PDB Short entry for 5JYN HEADER VIRAL PROTEIN 14-MAY-16 5JYN TITLE STRUCTURE OF THE TRANSMEMBRANE DOMAIN OF HIV-1 GP41 IN BICELLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN GP160; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: GP41 DOMAIN RESIDUES 670-709; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: ENV; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PMM-LR6 KEYWDS TRANSMEMBRANE DOMAIN, LIPID BILAYER, TRANSMEMBRANE TRIMER, VIRAL KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR J.DEV,Q.FU,D.PARK,B.CHEN,J.J.CHOU REVDAT 6 14-JUN-23 5JYN 1 REMARK REVDAT 5 04-DEC-19 5JYN 1 REMARK REVDAT 4 20-SEP-17 5JYN 1 COMPND JRNL REVDAT 3 20-JUL-16 5JYN 1 JRNL REVDAT 2 06-JUL-16 5JYN 1 JRNL REVDAT 1 29-JUN-16 5JYN 0 JRNL AUTH J.DEV,D.PARK,Q.FU,J.CHEN,H.J.HA,F.GHANTOUS,T.HERRMANN, JRNL AUTH 2 W.CHANG,Z.LIU,G.FREY,M.S.SEAMAN,B.CHEN,J.J.CHOU JRNL TITL STRUCTURAL BASIS FOR MEMBRANE ANCHORING OF HIV-1 ENVELOPE JRNL TITL 2 SPIKE. JRNL REF SCIENCE V. 353 172 2016 JRNL REFN ESSN 1095-9203 JRNL PMID 27338706 JRNL DOI 10.1126/SCIENCE.AAF7066 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.42, XPLOR-NIH 2.42 REMARK 3 AUTHORS : G. MARIUS CLORE , GUILLERMO BERMEJO, , JOHN REMARK 3 KUSZEWSKI, CHARLES D. SCHWIETERS, AND NICO TJANDRA REMARK 3 (XPLOR-NIH), G. MARIUS CLORE , GUILLERMO BERMEJO, , REMARK 3 JOHN KUSZEWSKI, CHARLES D. SCHWIETERS, AND NICO REMARK 3 TJANDRA (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5JYN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221430. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-13C; U-15N; 85%-2H] REMARK 210 HIV-1 GP41 TRANSMEMBRANE DOMAIN, 60 MM REGULAR 1,2-DIMYRISTOYL- REMARK 210 SN-GLYCERO-3-PHOSPHOCHOLINE (DMPC), 120 MM REGULAR 1,2- REMARK 210 DIHEXANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE (DHPC), 25 MM REGULAR MES, REMARK 210 0.1 % REGULAR NAN3, 95% H2O/5% D2O; 0.8 MM [U-13C; U-15N] HIV-1 REMARK 210 GP41 TRANSMEMBRANE DOMAIN, 60 MM ACYL CHAINS 2H LABELED 1,2- REMARK 210 DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE (DMPC), 120 MM ACYL REMARK 210 CHAINS 2H LABELED 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE REMARK 210 (DHPC), 25 MM REGULAR MES, 0.1 % REGULAR NAN3, 95% H2O/5% D2O; REMARK 210 0.4 MM [U-15N; U-2H] HIV-1 GP41 TRANSMEMBRANE DOMAIN, 0.4 MM [15% REMARK 210 13C] HIV-1 GP41 TRANSMEMBRANE DOMAIN, 60 MM ACYL CHAINS 2H REMARK 210 LABELED 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE (DMPC), 120 REMARK 210 MM ACYL CHAINS 2H LABELED 1,2-DIHEXANOYL-SN-GLYCERO-3- REMARK 210 PHOSPHOCHOLINE (DHPC), 25 MM REGULAR MES, 0.1 % REGULAR NAN3, 95% REMARK 210 H2O/5% D2O; 0.8 MM [U-15N] HIV-1 GP41 TRANSMEMBRANE DOMAIN, 60 REMARK 210 MM ACYL CHAINS 2H LABELED 1,2-DIMYRISTOYL-SN-GLYCERO-3- REMARK 210 PHOSPHOCHOLINE (DMPC), 120 MM ACYL CHAINS 2H LABELED 1,2- REMARK 210 DIHEXANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE (DHPC), 25 MM REGULAR MES, REMARK 210 0.1 % REGULAR NAN3, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D TROSY HNCA; 3D TROSY HNCOCA; REMARK 210 3D TROSY HNCACO; 3D 15N NOESY- REMARK 210 TROSY-HSQC; 3D 13C NOESY-HSQC REMARK 210 (METHYLS); 3D 15N NOESY-TROSY- REMARK 210 HSQC (LONG MIXING TIME); 2D 15N REMARK 210 TROSY-HSQC FOR GDDOTA TITRATION; REMARK 210 3D 15N NOESY-TROSY-HSQC (SHORT REMARK 210 MIXING TIME) REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR, NMRPIPE, XEASY, TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 150 