HEADER VIRAL PROTEIN 18-MAY-24 9FED TITLE SINGLE-CHAIN CHIMERIC PROTEIN MIMICKING THE INTERACTION BETWEEN HR1 TITLE 2 AND HR2 IN HIV GP41 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAINS: A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HIV-1 06TG.HT008; SOURCE 3 ORGANISM_TAXID: 587638; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GP41, HIV-1, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS,J.A.GAVIRA,F.CONEJERO-LARA,D.POLO-MEGIAS REVDAT 2 13-MAY-26 9FED 1 JRNL REVDAT 1 28-MAY-25 9FED 0 JRNL AUTH D.POLO-MEGIAS,M.CANO-MUNOZ,L.SANCHEZ-MARTINEZ,S.LESTANI, JRNL AUTH 2 C.MOOG,T.DECOVILLE,M.C.SALINAS-GARCIA,J.A.GAVIRA, JRNL AUTH 3 A.CAMARA-ARTIGAS,F.CONEJERO-LARA JRNL TITL INVESTIGATING THE ROLE OF A CONSERVED HYDROPHOBIC POCKET OF JRNL TITL 2 GP41 IN THE ANTI-HIV ACTIVITY OF FUSION INHIBITORS. JRNL REF PROTEIN SCI. V. 35 70593 2026 JRNL REFN ESSN 1469-896X JRNL PMID 42080310 JRNL DOI 10.1002/PRO.70593 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 9641 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.540 REMARK 3 FREE R VALUE TEST SET COUNT : 438 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.8400 - 3.3100 0.97 3060 136 0.1842 0.2003 REMARK 3 2 3.3100 - 2.6300 0.99 3055 163 0.2463 0.3374 REMARK 3 3 2.6300 - 2.3000 0.99 3088 139 0.2571 0.3259 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.273 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.079 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 1472 REMARK 3 ANGLE : 0.438 1981 REMARK 3 CHIRALITY : 0.027 233 REMARK 3 PLANARITY : 0.003 261 REMARK 3 DIHEDRAL : 3.400 196 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 32 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.8456 56.6096 -14.0997 REMARK 3 T TENSOR REMARK 3 T11: 0.3275 T22: 0.2879 REMARK 3 T33: 0.2565 T12: 0.0413 REMARK 3 T13: 0.0455 T23: 0.0201 REMARK 3 L TENSOR REMARK 3 L11: 8.6082 L22: 5.9654 REMARK 3 L33: 7.5598 L12: 2.4142 REMARK 3 L13: 2.9214 L23: 0.9475 REMARK 3 S TENSOR REMARK 3 S11: 0.0180 S12: 0.6432 S13: 0.5112 REMARK 3 S21: -0.2981 S22: -0.0922 S23: 0.4911 REMARK 3 S31: 0.2069 S32: -0.0264 S33: 0.0613 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 33 THROUGH 143 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.2843 56.5733 5.9888 REMARK 3 T TENSOR REMARK 3 T11: 0.2209 T22: 0.2450 REMARK 3 T33: 0.2723 T12: 0.0109 REMARK 3 T13: 0.0948 T23: 0.0451 REMARK 3 L TENSOR REMARK 3 L11: 4.4740 L22: 3.3098 REMARK 3 L33: 6.0879 L12: 2.7218 REMARK 3 L13: 4.0895 L23: 3.1968 REMARK 3 S TENSOR REMARK 3 S11: 0.1749 S12: -0.3293 S13: -0.1335 REMARK 3 S21: 0.3045 S22: -0.2079 S23: 0.0402 REMARK 3 S31: 0.2645 S32: -0.2154 S33: 0.0918 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 144 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.8673 55.0729 5.3990 REMARK 3 T TENSOR REMARK 3 T11: 0.3472 T22: 0.3014 REMARK 3 T33: 0.3435 T12: 0.0166 REMARK 3 T13: 0.0492 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 6.7008 L22: 1.2156 REMARK 3 L33: 7.6641 L12: 2.7576 REMARK 3 L13: 7.5122 L23: 3.2063 REMARK 3 S TENSOR REMARK 3 S11: 0.2375 S12: 0.0832 S13: -0.1861 REMARK 3 S21: 0.1987 S22: -0.0089 S23: -0.0866 REMARK 3 S31: 0.5930 S32: 0.0210 S33: -0.2459 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9FED COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1292138408. