HEADER IMMUNE SYSTEM 11-JUN-02 1M05 TITLE HLA B8 IN COMPLEX WITH AN EPSTEIN BARR VIRUS DETERMINANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-8 B*0801 ALPHA COMPND 3 CHAIN; COMPND 4 CHAIN: A, C; COMPND 5 FRAGMENT: RESIDUES 25-301; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: TRUNCATION MUTANT; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 10 CHAIN: B, D; COMPND 11 FRAGMENT: RESIDUES 21-119; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: EBNA-3 NUCLEAR PROTEIN; COMPND 15 CHAIN: E, F; COMPND 16 FRAGMENT: RESIDUES 193-201; COMPND 17 SYNONYM: EBNA-3A; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 16 OF THE PROTEIN IS NATURALLY FOUND IN EPSTEIN-BARR VIRUS. KEYWDS MHC CLASS I, HLA B8, EPSTEIN BARR VIRUS, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR L.KJER-NIELSEN,C.S.CLEMENTS,A.G.BROOKS,A.W.PURCELL,M.R.FONTES, AUTHOR 2 J.MCCLUSKEY,J.ROSSJOHN REVDAT 3 11-OCT-17 1M05 1 REMARK REVDAT 2 24-FEB-09 1M05 1 VERSN REVDAT 1 02-SEP-03 1M05 0 JRNL AUTH L.KJER-NIELSEN,C.S.CLEMENTS,A.G.BROOKS,A.W.PURCELL, JRNL AUTH 2 M.R.FONTES,J.MCCLUSKEY,J.ROSSJOHN JRNL TITL THE STRUCTURE OF HLA-B8 COMPLEXED TO AN IMMUNODOMINANT VIRAL JRNL TITL 2 DETERMINANT: PEPTIDE-INDUCED CONFORMATIONAL CHANGES AND A JRNL TITL 3 MODE OF MHC CLASS I DIMERIZATION. JRNL REF J.IMMUNOL. V. 169 5153 2003 JRNL REFN ISSN 0022-1767 JRNL PMID 12391232 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 73057 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3040 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6190 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 794 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1M05 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000016432. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76165 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1AGB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP 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 42.70000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.65000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.05000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.65000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.70000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.05000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: HLA B8 IS A HETERODIMERIC RECEPTOR 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, F 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 ALA A 41 REMARK 465 SER A 42 REMARK 465 PRO A 43 REMARK 465 ARG A 44 REMARK 465 GLU A 45 REMARK 465 GLU A 46 REMARK 465 PRO A 47 REMARK 465 ARG A 48 REMARK 465 ALA C 41 REMARK 465 SER C 42 REMARK 465 PRO C 43 REMARK 465 ARG C 44 REMARK 465 GLU C 45 REMARK 465 GLU C 46 REMARK 465 PRO C 47 REMARK 465 ARG C 48 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 C 268 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 425 O HOH C 477 1545 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 276 C - N - CA ANGL. DEV. = 19.7 DEGREES REMARK 500 PRO A 276 C - N - CD ANGL. DEV. = -32.2 DEGREES REMARK 500 ASP C 177 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP C 177 CB - CG - OD2 ANGL. DEV. = -7.