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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
