HEADER VIRAL PROTEIN 12-SEP-07 2JV6 TITLE YF ED3 PROTEIN NMR STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE PROTEIN E; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YELLOW FEVER VIRUS; SOURCE 3 ORGANISM_COMMON: YFV; SOURCE 4 ORGANISM_TAXID: 11089; SOURCE 5 STRAIN: ASIBI 17D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET-15; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PLASMID KEYWDS YELLOW FEVER, ENVELOP PROTEIN DOMAIN III, FLAVIVIRUS, ATP-BINDING, KEYWDS 2 CAPSID PROTEIN, CLEAVAGE ON PAIR OF BASIC RESIDUES, ENDOPLASMIC KEYWDS 3 RETICULUM, ENVELOPE PROTEIN, GLYCOPROTEIN, HELICASE, HYDROLASE, KEYWDS 4 MEMBRANE, METAL-BINDING, MULTIFUNCTIONAL ENZYME, NUCLEOTIDE-BINDING, KEYWDS 5 NUCLEOTIDYLTRANSFERASE, NUCLEUS, PHOSPHORYLATION, PROTEASE, KEYWDS 6 RIBONUCLEOPROTEIN, RNA REPLICATION, RNA-BINDING, RNA-DIRECTED RNA KEYWDS 7 POLYMERASE, SECRETED, SERINE PROTEASE, TRANSFERASE, TRANSMEMBRANE, KEYWDS 8 VIRAL NUCLEOPROTEIN, VIRION, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.E.VOLK,S.H.A.GANDHAM,F.J.MAY,A.ANDERSON,A.D.T.BARRETT, AUTHOR 2 D.G.GORENSTEIN REVDAT 3 16-MAR-22 2JV6 1 REMARK SEQADV REVDAT 2 24-FEB-09 2JV6 1 VERSN REVDAT 1 16-SEP-08 2JV6 0 JRNL AUTH D.E.VOLK,F.J.MAY,S.H.A.GANDHAM,A.ANDERSON,J.J.VON LINDERN, JRNL AUTH 2 D.W.BEASLEY,A.D.T.BARRETT,D.G.GORENSTEIN JRNL TITL YELLOW FEVER VIRUS ENVELOPE PROTEIN DOMAIN III: A JRNL TITL 2 CONVERGENCE OF STRUCTURE AND PHYLOGENETICS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 6 REMARK 3 AUTHORS : CASE, D.A. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JV6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000100330. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.8 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2 MM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN, 50 MM SODIUM CHLORIDE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HNCACB; 3D HCCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS, DGSA REMARK 210 -DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 OD1 ASP A 373 HG SER A 394 1.33 REMARK 500 HG1 THR A 317 OE1 GLU A 366 1.34 REMARK 500 OD2 ASP A 373 HG SER A 395 1.35 REMARK 500 HG1 THR A 358 OD1 ASP A 361 1.37 REMARK 500 O THR A 301 HG SER A 383 1.50 REMARK 500 HG SER A 288 O LYS A 293 1.54 REMARK 500 O ASP A 373 HG SER A 374 1.55 REMARK 500 O THR A 291 HG1 THR A 295 1.56 REMARK 500 O THR A 295 HG SER A 296 1.57 REMARK 500 O ILE A 376 HG1 THR A 386 1.58 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 2 CYS A 300 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 6 CYS A 300 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 8 ARG A 384 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 9 CYS A 300 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 11 CYS A 300 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 16 CYS A 300 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 20 ARG A 384 NE - CZ - NH1 ANGL. DEV. = 3.3 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 1 SER A 288 4.58 -69.82 REMARK 500 1 LEU A 340 -6.34 63.89 REMARK 500 1 ALA A 342 37.29 73.22 REMARK 500 1 ALA A 356 98.09 -69.16 REMARK 500 1 SER A 383 -8.34 -58.41 