HEADER VIRAL PROTEIN 07-OCT-16 5M1H TITLE STRUCTURE OF A SPUMARETROVIRUS GAG CENTRAL DOMAIN REVEALS AN ANCIENT TITLE 2 RETROVIRAL CAPSID COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PR71GAG; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN SPUMARETROVIRUS; SOURCE 3 ORGANISM_COMMON: SFVCPZ(HU); SOURCE 4 ORGANISM_TAXID: 11963; SOURCE 5 GENE: GAG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET47B KEYWDS GAG, VIRAL PROTEIN, FOAMY VIRUS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR I.A.TAYLOR,G.NICASTRO,N.BALL REVDAT 3 15-MAY-24 5M1H 1 REMARK REVDAT 2 23-NOV-16 5M1H 1 JRNL REVDAT 1 26-OCT-16 5M1H 0 JRNL AUTH N.J.BALL,G.NICASTRO,M.DUTTA,D.J.POLLARD,D.C.GOLDSTONE, JRNL AUTH 2 M.SANZ-RAMOS,A.RAMOS,E.MULLERS,K.STIRNNAGEL,N.STANKE, JRNL AUTH 3 D.LINDEMANN,J.P.STOYE,W.R.TAYLOR,P.B.ROSENTHAL,I.A.TAYLOR JRNL TITL STRUCTURE OF A SPUMARETROVIRUS GAG CENTRAL DOMAIN REVEALS AN JRNL TITL 2 ANCIENT RETROVIRAL CAPSID. JRNL REF PLOS PATHOG. V. 12 05981 2016 JRNL REFN ESSN 1553-7374 JRNL PMID 27829070 JRNL DOI 10.1371/JOURNAL.PPAT.1005981 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5M1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001707. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 20MM NACL, 20MM TRIS REMARK 210 PRESSURE : 1 PA REMARK 210 SAMPLE CONTENTS : 0.3 MM [U-13C; U-15N] PROTEIN, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 950 MHZ; 800 MHZ; 700 MHZ; 600 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 O LEU A 328 H ALA A 332 1.51 REMARK 500 O PRO A 344 HG CYS A 348 1.53 REMARK 500 O ILE A 398 H GLU A 402 1.56 REMARK 500 O LEU A 410 H LEU A 414 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 1 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES REMARK 500 3 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 4 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES REMARK 500 5 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 6 PHE A 386 CB - CG - CD1 ANGL. DEV. = -5.0 DEGREES REMARK 500 7 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 8 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 10 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 11 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 13 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 15 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 16 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 17 PHE A 386 CB - CG - CD1 ANGL. DEV. = -5.0 DEGREES REMARK 500 18 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES REMARK 500 19 PHE A 386 CB - CG - CD1 ANGL. DEV. = -4.6 DEGREES REMARK 500 20 PHE A 386 CB - CG - CD1 ANGL. DEV. = -5.0 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 ILE A 307 -63.79 34.71 REMARK 500 1 GLU A 316 165.35 55.75 REMARK 500 1 PRO A 318 -102.58 -88.09 REMARK 500 1 ARG A 319 -79.94 -102.36 REMARK 500 1 VAL A 338 -71.76 -57.78 REMARK 500 1 VAL A 341 66.43 32.62 REMARK 500 1 ILE A 359 -71.43 -48.24 REMARK 500 1 SER A 362 78.89 -63.70 REMARK 500 1 LEU A 363 -179.69 -61.14 REMARK 500 1 PRO A 365 25.32 -69.79 REMARK 500 1 THR A 385 159.54 66.27 REMARK 500 1 PRO A 387 54.10 -96.32 REMARK 500 1 