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 8 TYR A 681 CB TYR A 681 CG 0.090 REMARK 500 8 TYR C 681 CB TYR C 681 CG 0.090 REMARK 500 10 PHE A 699 CB PHE A 699 CG 0.103 REMARK 500 12 TYR C 681 CB TYR C 681 CG 0.094 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 5 TYR C 712 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 5 TYR C 712 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 12 TYR C 712 CB - CG - CD2 ANGL. DEV. = 4.0 DEGREES REMARK 500 12 TYR C 712 CB - CG - CD1 ANGL. DEV. = -3.8 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 LEU B 715 165.80 -46.56 REMARK 500 1 TRP C 678 -56.14 56.55 REMARK 500 2 LEU A 715 -117.87 -61.51 REMARK 500 2 TRP C 678 -40.44 -169.06 REMARK 500 2 LEU C 715 176.81 65.28 REMARK 500 3 TRP A 678 -76.94 -156.65 REMARK 500 3 TRP C 678 -30.00 -170.83 REMARK 500 3 LEU C 715 -67.87 65.56 REMARK 500 4 TRP A 678 102.74 54.87 REMARK 500 4 LEU A 715 70.63 50.05 REMARK 500 4 LEU B 715 170.15 -58.64 REMARK 500 4 TRP C 678 -71.30 -166.31 REMARK 500 5 TRP A 678 -74.21 -166.90 REMARK 500 5 LEU A 715 -79.01 57.95 REMARK 500 5 TRP B 678 -30.44 59.07 REMARK 500 5 LEU B 715 -57.09 -144.93 REMARK 500 5 LEU C 715 79.46 55.90 REMARK 500 6 TRP A 678 -77.66 -165.30 REMARK 500 6 TRP B 678 -47.31 -165.35 REMARK 500 6 TRP C 678 113.10 58.59 REMARK 500 6 LEU C 715 90.89 -56.94 REMARK 500 7 TRP A 678 -87.21 57.58 REMARK 500 7 TRP B 678 -74.18 -166.17 REMARK 500 7 LEU C 715 -101.39 51.92 REMARK 500 8 LEU A 715 42.44 -97.87 REMARK 500 8 LEU B 715 143.74 60.81 REMARK 500 9 LEU A 715 149.25 63.10 REMARK 500 9 LEU B 715 123.80 59.63 REMARK 500 9 LEU C 715 148.94 62.73 REMARK 500 10 LEU A 715 81.83 -68.10 REMARK 500 10 TRP C 678 -152.46 -82.96 REMARK 500 10 LEU C 715 94.64 -61.97 REMARK 500 11 TRP A 678 -78.02 -170.01 REMARK 500 11 LEU B 715 -57.02 -144.19 REMARK 500 11 LEU C 715 -49.93 -158.63 REMARK 500 12 TRP A 678 -13.74 -165.87 REMARK 500 12 TRP B 678 105.52 54.92 REMARK 500 13 LEU A 715 76.88 62.19 REMARK 500 13 LEU B 715 -77.09 -86.73 REMARK 500 13 TRP C 678 -106.20 -166.74 REMARK 500 14 TRP A 678 -104.97 -122.58 REMARK 500 14 LEU A 715 110.55 59.55 REMARK 500 14 TRP C 678 -59.86 67.93 REMARK 500 15 TRP A 678 128.30 60.22 REMARK 500 15 LEU C 715 -167.14 -65.81 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 14 ARG A 696 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30090 RELATED DB: BMRB DBREF 5JYN A 677 716 UNP Q74849 Q74849_9HIV1 670 709 DBREF 5JYN B 677 716 UNP Q74849 Q74849_9HIV1 670 709 DBREF 5JYN C 677 716 UNP Q74849 Q74849_9HIV1 670 709 SEQRES 1 A 40 ASN TRP LEU TRP TYR ILE ARG ILE PHE ILE ILE ILE VAL SEQRES 2 A 40 GLY SER LEU ILE GLY LEU ARG ILE VAL PHE ALA VAL LEU SEQRES 3 A 40 SER LEU VAL ASN ARG VAL ARG GLN GLY TYR SER PRO LEU SEQRES 4 A 40 SER SEQRES 1 B 40 ASN TRP LEU TRP TYR ILE ARG ILE PHE ILE ILE ILE VAL SEQRES 2 B 40 GLY SER LEU ILE GLY LEU ARG ILE VAL PHE ALA VAL LEU SEQRES 3 B 40 SER LEU VAL ASN ARG VAL ARG GLN GLY TYR SER PRO LEU SEQRES 4 B 40 SER SEQRES 1 C 40 ASN TRP LEU TRP TYR ILE ARG ILE PHE ILE ILE ILE VAL SEQRES 2 C 40 GLY SER LEU ILE GLY LEU ARG ILE VAL PHE ALA VAL LEU SEQRES 3 C 40 SER LEU VAL ASN ARG VAL ARG GLN GLY TYR SER PRO LEU SEQRES 4 C 40 SER HELIX 1 AA1 TRP A 678 ARG A 696 1 19 HELIX 2 AA2 ILE A 697 GLY A 711 1 15 HELIX 3 AA3 TRP B 678 ILE B 697 1 20 HELIX 4 AA4 VAL B 698 TYR B 712 1 15 HELIX 5 AA5 TRP C 678 ARG C 696 1 19 HELIX 6 AA6 VAL C 698 GLN C 710 1 13 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