HEADER VIRAL PROTEIN 17-FEB-07 2JO0 TITLE THE SOLUTION STRUCTURE OF THE MONOMERIC SPECIES OF THE C TERMINAL TITLE 2 DOMAIN OF THE CA PROTEIN OF HIV-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG-POL POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 278-363; COMPND 5 SYNONYM: PR160GAG-POL; COMPND 6 EC: 3.4.23.16; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: GAG-POL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET21B KEYWDS HIV, MONOMER, CAPSID PROTEIN, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR L.A.ALCARAZ,M.DEL ALAMO,F.N.BARRERA,M.G.MATEU,J.L.NEIRA REVDAT 4 20-DEC-23 2JO0 1 REMARK REVDAT 3 20-OCT-21 2JO0 1 REMARK SEQADV REVDAT 2 24-FEB-09 2JO0 1 VERSN REVDAT 1 31-JUL-07 2JO0 0 JRNL AUTH L.A.ALCARAZ,M.DEL ALAMO,F.N.BARRERA,M.G.MATEU,J.L.NEIRA JRNL TITL FLEXIBILITY IN HIV-1 ASSEMBLY SUBUNITS: SOLUTION STRUCTURE JRNL TITL 2 OF THE MONOMERIC C-TERMINAL DOMAIN OF THE CAPSID PROTEIN JRNL REF BIOPHYS.J. V. 93 1264 2007 JRNL REFN ISSN 0006-3495 JRNL PMID 17526561 JRNL DOI 10.1529/BIOPHYSJ.106.101089 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, AMBER 8 REMARK 3 AUTHORS : P GUNTERT, C MUMENTHALER AND K WUTHRICH (CYANA), REMARK 3 DA CASE, TA DARDEN, TE CHEATHAM, III, CL REMARK 3 SIMMERLING, J WANG, RE DUKE, (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JO0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000100072. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-15N] PROTEIN, 100 MM REMARK 210 POTASSIUM PHOSPHATE, 0.00001 MM REMARK 210 TSP, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 2D 1H-15N REMARK 210 HSQC; 3D 1H-15N NOESY; 3D 1H-15N REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.0, XWINNMR REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 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 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 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 PRO A 13 C - N - CA ANGL. DEV. = 10.6 DEGREES REMARK 500 1 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 5 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 6 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 6 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 7 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 9 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 12 LEU A 87 C - N - CA ANGL. DEV. = 15.7 DEGREES REMARK 500 13 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 17 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 18 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 19 ARG A 18 CD - NE - CZ ANGL. DEV. = 9.1 DEGREES REMARK 500 19 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 19 ARG A 18 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 20 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 20 VAL A 21 CA - CB - CG1 ANGL. DEV. = 10.2 DEGREES REMARK 500 20 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 20 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 21 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 21 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 22 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 22 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 23 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 27 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 28 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 28 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 29 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 4.7 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 THR A 4 101.10 -161.48 REMARK 500 1 LEU A 7 3.31 -63.30 REMARK 500 1 ARG A 10 9.40 -65.90 REMARK 500 1 GLN A 11 -63.12 -5.32 REMARK 500 1 PRO A 