HEADER VIRAL PROTEIN 16-JUL-19 6SAI TITLE NMR SOLUTION STRUCTURE OF HML-2 C-TERMINAL DIMER DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN ENDOGENOUS RETROVIRUS K; SOURCE 3 ORGANISM_TAXID: 45617; SOURCE 4 GENE: GAG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HUMAN-ENDOGENOUS-RETROVIRUSES, RETROVIRIDAE, ORTERVIRALES., VIRAL KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.NICASTRO,I.A.TAYLOR,N.J.BALL,A.RAMOS REVDAT 1 15-JAN-20 6SAI 0 JRNL AUTH O.ACTON,T.GRANT,G.NICASTRO,N.J.BALL,D.C.GOLDSTONE, JRNL AUTH 2 L.E.ROBERTSON,K.SADER,A.NANS,A.RAMOS,J.P.STOYE,I.A.TAYLOR, JRNL AUTH 3 P.B.ROSENTHAL JRNL TITL STRUCTURAL BASIS FOR FULLERENE GEOMETRY IN A HUMAN JRNL TITL 2 ENDOGENOUS RETROVIRUS CAPSID. JRNL REF NAT COMMUN V. 10 5822 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31862888 JRNL DOI 10.1038/S41467-019-13786-Y REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.BELSHAW REMARK 1 TITL LONG-TERM REINFECTION OF THE HUMAN GENOME BY ENDOGENOUS REMARK 1 TITL 2 RETROVIRUSES. REMARK 1 REF PROC NATL ACAD SCI U S A. V.14): 894-9 2004 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 15044706 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 6SAI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1292103309. 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 : 50 REMARK 210 PRESSURE : 1 MMHG REMARK 210 SAMPLE CONTENTS : 2.3 MM [U-13C; U-15N] HML-2 CTD, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D CBCA(CO)NH; 3D HNCO; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D 1H-15N REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA, XEASY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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: 1320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 O PRO A 49 HG SER A 53 1.57 REMARK 500 O PRO B 49 HG SER B 53 1.57 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 10 100.46 -52.26 REMARK 500 1 TYR A 44 -68.78 -104.08 REMARK 500 1 LYS A 59 108.95 -54.64 REMARK 500 1 ALA A 82 -74.35 66.33 REMARK 500 1 SER B 2 -179.74 -68.48 REMARK 500 1 SER B 10 100.35 -51.67 REMARK 500 1 TYR B 44 -68.71 -104.09 REMARK 500 1 LYS B 59 108.96 -54.70 REMARK 500 1 ALA B 82 -74.79 66.08 REMARK 500 2 SER A 10 95.45 -51.98 REMARK 500 2 LYS A 11 43.47 37.76 REMARK 500 2 TYR A 44 -67.92 -108.22 REMARK 500 2 ALA A 47 -179.13 -60.40 REMARK 500 2 LYS A 59 109.22 -53.45 REMARK 500 2 ALA A 64 96.63 -60.71 REMARK 500 2 ILE A 79 -88.91 -79.78 REMARK 500 2 ALA A 82 -71.13 68.25 REMARK 500 2 SER B 10 95.17 -52.07 REMARK 500 2 LYS B 11 43.93 37.90 REMARK 500 2 TYR B 44 -67.68 -108.17 REMARK 500 2 ALA B 47 -179.27 -60.44 REMARK 500 2 LYS B 59 109.34 -53.41 REMARK 500 2 ALA B 64 96.34 -61.19 REMARK 500 2 ILE B 79 -89.37 -79.55 REMARK 500 2 ALA B 82 -71.05 67.87 REMARK 500 3 SER A 2 -178.90 -67.57 REMARK 500 3 GLN A 8 116.65 -39.07 REMARK 500 3 SER A 10 100.51 -48.25 REMARK 