PDB Short entry for 2MK3 HEADER IMMUNE SYSTEM 23-JAN-14 2MK3 TITLE SOLUTION NMR STRUCTURE OF GP41 ECTODOMAIN MONOMER ON A DPC MICELLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSMEMBRANE GLYCOPROTEIN, CHIMERIC CONSTRUCT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 93-126; UNP RESIDUES 138-165; COMPND 5 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; SOURCE 6 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS HIV-1 ENV, MEMBRANE FUSION, GP41 ECTODOMAIN, PRE-HAIRPIN, CORES, KEYWDS 2 IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.ROCHE,J.M.LOUIS,A.GRISHAEV,J.YING,A.BAX REVDAT 2 19-MAR-14 2MK3 1 JRNL REVDAT 1 19-FEB-14 2MK3 0 JRNL AUTH J.ROCHE,J.M.LOUIS,A.GRISHAEV,J.YING,A.BAX JRNL TITL DISSOCIATION OF THE TRIMERIC GP41 ECTODOMAIN AT THE JRNL TITL 2 LIPID-WATER INTERFACE SUGGESTS AN ACTIVE ROLE IN HIV-1 JRNL TITL 3 ENV-MEDIATED MEMBRANE FUSION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 3425 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 24550514 JRNL DOI 10.1073/PNAS.1401397111 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MK3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-14. REMARK 100 THE RCSB ID CODE IS RCSB103708. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 4.0 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 100 MM [U-99% 2H] DPC, 50 MM REMARK 210 SODIUM PHOSPHATE, 93% H2O/7% D2O; REMARK 210 100 MM [U-99% 2H] DPC, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 93% H2O/7% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D HNCO; 3D 1H-15N REMARK 210 NOESY; 3D HCCH-TOCSY; 2D 1H-1H REMARK 210 NOESY; 2D 1H-15N ARTSY; 2D 1H-15N REMARK 210 TROSY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 900 MHZ; 500 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR_NIH 2.34 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 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 ASN A 9 H ALA A 13 1.59 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 16 40.93 -71.72 REMARK 500 1 GLN A 17 10.21 -157.87 REMARK 500 1 GLU A 43 -77.95 -42.29 REMARK 500 1 GLN A 66 -73.55 -158.81 REMARK 500 2 ALA A 16 37.07 -73.94 REMARK 500 2 GLN A 17 11.07 -151.78 REMARK 500 2 GLN A 66 -71.25 -155.73 REMARK 500 3 ALA A 16 37.81 -73.90 REMARK 500 3 GLN A 17 9.85 -151.67 REMARK 500 3 GLU A 43 -79.26 -42.55 REMARK 500 3 TRP A 44 -7.28 -58.93 REMARK 500 3 GLN A 63 25.45 -46.48 REMARK 500 3 GLN A 66 -70.04 -174.02 REMARK 500 4 ALA A 16 39.84 -71.40 REMARK 500 4 GLN A 17 11.75 -156.89 REMARK 500 4 GLU A 43 -77.83 -41.38 REMARK 500 4 TRP A 44 -6.92 -59.15 REMARK 500 4 GLN A 66 -72.40 -151.71 REMARK 500 5 ALA A 16 40.65 -70.02 REMARK 500 5 GLN A 17 12.67 -157.61 REMARK 500 5 GLU A 43 -77.78 -41.44 REMARK 500 5 TRP A 44 -7.02 -57.79 REMARK 500 5 GLN A 66 -72.94 -151.07 REMARK 500 6 ALA A 16 40.80 -73.49 REMARK 500 6 GLN A 17 8.85 -155.72 REMARK 500 6 GLU A 43 -77.17 -42.79 REMARK 500 6 TRP A 44 -8.81 -55.33 REMARK 500 6 GLN A 66 -72.66 -139.96 REMARK 500 7 ALA A 16 43.40 -65.40 REMARK 500 7 GLN A 17 22.27 -159.45 REMARK 500 7 GLN A 66 -71.50 -144.91 REMARK 500 8 ALA A 16 37.06 -73.43 REMARK 500 8 GLN A 17 10.81 -150.92 REMARK 500 8 GLU A 43 -79.79 -43.31 REMARK 500 8 TRP A 44 -8.63 -55.81 REMARK 500 8 GLN A 63 29.40 -43.18 REMARK 500 8 GLN A 66 -75.11 -174.29 REMARK 500 9 GLN A 5 -79.45 -44.20 REMARK 500 9 ALA A 16 45.06 -70.08 REMARK 500 9 GLN A 17 12.30 -160.22 REMARK 500 9 GLU A 43 -76.52 -42.21 REMARK 500 9 TRP A 44 -8.26 -57.96 REMARK 500 9 GLN A 66 -69.36 -144.30 REMARK 500 10 ALA A 13 -33.39 -38.65 REMARK 500 10 ALA A 16 30.42 -78.18 REMARK 500 10 LEU A 31 -70.79 -60.32 REMARK 500 10 GLU A 43 -80.16 -43.33 REMARK 500 10 TRP A 44 -7.97 -54.04 REMARK 500 10 GLN A 66 -66.14 -153.41 REMARK 500 11 ALA A 16 35.76 -74.33 REMARK 500 REMARK 500 THIS ENTRY HAS 95 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19750 RELATED DB: BMRB DBREF 2MK3 A 1 34 UNP D0VWW0 D0VWW0_9HIV1 93 126 DBREF 2MK3 A 41 68 UNP D0VWW0 D0VWW0_9HIV1 138 165 SEQADV 2MK3 GLY A -3 UNP D0VWW0 EXPRESSION TAG SEQADV 2MK3 SER A -2 UNP D0VWW0 EXPRESSION TAG SEQADV 2MK3 HIS A -1 UNP D0VWW0 EXPRESSION TAG SEQADV 2MK3 MET A 0 UNP D0VWW0 EXPRESSION TAG SEQADV 2MK3 SER A 35 UNP D0VWW0 LINKER SEQADV 2MK3 GLY A 36 UNP D0VWW0 LINKER SEQADV 2MK3 GLY A 37 UNP D0VWW0 LINKER SEQADV 2MK3 ARG A 38 UNP D0VWW0 LINKER SEQADV 2MK3 GLY A 39 UNP D0VWW0 LINKER SEQADV 2MK3 GLY A 40 UNP D0VWW0 LINKER SEQRES 1 A 72 GLY SER HIS MET SER GLY ILE VAL GLN GLN GLN ASN ASN SEQRES 2 A 72 LEU LEU ARG ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN SEQRES 3 A 72 LEU THR VAL TRP GLY ILE LYS GLN LEU GLN ALA ARG SER SEQRES 4 A 72 GLY GLY ARG GLY GLY TRP MET GLU TRP ASP ARG GLU ILE SEQRES 5 A 72 ASN ASN TYR THR SER LEU ILE HIS SER LEU ILE GLU GLU SEQRES 6 A 72 SER GLN ASN GLN GLN GLU LYS HELIX 1 1 GLY A 2 ALA A 16 1 15 HELIX 2 2 HIS A 19 ALA A 33 1 15 HELIX 3 3 TRP A 41 GLN A 63 1 23 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