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 29 -126.10 58.11 REMARK 500 ASN A 114 98.26 -170.65 REMARK 500 GLU A 180 29.10 -76.37 REMARK 500 HIS A 188 144.03 -170.32 REMARK 500 SER A 195 -169.14 -175.26 REMARK 500 GLN A 224 34.64 -88.23 REMARK 500 THR A 225 -34.97 -35.93 REMARK 500 ARG A 239 -16.71 71.20 REMARK 500 LYS A 243 149.23 -174.76 REMARK 500 GLU A 253 44.81 -90.13 REMARK 500 GLU A 275 155.22 178.73 REMARK 500 TRP B 60 -14.79 78.58 REMARK 500 ASP C 29 -122.97 57.71 REMARK 500 ASN C 114 98.73 -166.08 REMARK 500 GLU C 180 46.98 -84.17 REMARK 500 SER C 195 -156.76 -162.81 REMARK 500 GLN C 224 42.68 -91.00 REMARK 500 ARG C 239 -19.46 80.94 REMARK 500 TRP C 274 174.63 -59.42 REMARK 500 GLU C 275 76.03 -162.78 REMARK 500 TRP D 60 -7.75 76.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 101 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 38 OD1 REMARK 620 2 GLU B 36 OE2 147.0 REMARK 620 3 ASP B 38 OD2 51.1 97.0 REMARK 620 4 GLU C 19 OE2 86.0 99.6 109.1 REMARK 620 5 GLU C 19 OE1 89.8 119.4 140.1 52.4 REMARK 620 6 HOH C 278 O 96.8 95.0 96.6 148.4 96.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD D 101 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU D 36 OE2 REMARK 620 2 ASP D 38 OD1 146.6 REMARK 620 3 ASP D 38 OD2 95.6 51.4 REMARK 620 4 GLU A 19 OE2 103.9 85.0 107.4 REMARK 620 5 HOH A 278 O 95.6 93.8 97.7 146.2 REMARK 620 6 GLU A 19 OE1 123.4 87.2 136.9 50.1 96.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD D 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AGE RELATED DB: PDB REMARK 900 HLA B8 IN COMPLEX WITH A GAG PEPTIDE (FROM HIV) REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO THE AUTHOR, THIS IS A SITE REMARK 999 OF POLYMORPHISM IN THE EBNA 3 ANTIGEN. THE REMARK 999 9-MER PEPTIDE THAT WAS SYNTHESIZED HAD LEU REMARK 999 IN THE 9TH POSITION. DBREF 1M05 A 1 277 UNP P30460 1B08_HUMAN 25 301 DBREF 1M05 B 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 1M05 C 1 277 UNP P30460 1B08_HUMAN 25 301 DBREF 1M05 D 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 1M05 E 1 9 UNP P12977 EBN3_EBV 193 200 DBREF 1M05 F 1 9 UNP P12977 EBN3_EBV 193 200 SEQADV 1M05 LEU E 9 UNP P12977 ILE 201 SEE REMARK 999 SEQADV 1M05 LEU F 9 UNP P12977 ILE 201 SEE REMARK 999 SEQRES 1 A 277 GLY SER HIS SER MET ARG TYR PHE ASP THR ALA MET SER SEQRES 2 A 277 ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE SER VAL GLY SEQRES 3 A 277 TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER ASP SEQRES 4 A 277 ALA ALA SER PRO ARG GLU GLU PRO ARG ALA PRO TRP ILE SEQRES 5 A 277 GLU GLN GLU GLY PRO GLU TYR TRP ASP ARG ASN THR GLN SEQRES 6 A 277 ILE PHE LYS THR ASN THR GLN THR ASP ARG GLU SER LEU SEQRES 7 A 277 ARG ASN LEU ARG GLY TYR TYR ASN GLN SER GLU ALA GLY