859 0.000000 0.006932 0.00000 SCALE2 0.000000 0.013604 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017377 0.00000