1OK8 - Header Asymmetric Unit

HEADER VIRAL PROTEIN 19-JUL-03 1OK8

TITLE CRYSTAL STRUCTURE OF THE DENGUE 2 VIRUS ENVELOPE TITLE 2 GLYCOPROTEIN IN THE POSTFUSION CONFORMATION

COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR ENVELOPE PROTEIN E; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SOLUBLE ECTODOMAIN, RESIDUES 281-674; COMPND 5 SYNONYM: DENGUE VIRUS TYPE 2 MAJOR ENVELOPE PROTEIN E; COMPND 6 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS TYPE 2; SOURCE 3 ORGANISM_TAXID: 11060; SOURCE 4 STRAIN: PR159/S1; SOURCE 5 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: SCHNEIDER 2; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMTT

KEYWDS VIRAL PROTEIN, MEMBRANE FUSION, FLAVIVIRUS, FUSION PEPTIDE, KEYWDS 2 LOW-PH CONFORMATIONAL CHANGE, CLASS 2 FUSION PROTEIN,

EXPDTA X-RAY DIFFRACTION

AUTHOR Y.MODIS,S.C.HARRISON

REVDAT 3 25-JAN-12 1OK8 1 HEADER KEYWDS REMARK VERSN REVDAT 3 2 HETSYN FORMUL SITE REVDAT 2 24-FEB-09 1OK8 1 VERSN REVDAT 1 29-JAN-04 1OK8 0

JRNL AUTH Y.MODIS,S.OGATA,D.CLEMENTS,S.C.HARRISON JRNL TITL STRUCTURE OF THE DENGUE VIRUS ENVELOPE PROTEIN JRNL TITL 2 AFTER MEMBRANE FUSION JRNL REF NATURE V. 427 313 2004 JRNL REFN ISSN 0028-0836 JRNL PMID 14737159 JRNL DOI 10.1038/NATURE02165

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.MODIS,S.OGATA,D.CLEMENTS,S.C.HARRISON REMARK 1 TITL A LIGAND-BINDING POCKET IN THE DENGUE VIRUS REMARK 1 TITL 2 ENVELOPE GLYCOPROTEIN REMARK 1 REF PROC.NATL.ACAD.SCI.USA. V. 100 6986 2003 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 12759475 REMARK 1 DOI 10.1073/PNAS.0832193100

REMARK 2 REMARK 2 RESOLUTION. 2.0 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 441803.91 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.00 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 27450 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.8 REMARK 3 FREE R VALUE TEST SET COUNT : 1322 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.6 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3130 REMARK 3 BIN R VALUE (WORKING SET) : 0.273 REMARK 3 BIN FREE R VALUE : 0.306 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.3 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 174 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2962 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.3 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.1 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.49 REMARK 3 B22 (A**2) : 1.49 REMARK 3 B33 (A**2) : -2.98 REMARK 3 B12 (A**2) : 2.18 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.4 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.4 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.82 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.29 ; 3.00 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.22 ; 4.00 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.76 ; 5.00 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.41 ; 6.00 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : .355448 REMARK 3 BSOL : 47.9914 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 3 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1OK8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JUL-03. REMARK 100 THE PDBE ID CODE IS EBI-13085.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28677 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.20 REMARK 200 R MERGE FOR SHELL (I) : 0.39800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE, CNS REMARK 200 STARTING MODEL: PDB ENTRY 1OAM REMARK 200 REMARK 200 REMARK: THE THREE DOMAINS OF 1OAM WERE PLACED SEQUENTIALLY IN REMARK 200 THE FOLLOWING ORDER: DOMAIN II, DOMAIN I, DOMAIN III.

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.445 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-30% PEG 400, 0.08 M NACL, REMARK 280 0.1 M MOPS PH 7-8.

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.1 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 -0.500000 0.866025 0.000000 -38.07550 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 65.94870 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 38.07550 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 65.94870 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000

REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CL CL A1396 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2099 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2137 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2149 LIES ON A SPECIAL POSITION.

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 SER A 145 REMARK 465 GLY A 146 REMARK 465 GLU A 147 REMARK 465 GLU A 148 REMARK 465 HIS A 149 REMARK 465 ALA A 150 REMARK 465 VAL A 151 REMARK 465 GLY A 152 REMARK 465 ASN A 153 REMARK 465 ASP A 154 REMARK 465 THR A 155 REMARK 465 GLY A 156 REMARK 465 LYS A 157 REMARK 465 HIS A 158

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 O GLY A 281 O HOH A 2147 2.19 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 CYS A 30 CA - CB - SG ANGL. DEV. = 9.9 DEGREES REMARK 500 CYS A 121 CA - CB - SG ANGL. DEV. = -7.2 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 THR A 76 -4.45 69.78 REMARK 500 LYS A 88 -9.08 -59.99 REMARK 500 LYS A 202 -123.94 55.60 REMARK 500 ASN A 230 54.57 -95.30 REMARK 500 SER A 274 78.85 45.68 REMARK 500 LEU A 342 -31.57 -39.60 REMARK 500 GLU A 343 -100.36 -88.27 REMARK 500 LYS A 344 14.15 -160.33 REMARK 500 ARG A 350 -7.90 80.02 REMARK 500 GLU A 383 -43.38 -27.04 REMARK 500 PRO A 384 85.62 -60.84 REMARK 500 REMARK 500 REMARK: NULL

REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED.

REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED.

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1396 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR MONO-SACCHARIDE REMARK 800 NAG A1395 BOUND TO ASN A 67

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1L9K RELATED DB: PDB REMARK 900 DENGUE METHYLTRANSFERASE REMARK 900 RELATED ID: 1OAM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DENGUE 2 VIRUS REMARK 900 ENVELOPE PROTEIN IN COMPLEX WITH N-OCTYL- REMARK 900 BETA-D-GLUCOSIDE REMARK 900 RELATED ID: 1OAN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DENGUE 2 VIRUS REMARK 900 ENVELOPE PROTEIN

REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 100-108 FORM THE GLYCINE-RICH, HYDROPHOBIC FUSION REMARK 999 PEPTIDE (ALLISON ET AL., J.VIROL. 75, 4268-75 (2001)) REMARK 999 REMARK 999 THE MOLECULE CRYSTALLIZED LACKS THE LAST 101 RESIDUES OF E, REMARK 999 INCLUDING THE C-TERMINAL VIRAL TRANSMEMBRANE DOMAIN.

DBREF 1OK8 A 1 394 UNP P12823 POLG_DEN2P 281 674

SEQADV 1OK8 GLU A 71 UNP P12823 ASP 351 CONFLICT SEQADV 1OK8 ASN A 390 UNP P12823 ASP 670 CONFLICT

SEQRES 1 A 394 MET ARG CYS ILE GLY ILE SER ASN ARG ASP PHE VAL GLU SEQRES 2 A 394 GLY VAL SER GLY GLY SER TRP VAL ASP ILE VAL LEU GLU SEQRES 3 A 394 HIS GLY SER CYS VAL THR THR MET ALA LYS ASN LYS PRO SEQRES 4 A 394 THR LEU ASP PHE GLU LEU ILE LYS THR GLU ALA LYS GLN SEQRES 5 A 394 PRO ALA THR LEU ARG LYS TYR CYS ILE GLU ALA LYS LEU SEQRES 6 A 394 THR ASN THR THR THR GLU SER ARG CYS PRO THR GLN GLY SEQRES 7 A 394 GLU PRO THR LEU ASN GLU GLU GLN ASP LYS ARG PHE VAL SEQRES 8 A 394 CYS LYS HIS SER MET VAL ASP ARG GLY TRP GLY ASN GLY SEQRES 9 A 394 CYS GLY LEU PHE GLY LYS GLY GLY ILE VAL THR CYS ALA SEQRES 10 A 394 MET PHE THR CYS LYS LYS ASN MET GLU GLY LYS ILE VAL SEQRES 11 A 394 GLN PRO GLU ASN LEU GLU TYR THR VAL VAL ILE THR PRO SEQRES 12 A 394 HIS SER GLY GLU GLU HIS ALA VAL GLY ASN ASP THR GLY SEQRES 13 A 394 LYS HIS GLY LYS GLU VAL LYS ILE THR PRO GLN SER SER SEQRES 14 A 394 ILE THR GLU ALA GLU LEU THR GLY TYR GLY THR VAL THR SEQRES 15 A 394 MET GLU CYS SER PRO ARG THR GLY LEU ASP PHE ASN GLU SEQRES 16 A 394 MET VAL LEU LEU GLN MET LYS ASP LYS ALA TRP LEU VAL SEQRES 17 A 394 HIS ARG GLN TRP PHE LEU ASP LEU PRO LEU PRO TRP LEU SEQRES 18 A 394 PRO GLY ALA ASP THR GLN GLY SER ASN TRP ILE GLN LYS SEQRES 19 A 394 GLU THR LEU VAL THR PHE LYS ASN PRO HIS ALA LYS LYS SEQRES 20 A 394 GLN ASP VAL VAL VAL LEU GLY SER GLN GLU GLY ALA MET SEQRES 21 A 394 HIS THR ALA LEU THR GLY ALA THR GLU ILE GLN MET SER SEQRES 22 A 394 SER GLY ASN LEU LEU PHE THR GLY HIS LEU LYS CYS ARG SEQRES 23 A 394 LEU ARG MET ASP LYS LEU GLN LEU LYS GLY MET SER TYR SEQRES 24 A 394 SER MET CYS THR GLY LYS PHE LYS VAL VAL LYS GLU ILE SEQRES 25 A 394 ALA GLU THR GLN HIS GLY THR ILE VAL ILE ARG VAL GLN SEQRES 26 A 394 TYR GLU GLY ASP GLY SER PRO CYS LYS ILE PRO PHE GLU SEQRES 27 A 394 ILE MET ASP LEU GLU LYS ARG HIS VAL LEU GLY ARG LEU SEQRES 28 A 394 ILE THR VAL ASN PRO ILE VAL THR GLU LYS ASP SER PRO SEQRES 29 A 394 VAL ASN ILE GLU ALA GLU PRO PRO PHE GLY ASP SER TYR SEQRES 30 A 394 ILE ILE ILE GLY VAL GLU PRO GLY GLN LEU LYS LEU ASN SEQRES 31 A 394 TRP PHE LYS LYS

