HEADER VIRAL PROTEIN 07-OCT-16 5M1G 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, B; 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 G.NICASTRO,N.BALL,I.A.TAYLOR REVDAT 3 30-OCT-19 5M1G 1 REMARK REVDAT 2 23-NOV-16 5M1G 1 JRNL REVDAT 1 26-OCT-16 5M1G 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 5M1G 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_1200001728. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 20MM NACL, 20MM TRIS REMARK 210 PRESSURE : 1 PA REMARK 210 SAMPLE CONTENTS : 0.3 NM [U-13C; U-15N] GAG REMARK 210 PROTEIN, 0.5 MM [U-13C; U-15N; U- REMARK 210 2H] GAG PROTEIN, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY 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 : 1000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 PRO A 387 64.14 -66.88 REMARK 500 1 HIS A 389 -160.77 -65.25 REMARK 500 1 LEU A 391 -63.73 -155.23 REMARK 500 1 GLN A 417 24.19 -79.76 REMARK 500 1 PRO A 431 -60.46 -24.05 REMARK 500 1 GLU A 446 97.06 31.41 REMARK 500 1 PRO B 387 63.89 -66.83 REMARK 500 1 HIS B 389 -160.49 -65.20 REMARK 500 1 LEU B 391 -64.14 -155.15 REMARK 500 1 GLN B 417 24.44 -79.72 REMARK 500 1 PRO B 431 -60.35 -24.06 REMARK 500 1 GLU B 446 97.02 31.26 REMARK 500 2 PRO A 387 -72.84 -49.27 REMARK 500 2 MET A 388 49.36 74.36 REMARK 500 2 HIS A 389 -99.44 47.31 REMARK 500 2 GLN A 390 15.71 -146.36 REMARK 500 2 LEU A 391 -50.97 -169.15 REMARK 500 2 GLN A 417 24.30 -79.65 REMARK 500 2 PRO A 431 -70.52 -23.41 REMARK 500 2 GLU A 446 98.86 27.59 REMARK 500 2 ASP A 448 -161.79 -163.66 REMARK 500 2 PRO B 387 -72.67 -49.32 REMARK 500 2 MET B 388 49.54 73.98 REMARK 500 2 HIS B 389 -99.84 47.32 REMARK 500 2 GLN B 390 15.49 -145.99 REMARK 500 2 LEU B 391 -50.89 -169.15 REMARK 500 2 GLN B 417 24.47 -79.71 REMARK 500 2 PRO B 431 -70.50 -23.47 REMARK 500 2 GLU B 446 98.94 27.91 REMARK 500 2 ASP B 448 -162.14 -163.79 REMARK 500 3 GLN A 390 19.66 -175.49 REMARK 500 3 LEU A 391 -54.80 -169.76 REMARK 500 3 GLN A 417 24.43 -79.70 REMARK 500 3 PRO A 431 -65.66 -23.55 REMARK 500 3 GLU A 446 100.57 26.68 REMARK 500 3 ASP A 448 -162.04 -164.21 REMARK 500 3 ASP A 449 -71.01 -79.55 REMARK 500 3 GLN B 390 19.84 -175.89 REMARK 500 3 LEU B 391 -54.86 -169.91 REMARK 500 3 GLN B 417 24.52 -79.90 REMARK 500 3 PRO B 431 -65.58 -23.45 REMARK 500 3 GLU B 446 100.59 26.87 REMARK 500 3 ASP B 448 -161.95 -164.08 REMARK 500 3 ASP B 449 -71.21 -79.55 REMARK 500 4 PHE A 386 113.04 73.11 REMARK 500 4 PRO A 387 -70.73 -42.14 