HEADER VIRAL PROTEIN 01-MAY-13 2M7W TITLE INDEPENDENTLY VERIFIED STRUCTURE OF GP41-M-MAT, A MEMBRANE ASSOCIATED TITLE 2 MPER TRIMER FROM HIV-1 GP41 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MPER, GP41, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 18 AUTHOR J.W.MARTIN,P.N.REARDON,H.S.SAGE,D.S.MOSES,A.S.MUNIR,B.F.HAYNES, AUTHOR 2 L.D.SPICER,B.R.DONALD REVDAT 3 05-MAR-14 2M7W 1 JRNL REVDAT 2 22-JAN-14 2M7W 1 JRNL REVDAT 1 15-MAY-13 2M7W 0 JRNL AUTH P.N.REARDON,H.SAGE,S.M.DENNISON,J.W.MARTIN,B.R.DONALD, JRNL AUTH 2 S.M.ALAM,B.F.HAYNES,L.D.SPICER JRNL TITL STRUCTURE OF AN HIV-1-NEUTRALIZING ANTIBODY TARGET, THE JRNL TITL 2 LIPID-BOUND GP41 ENVELOPE MEMBRANE PROXIMAL REGION TRIMER. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 1391 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 24474763 JRNL DOI 10.1073/PNAS.1309842111 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH 2.33 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISCO USED TO COMPUTE MPER QUATERNARY REMARK 3 STRUCTURE, XPLOR-NIH USED TO COMPUTE MPER SUBUNIT STRUCTURE AND REMARK 3 LINKER/FOLDON TRIMER STRUCTURES AND ALSO FOR FULL-LENGTH REMARK 3 REFINEMENT. REMARK 4 REMARK 4 2M7W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-13. REMARK 100 THE RCSB ID CODE IS RCSB103320. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM PROTEIN, 50 MM SODIUM REMARK 210 PHOSPHATE, 100 MM [U-99% 2H] DPC, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HNCACB; 3D HN(CO)CA; 3D 1H-15N REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 950 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DISCO 1, X-PLOR_NIH 2.33 REMARK 210 METHOD USED : COMPLETE SEARCH, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 GLU A 38 CB GLU A 38 CG 0.117 REMARK 500 8 GLU B 38 CB GLU B 38 CG 0.117 REMARK 500 8 GLU C 38 CB GLU C 38 CG 0.117 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 6 PHE A 26 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 6 PHE A 26 CB - CG - CD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 6 PHE B 26 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 6 PHE B 26 CB - CG - CD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 6 PHE C 26 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 6 PHE C 26 CB - CG - CD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 10 TRP A 20 CB - CG - CD2 ANGL. DEV. = 7.9 DEGREES REMARK 500 10 TRP B 20 CB - CG - CD2 ANGL. DEV. = 7.9 DEGREES REMARK 500 10 TRP C 20 CB - CG - CD2 ANGL. DEV. = 8.0 DEGREES REMARK 500 11 TYR A 13 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 11 TYR A 13 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 11 TYR B 13 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 11 TYR B 13 CB - CG - CD1 ANGL. DEV. = 3.8 DEGREES REMARK 500 11 TYR B 57 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 11 TYR C 13 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 11 TYR C 13 CB - CG - CD1 ANGL. DEV. = 3.7 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 ALA A 6 66.36 67.34 REMARK 500 1 ASP A 17 41.97 39.03 REMARK 500 1 SER A 29 -136.29 41.60 REMARK 500 1 ASN A 32 0.96 84.62 REMARK 500 1 ALA B 6 66.31 67.47 REMARK 500 1 ASP B 17 42.10 38.91 REMARK 500 1 SER B 29 -136.26 41.48 REMARK 500 1 ASN B 32 0.86 84.68 REMARK 500 1 ALA C 6 66.39 67.41 REMARK 500 1 ASP C 17 41.91 39.05 REMARK 500 1 SER C 29 -136.23 41.63 REMARK 500 1 ASN C 32 0.91 84.73 REMARK 500 2 TYR A 2 -123.29 -97.97 REMARK 500 2 ILE A 3 -54.89 -148.99 REMARK 500 2 ALA A 6 53.93 79.81 REMARK 