500 3 LYS A 11 42.67 38.24 REMARK 500 3 TYR A 44 -66.39 -108.15 REMARK 500 3 ALA A 47 -179.94 -59.77 REMARK 500 3 LYS A 59 108.64 -54.73 REMARK 500 3 ALA A 82 -85.01 56.46 REMARK 500 3 SER B 2 -179.24 -67.88 REMARK 500 3 GLN B 8 116.77 -38.70 REMARK 500 3 SER B 10 100.60 -48.19 REMARK 500 3 LYS B 11 42.04 38.46 REMARK 500 3 TYR B 44 -66.39 -108.06 REMARK 500 3 ALA B 47 179.76 -59.72 REMARK 500 3 LYS B 59 108.81 -54.65 REMARK 500 3 ALA B 82 -85.19 56.68 REMARK 500 4 SER A 10 99.13 -54.25 REMARK 500 4 LYS A 11 46.52 34.56 REMARK 500 4 TYR A 44 -65.68 -109.05 REMARK 500 4 ALA A 47 -175.96 -64.33 REMARK 500 4 LYS A 59 108.40 -52.94 REMARK 500 4 ALA A 82 -75.67 68.37 REMARK 500 4 SER B 10 98.91 -54.73 REMARK 500 4 LYS B 11 46.60 34.99 REMARK 500 4 TYR B 44 -65.63 -109.05 REMARK 500 REMARK 500 THIS ENTRY HAS 242 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 17 ARG A 35 0.16 SIDE CHAIN REMARK 500 17 ARG B 35 0.16 SIDE CHAIN REMARK 500 19 ARG A 7 0.16 SIDE CHAIN REMARK 500 19 ARG B 7 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6SA9 RELATED DB: PDB REMARK 900 RELATED ID: 34419 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF HML-2 C-TERMINAL DIMER DOMAIN DBREF 6SAI A 1 91 UNP P87891 P87891_9RETR 198 288 DBREF 6SAI B 1 91 UNP P87891 P87891_9RETR 198 288 SEQADV 6SAI LEU A 92 UNP P87891 EXPRESSION TAG SEQADV 6SAI GLU A 93 UNP P87891 EXPRESSION TAG SEQADV 6SAI LEU B 92 UNP P87891 EXPRESSION TAG SEQADV 6SAI GLU B 93 UNP P87891 EXPRESSION TAG SEQRES 1 A 93 PRO SER PHE ASN THR VAL ARG GLN GLY SER LYS GLU PRO SEQRES 2 A 93 TYR PRO ASP PHE VAL ALA ARG LEU GLN ASP VAL ALA GLN SEQRES 3 A 93 LYS SER ILE ALA ASP GLU LYS ALA ARG LYS VAL ILE VAL SEQRES 4 A 93 GLU LEU MET ALA TYR GLU ASN ALA ASN PRO GLU CYS GLN SEQRES 5 A 93 SER ALA ILE LYS PRO LEU LYS GLY LYS VAL PRO ALA GLY SEQRES 6 A 93 SER ASP VAL ILE SER GLU TYR VAL LYS ALA CYS ASP GLY SEQRES 7 A 93 ILE GLY GLY ALA MET HIS LYS ALA MET LEU MET ALA GLN SEQRES 8 A 93 LEU GLU SEQRES 1 B 93 PRO SER PHE ASN THR VAL ARG GLN GLY SER LYS GLU PRO SEQRES 2 B 93 TYR PRO ASP PHE VAL ALA ARG LEU GLN ASP VAL ALA GLN SEQRES 3 B 93 LYS SER ILE ALA ASP GLU LYS ALA ARG LYS VAL ILE VAL SEQRES 4 B 93 GLU LEU MET ALA TYR GLU ASN ALA ASN PRO GLU CYS GLN SEQRES 5 B 93 SER ALA ILE LYS PRO LEU LYS GLY LYS VAL PRO ALA GLY SEQRES 6 B 93 SER ASP VAL ILE SER GLU TYR VAL LYS ALA CYS ASP GLY SEQRES 7 B 93 ILE GLY GLY ALA MET HIS LYS ALA MET LEU MET ALA GLN SEQRES 8 B 93 LEU GLU HELIX 1 AA1 PRO A 13 ILE A 29 1 17 HELIX 2 AA2 ASP A 31 ASN A 46 1 16 HELIX 3 AA3 CYS A 51 LYS A 56 1 6 HELIX 4 AA4 ASP A 67 CYS A 76 1 10 HELIX 5 AA5 ASP A 77 ILE A 79 5 3 HELIX 6 AA6 ALA A 82 LEU A 88 1 7 HELIX 7 AA7 PRO B 13 ILE B 29 1 17 HELIX 8 AA8 ASP B 31 ASN B 46 1 16 HELIX 9 AA9 CYS B 51 LYS B 56 1 6 HELIX 10 AB1 ASP B 67 CYS B 76 1 10 HELIX 11 AB2 ALA B 82 LEU B 88 1 7 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