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87313 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9644 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 19.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.54800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE, 30% (W/V) REMARK 280 PEG4000, PH 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 25.18150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.68000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.18150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.68000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 326 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLN A 82 REMARK 465 LEU A 83 REMARK 465 GLY A 84 REMARK 465 LYS A 85 REMARK 465 GLY A 86 REMARK 465 ASN A 87 REMARK 465 GLN A 88 REMARK 465 PRO A 89 REMARK 465 GLN A 90 REMARK 465 GLY A 195 REMARK 465 GLY A 196 REMARK 465 GLY A 197 REMARK 465 GLY A 198 REMARK 465 SER A 199 REMARK 465 HIS A 200 REMARK 465 HIS A 201 REMARK 465 HIS A 202 REMARK 465 HIS A 203 REMARK 465 HIS A 204 REMARK 465 HIS A 205 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 11 CG CD OE1 OE2 REMARK 470 GLU A 29 CG CD OE1 OE2 REMARK 470 GLU A 31 CG CD OE1 OE2 REMARK 470 ARG A 33 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 79 CG CD CE NZ REMARK 470 LYS A 93 CG CD CE NZ REMARK 470 GLU A 130 CG CD OE1 OE2 REMARK 470 GLN A 131 CG CD OE1 NE2 REMARK 470 GLN A 192 CG CD OE1 NE2 REMARK 470 GLN A 193 CG CD OE1 NE2 REMARK 470 LEU A 194 CG CD1 CD2 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 ASP A 92 -59.48 64.90 REMARK 500 REMARK 500 REMARK: NULL DBREF 9FED A 1 205 PDB 9FED 9FED 1 205 SEQRES 1 A 205 MET TYR THR SER LEU ILE HIS SER LEU ILE GLU GLU SER SEQRES 2 A 205 GLN ASN GLN GLN GLU LYS ASN GLU GLN GLU LEU LEU GLU SEQRES 3 A 205 LEU GLY GLU GLY GLU ALA ARG GLN GLU LEU SER GLY ILE SEQRES 4 A 205 VAL GLN LYS GLN ASN ASN LEU LEU ARG GLN ILE GLU ALA SEQRES 5 A 205 GLN GLN HIS LEU LEU GLN LEU THR VAL SER LYS ILE LYS SEQRES 6 A 205 GLN LEU GLN ALA ARG ILE LEU ALA VAL GLU ARG TYR LEU SEQRES 7 A 205 LYS ASP GLN GLN LEU GLY LYS GLY ASN GLN PRO GLN GLN SEQRES 8 A 205 ASP LYS LEU TYR ARG GLU VAL ALA LEU ILE ARG ALA GLN SEQRES 9 A 205 LEU GLN LYS ILE GLU SER GLU THR LEU GLN LEU LEU HIS SEQRES 10 A 205 GLN GLN ALA GLU ILE GLU ARG GLU LEU ASN ASN GLN GLU SEQRES 11 A 205 GLN GLU ILE GLY SER LEU LYS GLN ARG GLY LEU ILE ASP SEQRES 12 A 205 GLY PRO LEU LEU SER GLY ILE ASP GLN GLN GLN ASN ASN SEQRES 13 A 205 LEU LYS ARG ALA ILE GLU ALA GLN LYS HIS LEU LEU GLN SEQRES 14 A 205 LEU THR VAL TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE SEQRES 15 A 205 LEU ALA VAL GLU ARG TYR LEU LYS ASP GLN GLN LEU GLY SEQRES 16 A 205 GLY GLY GLY SER HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *29(H2 O) HELIX 1 AA1 TYR A 2 GLU A 26 1 25 HELIX 2 AA2 ALA A 32 ASP A 80 1 49 HELIX 3 AA3 ASP A 92 ARG A 139 1 48 HELIX 4 AA4 ASP A 143 LEU A 194 1 52 CRYST1 50.363 79.360 56.841 90.00 100.39 90.00 C 1 2 1 4 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 0.019856 0.000000 0.003641 0.00000 SCALE2 0.000000 0.012601 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017886 0.00000 MASTER 305 0 0 4 0 0 0 6 1492 1 0 16 END