HET NAG A1395 14 HET CL A1396 1

HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM CL CHLORIDE ION

FORMUL 2 NAG C8 H15 N O6 FORMUL 3 CL CL 1- FORMUL 4 HOH *205(H2 O)

HELIX 1 2 LEU A 82 ASP A 87 5 6 HELIX 2 5 ARG A 210 ASP A 215 1 6 HELIX 3 7 GLN A 256 LEU A 264 1 9

SHEET 1 AA 5 ILE A 4 GLY A 5 0 SHEET 2 AA 5 VAL A 31 MET A 34 1 N THR A 32 O ILE A 4 SHEET 3 AA 5 THR A 40 LYS A 51 -1 O LEU A 41 N THR A 33 SHEET 4 AA 5 LEU A 135 HIS A 144 -1 O GLU A 136 N GLU A 49 SHEET 5 AA 5 LYS A 160 ILE A 164 -1 O LYS A 160 N ILE A 141 SHEET 1 AB 4 ILE A 4 GLY A 5 0 SHEET 2 AB 4 VAL A 31 MET A 34 1 N THR A 32 O ILE A 4 SHEET 3 AB 4 THR A 40 LYS A 51 -1 O LEU A 41 N THR A 33 SHEET 4 AB 4 ASN A 276 PHE A 279 -1 O LEU A 277 N ALA A 50 SHEET 1 AC 5 PHE A 11 GLU A 13 0 SHEET 2 AC 5 GLY A 18 GLU A 26 -1 O TRP A 20 N VAL A 12 SHEET 3 AC 5 HIS A 282 ASP A 290 -1 O LEU A 283 N LEU A 25 SHEET 4 AC 5 GLY A 179 PRO A 187 -1 O THR A 182 N ARG A 288 SHEET 5 AC 5 ILE A 170 LEU A 175 -1 O THR A 171 N MET A 183 SHEET 1 AD 4 PHE A 90 ARG A 99 0 SHEET 2 AD 4 GLY A 109 ILE A 129 -1 O GLY A 109 N ARG A 99 SHEET 3 AD 4 ALA A 54 SER A 72 -1 O ALA A 54 N ILE A 129 SHEET 4 AD 4 TRP A 220 PRO A 222 -1 O LEU A 221 N LYS A 58 SHEET 1 AE 5 PHE A 90 ARG A 99 0 SHEET 2 AE 5 GLY A 109 ILE A 129 -1 O GLY A 109 N ARG A 99 SHEET 3 AE 5 MET A 196 MET A 201 -1 O LEU A 198 N LYS A 128 SHEET 4 AE 5 LYS A 204 HIS A 209 -1 O LYS A 204 N MET A 201 SHEET 5 AE 5 THR A 268 ILE A 270 -1 O THR A 268 N LEU A 207 SHEET 1 AF 2 VAL A 238 PHE A 240 0 SHEET 2 AF 2 VAL A 250 VAL A 252 -1 O VAL A 251 N THR A 239 SHEET 1 AG 3 PHE A 306 GLU A 314 0 SHEET 2 AG 3 ILE A 320 TYR A 326 -1 O VAL A 321 N ALA A 313 SHEET 3 AG 3 VAL A 365 ALA A 369 -1 O VAL A 365 N VAL A 324 SHEET 1 AH 2 CYS A 333 LYS A 334 0 SHEET 2 AH 2 ILE A 357 VAL A 358 -1 O VAL A 358 N CYS A 333 SHEET 1 AI 3 PHE A 337 ASP A 341 0 SHEET 2 AI 3 GLY A 374 ILE A 380 -1 O TYR A 377 N MET A 340 SHEET 3 AI 3 LEU A 387 LYS A 393 -1 O LEU A 387 N ILE A 380

SSBOND 1 CYS A 3 CYS A 30 1555 1555 2.03 SSBOND 2 CYS A 60 CYS A 121 1555 1555 2.05 SSBOND 3 CYS A 74 CYS A 105 1555 1555 2.04 SSBOND 4 CYS A 92 CYS A 116 1555 1555 2.04 SSBOND 5 CYS A 185 CYS A 285 1555 1555 2.05 SSBOND 6 CYS A 302 CYS A 333 1555 1555 2.04

LINK ND2 ASN A 67 C1 NAG A1395 1555 1555 1.45

CISPEP 1 SER A 331 PRO A 332 0 0.60

SITE 1 AC1 1 LYS A 110 SITE 1 AC2 2 ASN A 67 PHE A 90

CRYST1 76.151 76.151 130.775 90.00 90.00 120.00 P 3 2 1 6

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 0.013132 0.007582 0.000000 0.00000

SCALE2 0.000000 0.015163 0.000000 0.00000

SCALE3 0.000000 0.000000 0.007647 0.00000