HEADER VIRAL PROTEIN 09-NOV-22 8F3B TITLE HIV-1 GP41 COILED-COIL POCKET IQN22 COMPND MOL_ID: 1; COMPND 2 MOLECULE: IQN22; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HIV-1 M:B_HXB2R; SOURCE 4 ORGANISM_TAXID: 11706 KEYWDS HIV-1, GP41, COILED-COIL, POCKET, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.U.J.BRUUN,S.TANG,D.FERNANDEZ,P.S.KIM REVDAT 3 25-OCT-23 8F3B 1 REMARK REVDAT 2 05-APR-23 8F3B 1 JRNL REVDAT 1 08-MAR-23 8F3B 0 JRNL AUTH T.U.J.BRUUN,S.TANG,G.ERWIN,L.DEIS,D.FERNANDEZ,P.S.KIM JRNL TITL STRUCTURE-GUIDED STABILIZATION IMPROVES THE ABILITY OF THE JRNL TITL 2 HIV-1 GP41 HYDROPHOBIC POCKET TO ELICIT NEUTRALIZING JRNL TITL 3 ANTIBODIES. JRNL REF J.BIOL.CHEM. V. 299 03062 2023 JRNL REFN ESSN 1083-351X JRNL PMID 36841484 JRNL DOI 10.1016/J.JBC.2023.103062 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1-4122 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 11255 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 581 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 30.4800 - 3.1700 0.99 2817 150 0.2198 0.2460 REMARK 3 2 3.1700 - 2.5200 0.99 2655 141 0.2524 0.2662 REMARK 3 3 2.5200 - 2.2000 0.98 2629 144 0.2354 0.2970 REMARK 3 4 2.2000 - 2.0000 0.98 2573 146 0.2534 0.3559 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 1252 REMARK 3 ANGLE : 0.828 1670 REMARK 3 CHIRALITY : 0.047 195 REMARK 3 PLANARITY : 0.005 211 REMARK 3 DIHEDRAL : 14.049 516 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 7.2213 0.6165 21.5992 REMARK 3 T TENSOR REMARK 3 T11: 0.1324 T22: 0.2251 REMARK 3 T33: 0.2579 T12: 0.0134 REMARK 3 T13: -0.0133 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 1.3191 L22: 1.1712 REMARK 3 L33: 7.1264 L12: -0.0665 REMARK 3 L13: -1.1216 L23: 1.0665 REMARK 3 S TENSOR REMARK 3 S11: 0.0673 S12: 0.1251 S13: -0.0678 REMARK 3 S21: 0.0519 S22: -0.0786 S23: 0.0058 REMARK 3 S31: 0.0003 S32: -0.0615 S33: -0.0089 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 8F3B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1000269937. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11287 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 37.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.06400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 8F3A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M DI-AMMONIUM PHOSPHATE AND 40 % REMARK 280 MPD, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 13.67950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.80200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.10850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.80200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.67950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.10850 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL 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 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 ACY C 0 REMARK 465 ARG C 1 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 TRP A 35 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 35 CZ3 CH2 REMARK 470 LYS A 38 CG CD CE NZ REMARK 470 LYS B 17 CG CD CE NZ REMARK 470 MET C 2 CG SD CE REMARK 470 LYS C 3 CG CD CE NZ REMARK 470 LYS C 8 NZ REMARK 470 LYS C 18 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 HOH A 124 O HOH C 133 2.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 8F3B A 0 51 PDB 8F3B 8F3B 0 51 DBREF 8F3B B 0 51 PDB 8F3B 8F3B 0 51 DBREF 8F3B C 0 51 PDB 8F3B 8F3B 0 51 SEQRES 1 A 52 ACY ARG MET LYS GLN ILE GLU ASP LYS ILE GLU GLU ILE SEQRES 2 A 52 GLU SER LYS GLN LYS LYS ILE GLU ASN GLU ILE ALA ARG SEQRES 3 A 52 ILE LYS LYS LEU LEU GLN LEU THR VAL TRP GLY ILE LYS SEQRES 4 A 52 GLN LEU GLN ALA ARG ILE LEU ALA VAL GLU ARG TYR NH2 SEQRES 1 B 52 ACY ARG MET LYS GLN ILE GLU ASP LYS ILE GLU GLU ILE SEQRES 2 B 52 GLU SER LYS GLN LYS LYS ILE GLU ASN GLU ILE ALA ARG SEQRES 3 B 52 ILE LYS LYS LEU LEU GLN LEU THR VAL TRP GLY ILE LYS SEQRES 4 B 52 GLN LEU GLN ALA ARG ILE LEU ALA VAL GLU ARG TYR NH2 SEQRES 1 C 52 ACY ARG MET LYS GLN ILE GLU ASP LYS ILE GLU GLU ILE SEQRES 2 C 52 GLU SER LYS GLN LYS LYS ILE GLU ASN GLU ILE ALA ARG SEQRES 3 C 52 ILE LYS LYS LEU LEU GLN LEU THR VAL TRP GLY ILE LYS SEQRES 4 C 52 GLN LEU GLN ALA ARG ILE LEU ALA VAL GLU ARG TYR NH2 HET ACY A 0 3 HET NH2 A 51 1 HET ACY B 0 3 HET NH2 B 51 1 HET NH2 C 51 1 HETNAM ACY ACETIC ACID HETNAM NH2 AMINO GROUP FORMUL 1 ACY 2(C2 H4 O2) FORMUL 1 NH2 3(H2 N) FORMUL 4 HOH *69(H2 O) HELIX 1 AA1 ARG A 1 ARG A 49 1 49 HELIX 2 AA2 ARG B 1 TYR B 50 1 50 HELIX 3 AA3 LYS C 3 TYR C 50 1 48 LINK C ACY A 0 N ARG A 1 1555 1555 1.34 LINK C TYR A 50 N NH2 A 51 1555 1555 1.33 LINK C ACY B 0 N ARG B 1 1555 1555 1.34 LINK C TYR B 50 N NH2 B 51 1555 1555 1.32 LINK C TYR C 50 N NH2 C 51 1555 1555 1.33 CRYST1 27.359 38.217 151.604 90.00 90.00 90.00 P 21 21 21 12 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 0.036551 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026166 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006596 0.00000 HETATM 1 C ACY A 0 11.731 9.249 56.530 1.00 55.36 C ANISOU 1 C ACY A 0 7721 8804 4507 -1779 -296 -874 C HETATM 2 O ACY A 0 11.461 9.564 55.368 1.00 63.80 O ANISOU 2 O ACY A 0 8801 9659 5783 -1789 -225 -873 O HETATM 3 CH3 ACY A 0 11.863 10.310 57.614 1.00 53.56 C ANISOU 3 CH3 ACY A 0 7628 8655 4067 -2042 -244 -1053 C