HEADER CELL ADHESION 14-OCT-14 3X0G TITLE CRYSTAL STRUCTURE OF THE ECTODOMAIN OF AFRICAN GREEN MONKEY CD81 LARGE TITLE 2 EXTRACELLULAR LOOP (AGMCD81-LEL) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD81; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LARGE EXTRACELLULAR LOOP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHLOROCEBUS SABAEUS; SOURCE 3 ORGANISM_TAXID: 60711; SOURCE 4 GENE: CD81; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS DISULFIDE BOND, HELICAL BUNDLE, IMMUNE CELL ADHESION, MORPHOLOGY, KEYWDS 2 ACTIVATION, PROLIFERATION, DIFFERENTIATION, MEMBRANE, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR M.ZHANG,S.CUI REVDAT 4 08-NOV-23 3X0G 1 REMARK REVDAT 3 24-AUG-22 3X0G 1 JRNL REMARK REVDAT 2 08-JUL-15 3X0G 1 JRNL REVDAT 1 01-JUL-15 3X0G 0 JRNL AUTH W.YANG,M.ZHANG,X.CHI,X.LIU,B.QIN,S.CUI JRNL TITL AN INTRAMOLECULAR BOND AT CLUSTER OF DIFFERENTIATION 81 JRNL TITL 2 ECTODOMAIN IS IMPORTANT FOR HEPATITIS C VIRUS ENTRY. JRNL REF FASEB J. V. 29 4214 2015 JRNL REFN ESSN 1530-6860 JRNL PMID 26116703 JRNL DOI 10.1096/FJ.15-272880 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 7565 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.590 REMARK 3 FREE R VALUE TEST SET COUNT : 347 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 25.2780 - 2.3928 1.00 3778 190 0.2271 0.2485 REMARK 3 2 2.3928 - 1.8995 0.94 3440 157 0.2419 0.2711 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 33.59 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.05330 REMARK 3 B22 (A**2) : 0.83440 REMARK 3 B33 (A**2) : 4.21890 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.009 751 REMARK 3 ANGLE : 1.163 1012 REMARK 3 CHIRALITY : 0.065 120 REMARK 3 PLANARITY : 0.004 127 REMARK 3 DIHEDRAL : 17.478 270 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 3X0G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000097022. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS PACKAGE REMARK 200 DATA SCALING SOFTWARE : XDS PACKAGE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7580 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.899 REMARK 200 RESOLUTION RANGE LOW (A) : 27.878 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 5.930 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.52 REMARK 200 R MERGE FOR SHELL (I) : 0.48500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.420 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: 4BKH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% ETHANOL, 5% MPD, 0.1M TRIS PH 8.5, REMARK 280 200MM SODIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 19.57800 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.95750 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 19.57800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.95750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -94.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 39.15600 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 138 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O4 MPD A 301 HO2 MPD A 303 1.36 REMARK 500 O HOH A 422 O HOH A 430 1.93 REMARK 500 O HOH A 444 O HOH A 455 1.95 REMARK 500 O HOH A 445 O HOH A 447 2.12 REMARK 500 O4 MPD A 301 O2 MPD A 303 2.19 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 MPD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G8Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CD81 EXTRACELLULAR DOMAIN REMARK 900 RELATED ID: 1IV5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CD81 EXTRACELLULAR DOMAIN REMARK 900 RELATED ID: 3X0E RELATED DB: PDB REMARK 900 RELATED ID: 3X0F RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT REMARK 999 KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. DBREF 3X0G A 110 202 PDB 3X0G 3X0G 110 202 SEQRES 1 A 93 SER HIS MET PHE VAL ASN LYS ASP GLN ILE ALA LYS ASP SEQRES 2 A 93 VAL LYS GLN PHE TYR ASP GLN ALA LEU GLN GLN ALA VAL SEQRES 3 A 93 VAL ASP ASP ASP ALA ASN ASN ALA LYS ALA VAL VAL LYS SEQRES 4 A 93 THR PHE HIS GLU THR VAL ASP CYS CYS GLY SER SER THR SEQRES 5 A 93 LEU ALA ALA LEU THR THR SER VAL LEU LYS ASN ASN LEU SEQRES 6 A 93 CYS PRO SER GLY SER ASN ILE ILE SER ASN LEU LEU LYS SEQRES 7 A 93 LYS ASP CYS HIS GLN LYS ILE ASP ASP PHE PHE SER GLY SEQRES 8 A 93 LYS LEU HET MPD A 301 22 HET MPD A 302 22 HET MPD A 303 22 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 MPD 3(C6 H14 O2) FORMUL 5 HOH *56(H2 O) HELIX 1 1 ASN A 115 ASP A 137 1 23 HELIX 2 2 ALA A 140 ASP A 155 1 16 HELIX 3 3 LEU A 165 ASN A 172 1 8 HELIX 4 4 ILE A 182 LYS A 187 5 6 HELIX 5 5 ASP A 189 GLY A 200 1 12 SSBOND 1 CYS A 156 CYS A 190 1555 1555 2.03 SSBOND 2 CYS A 157 CYS A 175 1555 1555 2.01 SITE 1 AC1 6 VAL A 154 ILE A 194 PHE A 197 PHE A 198 SITE 2 AC1 6 MPD A 302 MPD A 303 SITE 1 AC2 7 PHE A 126 PHE A 150 VAL A 154 LEU A 185 SITE 2 AC2 7 MPD A 301 MPD A 303 HOH A 456 SITE 1 AC3 4 VAL A 123 PHE A 150 MPD A 301 MPD A 302 CRYST1 39.156 39.700 59.915 90.00 90.00 90.00 P 21 2 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 0.025539 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025189 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016690 0.00000