MET A 388 8.16 58.02 REMARK 500 1 ALA A 471 -75.57 -161.96 REMARK 500 1 ARG A 472 71.04 -66.26 REMARK 500 1 SER A 475 61.16 68.91 REMARK 500 2 ILE A 307 -63.62 41.03 REMARK 500 2 GLU A 316 168.21 53.97 REMARK 500 2 PRO A 318 -105.51 -96.94 REMARK 500 2 ARG A 319 -86.26 -86.52 REMARK 500 2 VAL A 338 -70.62 -57.81 REMARK 500 2 VAL A 341 70.14 33.24 REMARK 500 2 ILE A 359 -72.81 -47.77 REMARK 500 2 SER A 362 80.31 -63.62 REMARK 500 2 LEU A 363 -170.82 -60.35 REMARK 500 2 THR A 385 154.79 66.64 REMARK 500 2 PRO A 387 54.55 -96.09 REMARK 500 2 MET A 388 -7.44 60.00 REMARK 500 2 ALA A 471 -79.38 -159.06 REMARK 500 2 ARG A 472 73.60 -61.41 REMARK 500 3 GLU A 316 170.24 52.46 REMARK 500 3 PRO A 317 150.67 -49.63 REMARK 500 3 PRO A 318 -104.71 -93.37 REMARK 500 3 ARG A 319 -84.58 -95.17 REMARK 500 3 VAL A 338 -72.48 -63.49 REMARK 500 3 VAL A 341 67.40 33.89 REMARK 500 3 ILE A 359 -72.25 -49.62 REMARK 500 3 SER A 362 70.55 -69.18 REMARK 500 3 LEU A 363 172.31 -55.03 REMARK 500 3 PRO A 365 -9.98 -53.30 REMARK 500 3 THR A 385 164.39 64.12 REMARK 500 3 PRO A 387 54.14 -99.37 REMARK 500 3 MET A 388 -0.53 59.50 REMARK 500 3 ALA A 471 -72.92 -162.18 REMARK 500 3 ARG A 472 68.87 -61.33 REMARK 500 4 GLU A 316 169.42 53.52 REMARK 500 4 PRO A 317 151.39 -44.06 REMARK 500 4 PRO A 318 -108.00 -97.97 REMARK 500 4 ARG A 319 -82.02 -92.47 REMARK 500 4 VAL A 338 -72.99 -59.17 REMARK 500 REMARK 500 THIS ENTRY HAS 294 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34050 RELATED DB: BMRB REMARK 900 STRUCTURE OF A SPUMARETROVIRUS GAG CENTRAL DOMAIN REVEALS AN REMARK 900 ANCIENT RETROVIRAL CAPSID DBREF 5M1H A 300 477 UNP P14349 GAG_FOAMV 300 477 SEQADV 5M1H ASP A 449 UNP P14349 ASN 449 ENGINEERED MUTATION SEQADV 5M1H LEU A 478 UNP P14349 EXPRESSION TAG SEQADV 5M1H GLU A 479 UNP P14349 EXPRESSION TAG SEQRES 1 A 180 PRO ILE GLY THR VAL ILE PRO ILE GLN HIS ILE ARG SER SEQRES 2 A 180 VAL THR GLY GLU PRO PRO ARG ASN PRO ARG GLU ILE PRO SEQRES 3 A 180 ILE TRP LEU GLY ARG ASN ALA PRO ALA ILE ASP GLY VAL SEQRES 4 A 180 PHE PRO VAL THR THR PRO ASP LEU ARG CYS ARG ILE ILE SEQRES 5 A 180 ASN ALA ILE LEU GLY GLY ASN ILE GLY LEU SER LEU THR SEQRES 6 A 180 PRO GLY ASP CYS LEU THR TRP ASP SER ALA VAL ALA THR SEQRES 7 A 180 LEU PHE ILE ARG THR HIS GLY THR PHE PRO MET HIS GLN SEQRES 8 A 180 LEU GLY ASN VAL ILE LYS GLY ILE VAL ASP GLN GLU GLY SEQRES 9 A 180 VAL ALA THR ALA TYR THR LEU GLY MET MET LEU SER GLY SEQRES 10 A 180 GLN ASN TYR GLN LEU VAL SER GLY ILE ILE ARG GLY TYR SEQRES 11 A 180 LEU PRO GLY GLN ALA VAL VAL THR ALA LEU GLN GLN ARG SEQRES 12 A 180 LEU ASP GLN GLU ILE ASP ASP GLN THR ARG ALA GLU THR SEQRES 13 A 180 PHE ILE GLN HIS LEU ASN ALA VAL TYR GLU ILE LEU GLY SEQRES 14 A 180 LEU ASN ALA ARG GLY GLN SER ILE ARG LEU GLU HELIX 1 AA1 ILE A 307 GLY A 315 1 9 HELIX 2 AA2 GLU A 323 PHE A 339 1 17 HELIX 3 AA3 THR A 343 GLY A 356 1 14 HELIX 4 AA4 THR A 370 HIS A 383 1 14 HELIX 5 AA5 GLN A 390 GLU A 402 1 13 HELIX 6 AA6 GLY A 403 GLY A 416 1 14 HELIX 7 AA7 ASN A 418 GLY A 428 1 11 HELIX 8 AA8 GLY A 432 GLU A 446 1 15 HELIX 9 AA9 ASP A 448 LEU A 467 1 20 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