SEQRES 8 A 277 SER HIS THR LEU GLN SER MET TYR GLY CYS ASP VAL GLY SEQRES 9 A 277 PRO ASP GLY ARG LEU LEU ARG GLY HIS ASN GLN TYR ALA SEQRES 10 A 277 TYR ASP GLY LYS ASP TYR ILE ALA LEU ASN GLU ASP LEU SEQRES 11 A 277 ARG SER TRP THR ALA ALA ASP THR ALA ALA GLN ILE THR SEQRES 12 A 277 GLN ARG LYS TRP GLU ALA ALA ARG VAL ALA GLU GLN ASP SEQRES 13 A 277 ARG ALA TYR LEU GLU GLY THR CYS VAL GLU TRP LEU ARG SEQRES 14 A 277 ARG TYR LEU GLU ASN GLY LYS ASP THR LEU GLU ARG ALA SEQRES 15 A 277 ASP PRO PRO LYS THR HIS VAL THR HIS HIS PRO ILE SER SEQRES 16 A 277 ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU GLY PHE SEQRES 17 A 277 TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP GLY SEQRES 18 A 277 GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR ARG SEQRES 19 A 277 PRO ALA GLY ASP ARG THR PHE GLN LYS TRP ALA ALA VAL SEQRES 20 A 277 VAL VAL PRO SER GLY GLU GLU GLN ARG TYR THR CYS HIS SEQRES 21 A 277 VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU ARG SEQRES 22 A 277 TRP GLU PRO SER SEQRES 1 B 99 ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG HIS SEQRES 2 B 99 PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS TYR SEQRES 3 B 99 VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP LEU SEQRES 4 B 99 LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SER SEQRES 5 B 99 ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU LEU SEQRES 6 B 99 TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU TYR SEQRES 7 B 99 ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO LYS SEQRES 8 B 99 ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 C 277 GLY SER HIS SER MET ARG TYR PHE ASP THR ALA MET SER SEQRES 2 C 277 ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE SER VAL GLY SEQRES 3 C 277 TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER ASP SEQRES 4 C 277 ALA ALA SER PRO ARG GLU GLU PRO ARG ALA PRO TRP ILE SEQRES 5 C 277 GLU GLN GLU GLY PRO GLU TYR TRP ASP ARG ASN THR GLN SEQRES 6 C 277 ILE PHE LYS THR ASN THR GLN THR ASP ARG GLU SER LEU SEQRES 7 C 277 ARG ASN LEU ARG GLY TYR TYR ASN GLN SER GLU ALA GLY SEQRES 8 C 277 SER HIS THR LEU GLN SER MET TYR GLY CYS ASP VAL GLY SEQRES 9 C 277 PRO ASP GLY ARG LEU LEU ARG GLY HIS ASN GLN TYR ALA SEQRES 10 C 277 TYR ASP GLY LYS ASP TYR ILE ALA LEU ASN GLU ASP LEU SEQRES 11 C 277 ARG SER TRP THR ALA ALA ASP THR ALA ALA GLN ILE THR SEQRES 12 C 277 GLN ARG LYS TRP GLU ALA ALA ARG VAL ALA GLU GLN ASP SEQRES 13 C 277 ARG ALA TYR LEU GLU GLY THR CYS VAL GLU TRP LEU ARG SEQRES 14 C 277 ARG TYR LEU GLU ASN GLY LYS ASP THR LEU GLU ARG ALA SEQRES 15 C 277 ASP PRO PRO LYS THR HIS VAL THR HIS HIS PRO ILE SER SEQRES 16 C 277 ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU GLY PHE SEQRES 17 C 277 TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP GLY SEQRES 18 C 277 GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR ARG SEQRES 19 C 277 PRO ALA GLY ASP ARG THR PHE GLN LYS TRP ALA ALA VAL SEQRES 20 C 277 VAL VAL