REMARK 500 4 HIS A 389 -82.91 61.35 REMARK 500 4 GLN A 390 14.47 -167.92 REMARK 500 4 LEU A 391 -48.23 -169.53 REMARK 500 4 GLU A 446 101.01 19.29 REMARK 500 REMARK 500 THIS ENTRY HAS 302 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 19 ARG A 442 0.09 SIDE CHAIN REMARK 500 19 ARG B 442 0.09 SIDE CHAIN REMARK 500 20 ARG A 442 0.09 SIDE CHAIN REMARK 500 20 ARG B 442 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34049 RELATED DB: BMRB REMARK 900 STRUCTURE OF A SPUMARETROVIRUS GAG CENTRAL DOMAIN REVEALS AN REMARK 900 ANCIENT RETROVIRAL CAPSID DBREF 5M1G A 381 477 UNP P14349 GAG_FOAMV 381 477 DBREF 5M1G B 381 477 UNP P14349 GAG_FOAMV 381 477 SEQADV 5M1G ASP A 449 UNP P14349 ASN 449 CONFLICT SEQADV 5M1G LEU A 478 UNP P14349 EXPRESSION TAG SEQADV 5M1G GLU A 479 UNP P14349 EXPRESSION TAG SEQADV 5M1G ASP B 449 UNP P14349 ASN 449 CONFLICT SEQADV 5M1G LEU B 478 UNP P14349 EXPRESSION TAG SEQADV 5M1G GLU B 479 UNP P14349 EXPRESSION TAG SEQRES 1 A 99 ARG THR HIS GLY THR PHE PRO MET HIS GLN LEU GLY ASN SEQRES 2 A 99 VAL ILE LYS GLY ILE VAL ASP GLN GLU GLY VAL ALA THR SEQRES 3 A 99 ALA TYR THR LEU GLY MET MET LEU SER GLY GLN ASN TYR SEQRES 4 A 99 GLN LEU VAL SER GLY ILE ILE ARG GLY TYR LEU PRO GLY SEQRES 5 A 99 GLN ALA VAL VAL THR ALA LEU GLN GLN ARG LEU ASP GLN SEQRES 6 A 99 GLU ILE ASP ASP GLN THR ARG ALA GLU THR PHE ILE GLN SEQRES 7 A 99 HIS LEU ASN ALA VAL TYR GLU ILE LEU GLY LEU ASN ALA SEQRES 8 A 99 ARG GLY GLN SER ILE ARG LEU GLU SEQRES 1 B 99 ARG THR HIS GLY THR PHE PRO MET HIS GLN LEU GLY ASN SEQRES 2 B 99 VAL ILE LYS GLY ILE VAL ASP GLN GLU GLY VAL ALA THR SEQRES 3 B 99 ALA TYR THR LEU GLY MET MET LEU SER GLY GLN ASN TYR SEQRES 4 B 99 GLN LEU VAL SER GLY ILE ILE ARG GLY TYR LEU PRO GLY SEQRES 5 B 99 GLN ALA VAL VAL THR ALA LEU GLN GLN ARG LEU ASP GLN SEQRES 6 B 99 GLU ILE ASP ASP GLN THR ARG ALA GLU THR PHE ILE GLN SEQRES 7 B 99 HIS LEU ASN ALA VAL TYR GLU ILE LEU GLY LEU ASN ALA SEQRES 8 B 99 ARG GLY GLN SER ILE ARG LEU GLU HELIX 1 AA1 GLY A 392 GLU A 402 1 11 HELIX 2 AA2 GLY A 403 GLY A 416 1 14 HELIX 3 AA3 ASN A 418 ARG A 427 1 10 HELIX 4 AA4 GLY A 432 GLU A 446 1 15 HELIX 5 AA5 ASP A 449 THR A 455 1 7 HELIX 6 AA6 THR A 455 GLY A 468 1 14 HELIX 7 AA7 GLY B 392 GLU B 402 1 11 HELIX 8 AA8 GLY B 403 GLY B 416 1 14 HELIX 9 AA9 ASN B 418 ARG B 427 1 10 HELIX 10 AB1 GLY B 432 GLU B 446 1 15 HELIX 11 AB2 ASP B 449 THR B 455 1 7 HELIX 12 AB3 THR B 455 GLY B 468 1 14 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