13 33.42 -61.73 REMARK 500 1 PHE A 17 -72.20 -41.66 REMARK 500 1 ARG A 29 7.44 -44.81 REMARK 500 1 GLN A 32 54.13 -154.34 REMARK 500 1 SER A 34 16.80 -63.41 REMARK 500 1 ASN A 39 20.09 -59.97 REMARK 500 1 MET A 41 -45.10 -139.67 REMARK 500 1 ASN A 49 -28.00 50.83 REMARK 500 1 ALA A 50 -179.70 46.79 REMARK 500 1 ASP A 53 -73.83 -59.76 REMARK 500 1 LEU A 61 57.35 -93.32 REMARK 500 1 PRO A 63 35.75 -75.32 REMARK 500 1 ALA A 64 5.59 57.87 REMARK 500 1 ALA A 65 -69.37 -135.72 REMARK 500 1 HIS A 82 51.83 -143.58 REMARK 500 2 ILE A 6 -68.93 -164.71 REMARK 500 2 ASP A 8 -40.43 -158.31 REMARK 500 2 GLU A 15 -44.35 -148.09 REMARK 500 2 PRO A 16 43.31 -81.52 REMARK 500 2 ALA A 33 0.95 55.51 REMARK 500 2 SER A 34 40.25 -69.92 REMARK 500 2 GLN A 35 47.70 -70.45 REMARK 500 2 ASN A 39 -70.64 4.42 REMARK 500 2 LEU A 45 17.70 -152.50 REMARK 500 2 LEU A 46 -179.69 179.58 REMARK 500 2 ASN A 49 4.36 -66.13 REMARK 500 2 PRO A 63 40.69 -76.34 REMARK 500 2 ALA A 64 -3.85 59.03 REMARK 500 2 ALA A 65 -58.68 -133.07 REMARK 500 2 VAL A 77 21.03 -63.56 REMARK 500 2 HIS A 82 49.11 30.39 REMARK 500 3 SER A 5 173.42 -53.97 REMARK 500 3 LEU A 7 -12.39 -42.91 REMARK 500 3 ARG A 10 55.90 -0.48 REMARK 500 3 GLN A 11 102.94 -36.84 REMARK 500 3 LYS A 14 -98.46 -20.38 REMARK 500 3 PRO A 16 39.71 -79.68 REMARK 500 3 ARG A 29 12.51 -65.40 REMARK 500 3 GLU A 31 -63.07 -139.86 REMARK 500 3 ALA A 33 -17.19 50.05 REMARK 500 3 GLN A 35 48.61 32.32 REMARK 500 3 ASN A 39 -36.75 9.61 REMARK 500 3 ALA A 40 -146.14 -71.82 REMARK 500 3 GLU A 43 -9.63 -54.66 REMARK 500 3 THR A 44 97.29 -57.70 REMARK 500 3 ILE A 57 -62.17 -95.52 REMARK 500 REMARK 500 THIS ENTRY HAS 590 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 1 ARG A 18 0.12 SIDE CHAIN REMARK 500 1 TYR A 25 0.08 SIDE CHAIN REMARK 500 4 ARG A 23 0.10 SIDE CHAIN REMARK 500 6 TYR A 20 0.07 SIDE CHAIN REMARK 500 6 TYR A 25 0.09 SIDE CHAIN REMARK 500 7 ARG A 10 0.08 SIDE CHAIN REMARK 500 7 TYR A 25 0.08 SIDE CHAIN REMARK 500 8 ARG A 23 0.09 SIDE CHAIN REMARK 500 10 TYR A 25 0.10 SIDE CHAIN REMARK 500 11 TYR A 25 0.09 SIDE CHAIN REMARK 500 14 TYR A 25 0.15 SIDE CHAIN REMARK 500 16 TYR A 25 0.08 SIDE CHAIN REMARK 500 16 ARG A 85 0.13 SIDE CHAIN REMARK 500 17 PHE A 24 0.12 SIDE CHAIN REMARK 500 18 PHE A 24 0.12 SIDE CHAIN REMARK 500 20 ARG A 18 0.13 SIDE CHAIN REMARK 500 21 TYR A 25 0.08 SIDE CHAIN REMARK 500 22 ARG A 10 0.11 SIDE CHAIN REMARK 500 23 ARG A 10 0.08 SIDE CHAIN REMARK 500 24 ARG A 18 0.11 SIDE CHAIN REMARK 500 24 PHE A 24 0.09 SIDE CHAIN REMARK 500 25 ARG A 10 0.10 SIDE CHAIN REMARK 500 26 PHE A 24 0.09 SIDE CHAIN REMARK 500 27 TYR A 25 0.13 SIDE CHAIN REMARK 500 28 ARG A 18 0.11 SIDE CHAIN REMARK 500 28 TYR A 20 0.09 SIDE CHAIN REMARK 500 28 ARG A 29 0.09 SIDE CHAIN REMARK 500 29 TYR A 25 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A43 RELATED DB: PDB REMARK 900 DIMERIC PROTEIN DBREF 2JO0 A 2 87 UNP P35963 POL_HV1Y2 278 363 SEQADV 2JO0 MET A 1 UNP P35963 EXPRESSION TAG SEQADV 2JO0 ALA A 40 UNP P35963 TRP 316 ENGINEERED MUTATION SEQRES 1 A 87 MET SER PRO THR SER ILE LEU ASP ILE ARG GLN GLY PRO SEQRES 2 A 87 LYS GLU PRO PHE ARG ASP TYR VAL ASP ARG PHE TYR LYS SEQRES 3 A 87 THR LEU ARG ALA GLU GLN ALA SER GLN GLU VAL LYS ASN SEQRES 4 A 87 ALA MET THR GLU THR LEU LEU VAL GLN ASN ALA ASN PRO SEQRES 5 A 87 ASP CYS LYS THR ILE LEU LYS ALA LEU GLY PRO ALA ALA SEQRES 6 A 87 THR LEU GLU GLU MET MET THR ALA CYS GLN GLY VAL GLY SEQRES 7 A 87 GLY PRO GLY HIS LYS ALA ARG VAL LEU HELIX 1 1 SER A 5 ARG A 10 1 6 HELIX 2 2 PRO A 16 ARG A 29 1 14 HELIX 3 3 ASN A 51 LYS A 59 1 9 HELIX 4 4 THR A 66 CYS A 74 1 9 HELIX 5 5 GLN A 75 VAL A 77 5 3 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