PRO SER GLY GLU GLU GLN ARG TYR THR CYS HIS SEQRES 21 C 277 VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU ARG SEQRES 22 C 277 TRP GLU PRO SER SEQRES 1 D 99 ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG HIS SEQRES 2 D 99 PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS TYR SEQRES 3 D 99 VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP LEU SEQRES 4 D 99 LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SER SEQRES 5 D 99 ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU LEU SEQRES 6 D 99 TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU TYR SEQRES 7 D 99 ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO LYS SEQRES 8 D 99 ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 E 9 PHE LEU ARG GLY ARG ALA TYR GLY LEU SEQRES 1 F 9 PHE LEU ARG GLY ARG ALA TYR GLY LEU HET CD B 101 1 HET CD D 101 1 HETNAM CD CADMIUM ION FORMUL 7 CD 2(CD 2+) FORMUL 9 HOH *794(H2 O) HELIX 1 1 ALA A 49 GLN A 54 1 6 HELIX 2 2 GLY A 56 TYR A 85 1 30 HELIX 3 3 ASP A 137 ALA A 150 1 14 HELIX 4 4 ARG A 151 GLY A 162 1 12 HELIX 5 5 GLY A 162 GLY A 175 1 14 HELIX 6 6 GLY A 175 GLU A 180 1 6 HELIX 7 7 THR A 225 THR A 228 5 4 HELIX 8 8 ALA C 49 GLN C 54 1 6 HELIX 9 9 GLY C 56 TYR C 85 1 30 HELIX 10 10 ASP C 137 ALA C 150 1 14 HELIX 11 11 ARG C 151 GLY C 162 1 12 HELIX 12 12 GLY C 162 GLY C 175 1 14 HELIX 13 13 GLY C 175 GLU C 180 1 6 SHEET 1 A 7 THR A 31 ASP A 37 0 SHEET 2 A 7 ARG A 21 VAL A 28 -1 N SER A 24 O PHE A 36 SHEET 3 A 7 HIS A 3 MET A 12 -1 N THR A 10 O ILE A 23 SHEET 4 A 7 THR A 94 VAL A 103 -1 O LEU A 95 N ALA A 11 SHEET 5 A 7 LEU A 109 TYR A 118 -1 O LEU A 110 N ASP A 102 SHEET 6 A 7 LYS A 121 LEU A 126 -1 O TYR A 123 N TYR A 116 SHEET 7 A 7 TRP A 133 ALA A 135 -1 O THR A 134 N ALA A 125 SHEET 1 B 4 LYS A 186 HIS A 191 0 SHEET 2 B 4 GLU A 198 PHE A 208 -1 O LEU A 206 N LYS A 186 SHEET 3 B 4 PHE A 241 PRO A 250 -1 O VAL A 247 N LEU A 201 SHEET 4 B 4 GLU A 229 LEU A 230 -1 N GLU A 229 O ALA A 246 SHEET 1 C 4 LYS A 186 HIS A 191 0 SHEET 2 C 4 GLU A 198 PHE A 208 -1 O LEU A 206 N LYS A 186 SHEET 3 C 4 PHE A 241 PRO A 250 -1 O VAL A 247 N LEU A 201 SHEET 4 C 4 ARG A 234 PRO A 235 -1 N ARG A 234 O GLN A 242 SHEET 1 D 4 GLU A 222 ASP A 223 0 SHEET 2 D 4 THR A 214 ARG A 219 -1 N ARG A 219 O GLU A 222 SHEET 3 D 4 TYR A 257 GLN A 262 -1 O HIS A 260 N THR A 216 SHEET 4 D 4 LEU A 270 LEU A 272 -1 O LEU A 272 N CYS A 259 SHEET 1 E 4 LYS B 6 SER B 11 0 SHEET 2 E 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 E 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 E 4 GLU B 50 HIS B 51 -1 N GLU B 50 O TYR B 67 SHEET 1 F 4 LYS B 6 SER B 11 0 SHEET 2 F 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 F 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 F 4 SER B 55 PHE B 56 -1 N SER B 55 O TYR B 63 SHEET 1 G 4 GLU B 44 ARG B 45 0 SHEET 2 G 4 GLU B 36 LYS B 41 -1 N LYS B 41 O GLU B 44 SHEET 3 G 4 TYR B 78 ASN B 83 -1 O ALA B 79 N LEU B 40 SHEET 4 G 4 LYS B 91 LYS B 94 -1 O