REMARK 500 1 SER A 394 -83.22 -120.96 REMARK 500 2 ALA A 289 38.86 -75.34 REMARK 500 2 LEU A 340 -7.96 64.94 REMARK 500 2 ALA A 342 35.48 82.37 REMARK 500 2 SER A 383 -6.96 -59.87 REMARK 500 2 GLU A 392 105.05 -22.91 REMARK 500 2 SER A 394 -101.98 -133.22 REMARK 500 3 LYS A 293 70.21 -104.13 REMARK 500 3 SER A 296 120.06 -171.94 REMARK 500 3 PRO A 325 -67.30 -97.40 REMARK 500 3 ALA A 356 90.16 -65.78 REMARK 500 3 SER A 383 -7.61 -58.95 REMARK 500 3 GLU A 392 102.73 50.71 REMARK 500 3 SER A 394 8.74 -54.92 REMARK 500 3 ILE A 396 -17.48 -144.48 REMARK 500 4 THR A 291 -73.44 -42.69 REMARK 500 4 LEU A 292 3.80 -65.66 REMARK 500 4 SER A 296 134.53 -174.73 REMARK 500 4 LYS A 303 97.01 -61.06 REMARK 500 4 PRO A 325 -76.53 -103.05 REMARK 500 4 LEU A 340 -10.83 63.48 REMARK 500 4 ALA A 356 85.23 -69.20 REMARK 500 4 SER A 383 -4.30 -56.58 REMARK 500 5 SER A 296 103.44 -161.25 REMARK 500 5 LYS A 303 98.81 -66.44 REMARK 500 5 ALA A 356 75.39 -66.86 REMARK 500 5 ASP A 361 119.12 -39.22 REMARK 500 5 SER A 383 6.04 -52.14 REMARK 500 5 SER A 394 -44.58 -148.64 REMARK 500 6 ALA A 289 22.02 -69.92 REMARK 500 6 LEU A 340 -1.39 61.80 REMARK 500 6 SER A 394 -81.11 -135.47 REMARK 500 7 ALA A 289 21.98 -66.60 REMARK 500 7 THR A 291 -92.71 23.28 REMARK 500 7 SER A 296 135.60 -170.37 REMARK 500 7 LYS A 298 95.43 -66.76 REMARK 500 7 LYS A 303 95.01 -66.98 REMARK 500 7 LEU A 340 -6.02 65.27 REMARK 500 7 VAL A 352 107.77 -58.78 REMARK 500 7 ALA A 356 84.63 -66.00 REMARK 500 7 SER A 394 -79.59 -135.26 REMARK 500 8 ALA A 289 11.21 -69.52 REMARK 500 8 LYS A 293 64.19 -103.34 REMARK 500 8 SER A 296 124.81 -171.44 REMARK 500 8 LYS A 303 95.46 -61.87 REMARK 500 REMARK 500 THIS ENTRY HAS 163 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 370 PHE A 371 6 149.44 REMARK 500 SER A 357 THR A 358 10 147.88 REMARK 500 ALA A 342 ALA A 343 20 149.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15034 RELATED DB: BMRB DBREF 2JV6 A 288 398 UNP Q6J3P1 POLG_YEFVC 573 683 SEQADV 2JV6 MET A 287 UNP Q6J3P1 INITIATING METHIONINE SEQRES 1 A 112 MET SER ALA LEU THR LEU LYS GLY THR SER TYR LYS MET SEQRES 2 A 112 CYS THR ASP LYS MET SER PHE VAL LYS ASN PRO THR ASP SEQRES 3 A 112 THR GLY HIS GLY THR VAL VAL MET GLN VAL LYS VAL PRO SEQRES 4 A 112 LYS GLY ALA PRO CYS LYS ILE PRO VAL ILE VAL ALA ASP SEQRES 5 A 112 ASP LEU THR ALA ALA ILE ASN LYS GLY ILE LEU VAL THR SEQRES 6 A 112 VAL ASN PRO ILE ALA SER THR ASN ASP ASP GLU VAL LEU SEQRES 7 A 112 ILE GLU VAL ASN PRO PRO PHE GLY ASP SER TYR ILE ILE SEQRES 8 A 112 VAL GLY THR GLY ASP SER ARG LEU THR TYR GLN TRP HIS SEQRES 9 A 112 LYS GLU GLY SER SER ILE GLY LYS SHEET 1 A 4 SER A 305 ASP A 312 0 SHEET 2 A 4 VAL A 318 LYS A 323 -1 O LYS A 323 N SER A 305 SHEET 3 A 4 GLU A 362 ASN A 368 -1 O ILE A 365 N MET A 320 SHEET 4 A 4 ILE A 348 LEU A 349 -1 N ILE A 348 O ASN A 368 SHEET 1 B 2 CYS A 330 LYS A 331 0 SHEET 2 B 2 ILE A 355 ALA A 356 -1 O ALA A 356 N CYS A 330 SHEET 1 C 3 VAL A 334 ALA A 337 0 SHEET 2 C 3 TYR A 375 VAL A 378 -1 O ILE A 377 N ILE A 335 SHEET 3 C 3 LEU A 385 GLN A 388 -1 O TYR A 387 N ILE A 376 SSBOND 1 CYS A 300 CYS A 330 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1