500 2 ASN A 32 -14.22 -160.78 REMARK 500 2 TYR B 2 -123.38 -97.94 REMARK 500 2 ILE B 3 -54.86 -148.97 REMARK 500 2 ALA B 6 53.89 79.89 REMARK 500 2 ASN B 32 -14.19 -160.85 REMARK 500 2 TYR C 2 -123.46 -97.88 REMARK 500 2 ILE C 3 -54.85 -148.86 REMARK 500 2 ALA C 6 53.78 79.95 REMARK 500 2 ASN C 32 -14.22 -160.87 REMARK 500 3 TYR A 2 -123.08 -97.44 REMARK 500 3 ILE A 3 -45.55 -149.02 REMARK 500 3 ALA A 6 66.82 65.87 REMARK 500 3 ASP A 9 -3.62 -150.03 REMARK 500 3 ASP A 17 41.42 38.18 REMARK 500 3 ASN A 32 -10.11 -162.06 REMARK 500 3 TYR B 2 -122.98 -97.54 REMARK 500 3 ILE B 3 -45.49 -149.10 REMARK 500 3 ALA B 6 66.90 65.84 REMARK 500 3 ASP B 9 -3.59 -150.02 REMARK 500 3 ASP B 17 41.45 38.18 REMARK 500 3 ASN B 32 -10.21 -161.90 REMARK 500 3 TYR C 2 -123.15 -97.58 REMARK 500 3 ILE C 3 -45.45 -148.98 REMARK 500 3 ALA C 6 67.01 65.77 REMARK 500 3 ASP C 9 -3.68 -149.98 REMARK 500 3 ASP C 17 41.51 38.07 REMARK 500 3 ASN C 32 -10.41 -161.91 REMARK 500 4 TYR A 2 -77.69 -135.02 REMARK 500 4 ILE A 3 -45.92 -156.24 REMARK 500 4 ASP A 9 -3.42 -157.12 REMARK 500 4 LEU A 27 -73.93 -74.99 REMARK 500 4 SER A 30 -22.49 -163.63 REMARK 500 4 TYR B 2 -77.61 -135.07 REMARK 500 4 ILE B 3 -45.89 -156.31 REMARK 500 4 ASP B 9 -3.52 -157.07 REMARK 500 REMARK 500 THIS ENTRY HAS 302 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LP7 RELATED DB: PDB REMARK 900 PARALLEL VALIDATION OF STRUCTURE USING INDEPENDENT REMARK 900 METHODOLOGY REMARK 900 RELATED ID: 19215 RELATED DB: BMRB DBREF 2M7W A 1 59 UNP M1E1E4 M1E1E4_9HIV1 1 59 DBREF 2M7W B 1 59 UNP M1E1E4 M1E1E4_9HIV1 1 59 DBREF 2M7W C 1 59 UNP M1E1E4 M1E1E4_9HIV1 1 59 SEQRES 1 A 59 GLY TYR ILE PRO GLU ALA PRO ARG ASP GLY GLN ALA TYR SEQRES 2 A 59 VAL ARG LYS ASP GLY GLU TRP VAL LEU LEU SER THR PHE SEQRES 3 A 59 LEU GLY SER SER GLY ASN GLU GLN GLU LEU LEU GLU LEU SEQRES 4 A 59 ASP LYS TRP ALA SER LEU TRP ASN TRP PHE ASN ILE THR SEQRES 5 A 59 ASN TRP LEU TRP TYR ILE LYS SEQRES 1 B 59 GLY TYR ILE PRO GLU ALA PRO ARG ASP GLY GLN ALA TYR SEQRES 2 B 59 VAL ARG LYS ASP GLY GLU TRP VAL LEU LEU SER THR PHE SEQRES 3 B 59 LEU GLY SER SER GLY ASN GLU GLN GLU LEU LEU GLU LEU SEQRES 4 B 59 ASP LYS TRP ALA SER LEU TRP ASN TRP PHE ASN ILE THR SEQRES 5 B 59 ASN TRP LEU TRP TYR ILE LYS SEQRES 1 C 59 GLY TYR ILE PRO GLU ALA PRO ARG ASP GLY GLN ALA TYR SEQRES 2 C 59 VAL ARG LYS ASP GLY GLU TRP VAL LEU LEU SER THR PHE SEQRES 3 C 59 LEU GLY SER SER GLY ASN GLU GLN GLU LEU LEU GLU LEU SEQRES 4 C 59 ASP LYS TRP ALA SER LEU TRP ASN TRP PHE ASN ILE THR SEQRES 5 C 59 ASN TRP LEU TRP TYR ILE LYS HELIX 1 1 LEU A 23 GLY A 28 1 6 HELIX 2 2 ASN A 32 TRP A 48 1 17 HELIX 3 3 PHE A 49 LYS A 59 1 11 HELIX 4 4 LEU B 23 GLY B 28 1 6 HELIX 5 5 ASN B 32 TRP B 48 1 17 HELIX 6 6 PHE B 49 LYS B 59 1 11 HELIX 7 7 LEU C 23 GLY C 28 1 6 HELIX 8 8 ASN C 32 TRP C 48 1 17 HELIX 9 9 PHE C 49 LYS C 59 1 11 SHEET 1 A 4 GLU A 19 VAL A 21 0 SHEET 2 A 4 ALA A 12 LYS A 16 -1 N VAL A 14 O VAL A 21 SHEET 3 A 4 ALA C 12 LYS C 16 -1 O TYR C 13 N ARG A 15 SHEET 4 A 4 GLU C 19 VAL C 21 -1 O VAL C 21 N VAL C 14 SHEET 1 B 4 GLU B 19 VAL B 21 0 SHEET 2 B 4 ALA B 12 LYS B 16 -1 N VAL B 14 O VAL B 21 SHEET 3 B 4 ALA C 12 LYS C 16 -1 O ARG C 15 N TYR B 13 SHEET 4 B 4 GLU C 19 VAL C 21 -1 O VAL C 21 N VAL C 14 SHEET 1 C 4 GLU A 19 VAL A 21 0 SHEET 2 C 4 ALA A 12 LYS A 16 -1 N VAL A 14 O VAL A 21 SHEET 3 C 4 ALA B 12 LYS B 16 -1 O ARG B 15 N TYR A 13 SHEET 4 C 4 GLU B 19 VAL B 21 -1 O VAL B 21 N VAL B 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 202 0 0 9 12 0 0 6 0 0 0 15 END