PDB Short entry for 2PJV HEADER VIRAL PROTEIN 16-APR-07 2PJV TITLE SOLUTION STRUCTURE OF HIV-1 GP41 FUSION DOMAIN BOUND TO DPC MICELLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 23 N-TERMINAL RESIDUES; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 STRAIN: LAVMAL; SOURCE 5 GENE: ENV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BLR(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET31B(+) KEYWDS HIV, GP41, FUSION, MEMBRANE, PROTEIN, DPC, VIRUS, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 38 AUTHOR Y.LI,L.K.TAMM REVDAT 5 20-OCT-21 2PJV 1 REMARK SEQADV REVDAT 4 31-JAN-18 2PJV 1 AUTHOR REMARK REVDAT 3 24-FEB-09 2PJV 1 VERSN REVDAT 2 14-AUG-07 2PJV 1 JRNL REVDAT 1 01-MAY-07 2PJV 0 JRNL AUTH Y.LI,L.K.TAMM JRNL TITL STRUCTURE AND PLASTICITY OF THE HUMAN IMMUNODEFICIENCY VIRUS JRNL TITL 2 GP41 FUSION DOMAIN IN LIPID MICELLES AND BILAYERS. JRNL REF BIOPHYS.J. V. 93 876 2007 JRNL REFN ISSN 0006-3495 JRNL PMID 17513369 JRNL DOI 10.1529/BIOPHYSJ.106.102335 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR, OPAL 2.6 REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2PJV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000042457. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM N15-PEPTIDE IN THE PRESENCE REMARK 210 OF 200 MM D38-DPC IN 0.05% NAN3, REMARK 210 5 MM DTT, 20 MM D4-ACETIC ACID, REMARK 210 95% H2O/5% D2O; 2 MM PEPTIDE IN REMARK 210 THE PRESENCE OF 400 MM D38-DPC REMARK 210 IN 0.05% NAN3, 5 MM DTT, 20 MM REMARK 210 D4-ACETIC ACID, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.4, SPARKY 3.110, DYANA REMARK 210 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 38 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 38 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-38 REMARK 465 RES C SSSEQI REMARK 465 GLY A 25 REMARK 465 GLY A 26 REMARK 465 LYS A 27 REMARK 465 LYS A 28 REMARK 465 LYS A 29 REMARK 465 LYS A 30 REMARK 465 LYS A 31 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 VAL A 2 -72.26 -139.83 REMARK 500 2 VAL A 2 -68.00 66.27 REMARK 500 2 ALA A 21 15.24 50.64 REMARK 500 3 VAL A 2 -74.86 -134.18 REMARK 500 3 ALA A 21 46.97 -70.57 REMARK 500 5 SER A 17 47.06 -73.78 REMARK 500 6 VAL A 2 -75.05 -139.92 REMARK 500 6 ALA A 21 -57.15 65.57 REMARK 500 7 VAL A 2 -19.77 -33.87 REMARK 500 9 VAL A 2 -70.22 66.41 REMARK 500 9 SER A 17 48.82 -63.73 REMARK 500 10 VAL A 2 -68.22 68.07 REMARK 500 11 VAL A 2 -74.51 -137.91 REMARK 500 11 VAL A 19 151.23 -43.83 REMARK 500 12 VAL A 2 -70.83 -140.29 REMARK 500 12 VAL A 19 151.71 -43.94 REMARK 500 13 VAL A 2 -16.36 -40.26 REMARK 500 13 THR A 18 47.39 -82.30 REMARK 500 14 SER A 17 -100.50 -85.67 REMARK 500 14 VAL A 19 154.96 -44.28 REMARK 500 15 VAL A 2 -75.24 -137.81 REMARK 500 16 THR A 18 -70.17 -74.21 REMARK 500 16 VAL A 19 153.86 -44.15 REMARK 500 16 ALA A 21 28.44 48.87 REMARK 500 17 SER A 17 64.22 -69.80 REMARK 500 18 VAL A 2 -76.60 -142.52 REMARK 500 18 SER A 17 60.59 -67.49 REMARK 500 18 THR A 18 86.52 -68.43 REMARK 500 18 VAL A 19 156.02 -43.89 REMARK 500 18 ALA A 21 94.72 95.74 REMARK 500 19 VAL A 2 -63.96 64.90 REMARK 500 19 SER A 17 80.18 -67.38 REMARK 500 20 SER A 17 92.03 -63.98 REMARK 500 20 ALA A 21 80.57 61.00 REMARK 500 21 ALA A 21 -86.59 -164.07 REMARK 500 22 VAL A 2 -72.52 68.74 REMARK 500 23 THR A 18 -79.26 -90.56 REMARK 500 23 ALA A 21 60.87 -68.72 REMARK 500 24 VAL A 2 -71.61 66.87 REMARK 500 24 ALA A 21 13.78 59.94 REMARK 500 25 ALA A 21 -48.09 -155.32 REMARK 500 26 THR A 18 -79.55 -90.02 REMARK 500 27 VAL A 2 -73.89 67.05 REMARK 500 27 VAL A 19 158.70 -43.99 REMARK 500 27 ALA A 21 -13.25 56.58 REMARK 500 28 THR A 18 -91.00 -90.47 REMARK 500 28 ALA A 21 45.20 -74.32 REMARK 500 29 VAL A 2 -72.61 -140.54 REMARK 500 30 VAL A 19 -19.96 -43.84 REMARK 500 31 VAL A 2 -51.00 -120.90 REMARK 500 REMARK 500 THIS ENTRY HAS 66 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 SER A 23 GLY A 24 2 -138.50 REMARK 500 SER A 23 GLY A 24 3 -138.82 REMARK 500 SER A 23 GLY A 24 5 -141.82 REMARK 500 SER A 23 GLY A 24 6 -138.50 REMARK 500 SER A 23 GLY A 24 7 -141.67 REMARK 500 SER A 23 GLY A 24 9 -141.26 REMARK 500 SER A 23 GLY A 24 11 -138.97 REMARK 500 SER A 23 GLY A 24 14 -140.00 REMARK 500 THR A 18 VAL A 19 15 145.82 REMARK 500 THR A 18 VAL A 19 16 147.72 REMARK 500 SER A 23 GLY A 24 16 -138.59 REMARK 500 VAL A 19 GLY A 20 17 143.24 REMARK 500 SER A 23 GLY A 24 18 -140.57 REMARK 500 SER A 23 GLY A 24 20 -149.34 REMARK 500 SER A 23 GLY A 24 21 -138.47 REMARK 500 SER A 23 GLY A 24 22 -138.72 REMARK 500 SER A 23 GLY A 24 23 -147.00 REMARK 500 SER A 23 GLY A 24 24 -138.89 REMARK 500 SER A 23 GLY A 24 25 -144.48 REMARK 500 SER A 23 GLY A 24 27 -138.49 REMARK 500 SER A 23 GLY A 24 28 -139.28 REMARK 500 SER A 23 GLY A 24 32 -138.52 REMARK 500 SER A 23 GLY A 24 33 -139.14 REMARK 500 SER A 23 GLY A 24 35 -141.43 REMARK 500 SER A 23 GLY A 24 36 -138.76 REMARK 500 THR A 18 VAL A 19 37 146.93 REMARK 500 SER A 23 GLY A 24 37 -139.01 REMARK 500 SER A 23 GLY A 24 38 -139.47 REMARK 500 REMARK 500 REMARK: NULL DBREF 2PJV A 1 23 UNP P19551 ENV_HV1MF 510 532 SEQADV 2PJV VAL A 19 UNP P19551 MET 528 ENGINEERED MUTATION SEQADV 2PJV GLY A 24 UNP P19551 CLONING ARTIFACT SEQADV 2PJV GLY A 25 UNP P19551 CLONING ARTIFACT SEQADV 2PJV GLY A 26 UNP P19551 CLONING ARTIFACT SEQADV 2PJV LYS A 27 UNP P19551 CLONING ARTIFACT SEQADV 2PJV LYS A 28 UNP P19551 CLONING ARTIFACT SEQADV 2PJV LYS A 29 UNP P19551 CLONING ARTIFACT SEQADV 2PJV LYS A 30 UNP P19551 CLONING ARTIFACT SEQADV 2PJV LYS A 31 UNP P19551 CLONING ARTIFACT SEQRES 1 A 31 ALA VAL GLY ILE GLY ALA LEU PHE LEU GLY PHE LEU GLY SEQRES 2 A 31 ALA ALA GLY SER THR VAL GLY ALA ALA SER GLY GLY GLY SEQRES 3 A 31 LYS LYS LYS LYS LYS HELIX 1 1 GLY A 3 GLY A 10 1 8 HELIX 2 2 GLY A 10 ALA A 15 1 6 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