LYS B 91 N VAL B 82 SHEET 1 H 7 THR C 31 ASP C 37 0 SHEET 2 H 7 ARG C 21 VAL C 28 -1 N GLY C 26 O PHE C 33 SHEET 3 H 7 HIS C 3 MET C 12 -1 N THR C 10 O ILE C 23 SHEET 4 H 7 THR C 94 VAL C 103 -1 O LEU C 95 N ALA C 11 SHEET 5 H 7 LEU C 109 TYR C 118 -1 O LEU C 110 N ASP C 102 SHEET 6 H 7 LYS C 121 LEU C 126 -1 O ILE C 124 N TYR C 116 SHEET 7 H 7 TRP C 133 ALA C 135 -1 O THR C 134 N ALA C 125 SHEET 1 I 4 LYS C 186 HIS C 191 0 SHEET 2 I 4 LEU C 201 PHE C 208 -1 O LEU C 206 N LYS C 186 SHEET 3 I 4 PHE C 241 VAL C 247 -1 O ALA C 245 N CYS C 203 SHEET 4 I 4 THR C 228 LEU C 230 -1 N GLU C 229 O ALA C 246 SHEET 1 J 4 LYS C 186 HIS C 191 0 SHEET 2 J 4 LEU C 201 PHE C 208 -1 O LEU C 206 N LYS C 186 SHEET 3 J 4 PHE C 241 VAL C 247 -1 O ALA C 245 N CYS C 203 SHEET 4 J 4 ARG C 234 PRO C 235 -1 N ARG C 234 O GLN C 242 SHEET 1 K 4 GLU C 222 ASP C 223 0 SHEET 2 K 4 THR C 214 ARG C 219 -1 N ARG C 219 O GLU C 222 SHEET 3 K 4 TYR C 257 GLN C 262 -1 O HIS C 260 N THR C 216 SHEET 4 K 4 LEU C 270 LEU C 272 -1 O LEU C 272 N CYS C 259 SHEET 1 L 4 LYS D 6 SER D 11 0 SHEET 2 L 4 ASN D 21 PHE D 30 -1 O ASN D 24 N TYR D 10 SHEET 3 L 4 PHE D 62 PHE D 70 -1 O PHE D 70 N ASN D 21 SHEET 4 L 4 GLU D 50 HIS D 51 -1 N GLU D 50 O TYR D 67 SHEET 1 M 4 LYS D 6 SER D 11 0 SHEET 2 M 4 ASN D 21 PHE D 30 -1 O ASN D 24 N TYR D 10 SHEET 3 M 4 PHE D 62 PHE D 70 -1 O PHE D 70 N ASN D 21 SHEET 4 M 4 SER D 55 PHE D 56 -1 N SER D 55 O TYR D 63 SHEET 1 N 4 GLU D 44 ARG D 45 0 SHEET 2 N 4 ILE D 35 LYS D 41 -1 N LYS D 41 O GLU D 44 SHEET 3 N 4 TYR D 78 HIS D 84 -1 O ALA D 79 N LEU D 40 SHEET 4 N 4 LYS D 91 LYS D 94 -1 O LYS D 91 N VAL D 82 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.05 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.02 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.03 SSBOND 4 CYS C 101 CYS C 164 1555 1555 2.05 SSBOND 5 CYS C 203 CYS C 259 1555 1555 2.02 SSBOND 6 CYS D 25 CYS D 80 1555 1555 2.03 LINK CD CD B 101 OD1 ASP B 38 1555 1555 2.50 LINK CD CD B 101 OE2 GLU B 36 1555 1555 2.45 LINK CD CD B 101 OD2 ASP B 38 1555 1555 2.59 LINK CD CD D 101 OE2 GLU D 36 1555 1555 2.47 LINK CD CD D 101 OD1 ASP D 38 1555 1555 2.48 LINK CD CD D 101 OD2 ASP D 38 1555 1555 2.59 LINK CD CD B 101 OE2 GLU C 19 1555 3645 2.53 LINK CD CD B 101 OE1 GLU C 19 1555 3645 2.47 LINK CD CD B 101 O HOH C 278 1555 3645 2.66 LINK CD CD D 101 OE2 GLU A 19 1555 3655 2.56 LINK CD CD D 101 O HOH A 278 1555 3655 2.61 LINK CD CD D 101 OE1 GLU A 19 1555 3655 2.65 CISPEP 1 TYR A 209 PRO A 210 0 -0.03 CISPEP 2 HIS B 31 PRO B 32 0 -0.03 CISPEP 3 TYR C 209 PRO C 210 0 -0.34 CISPEP 4 HIS D 31 PRO D 32 0 0.31 SITE 1 AC1 4 GLU B 36 ASP B 38 GLU C 19 HOH C 278 SITE 1 AC2 4 GLU A 19 HOH A 278 GLU D 36 ASP D 38 CRYST1 85.400 90.100 125.300 90.00 90.00 90.00 P 21 21 21 8 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 0.011710 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011099 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007981 0.00000