HEADER VIRAL PROTEIN 24-FEB-16 5IDL TITLE CRYSTAL STRUCTURE OF THE GERMLINE-TARGETING HIV-1 GP120 ENGINEERED TITLE 2 OUTER DOMAIN, EOD-GT8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GERMLINE-TARGETING HIV-1 GP120 ENGINEERED OUTER DOMAIN, COMPND 3 EOD-GT8; COMPND 4 CHAIN: A; 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: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS HIV ENV, GERMLINE-TARGETING IMMUNOGEN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.P.JULIEN,J.ERENO-ORBEA,J.G.JARDINE,W.R.SCHIEF,I.A.WILSON REVDAT 5 27-SEP-23 5IDL 1 HETSYN REVDAT 4 29-JUL-20 5IDL 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 11-DEC-19 5IDL 1 REMARK REVDAT 2 20-SEP-17 5IDL 1 JRNL REMARK REVDAT 1 05-OCT-16 5IDL 0 JRNL AUTH J.G.JARDINE,D.W.KULP,C.HAVENAR-DAUGHTON,A.SARKAR,B.BRINEY, JRNL AUTH 2 D.SOK,F.SESTERHENN,J.ERENO-ORBEA,O.KALYUZHNIY,I.DERESA,X.HU, JRNL AUTH 3 S.SPENCER,M.JONES,E.GEORGESON,Y.ADACHI,M.KUBITZ,A.C.DECAMP, JRNL AUTH 4 J.P.JULIEN,I.A.WILSON,D.R.BURTON,S.CROTTY,W.R.SCHIEF JRNL TITL HIV-1 BROADLY NEUTRALIZING ANTIBODY PRECURSOR B CELLS JRNL TITL 2 REVEALED BY GERMLINE-TARGETING IMMUNOGEN. JRNL REF SCIENCE V. 351 1458 2016 JRNL REFN ESSN 1095-9203 JRNL PMID 27013733 JRNL DOI 10.1126/SCIENCE.AAD9195 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 3332 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.258 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 243 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 0.0000 - 3.6533 0.99 1585 177 0.2357 0.2762 REMARK 3 2 3.6533 - 2.9004 0.95 1413 157 0.0000 0.3498 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 62.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.35 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 1278 REMARK 3 ANGLE : 0.455 1745 REMARK 3 CHIRALITY : 0.042 206 REMARK 3 PLANARITY : 0.003 220 REMARK 3 DIHEDRAL : 13.888 756 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5IDL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218632. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3333 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.840 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.77900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: 4JPJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2% (V/V) PEG 400, 2M AMMONIUM SULFATE, REMARK 280 0.1M HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 17.16500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.99500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.53000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.99500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.16500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.53000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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. (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 GLY A 28 REMARK 465 GLY A 29 REMARK 465 TYR A 30 REMARK 465 SER A 31 REMARK 465 ASN A 32 REMARK 465 SER A 138 REMARK 465 GLY A 139 REMARK 465 GLY A 140 REMARK 465 SER A 171 REMARK 465 THR A 172 REMARK 465 GLY A 173 REMARK 465 THR A 174 REMARK 465 LYS A 175 REMARK 465 HIS A 176 REMARK 465 HIS A 177 REMARK 465 HIS A 178 REMARK 465 HIS A 179 REMARK 465 HIS A 180 REMARK 465 HIS A 181 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 ASP A 1 CG OD1 OD2 REMARK 470 ARG A 46 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 47 CG OD1 OD2 REMARK 470 ARG A 50 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 81 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 143 CG CD OE1 OE2 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 GLN A 61 -38.81 67.31 REMARK 500 ASP A 79 109.99 -160.97 REMARK 500 PHE A 164 77.20 -116.54 REMARK 500 ALA A 165 54.05 -161.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 5IDL A 1 181 PDB 5IDL 5IDL 1 181 SEQRES 1 A 181 ASP THR ILE THR LEU PRO CYS ARG PRO ALA PRO PRO PRO SEQRES 2 A 181 HIS CYS SER SER ASN ILE THR GLY LEU ILE LEU THR ARG SEQRES 3 A 181 GLN GLY GLY TYR SER ASN ALA ASN THR VAL ILE PHE ARG SEQRES 4 A 181 PRO SER GLY GLY ASP TRP ARG ASP ILE ALA ARG CYS GLN SEQRES 5 A 181 ILE ALA GLY THR VAL VAL SER THR GLN LEU PHE LEU ASN SEQRES 6 A 181 GLY SER LEU ALA GLU GLU GLU VAL VAL ILE ARG SER GLU SEQRES 7 A 181 ASP TRP ARG ASP ASN ALA LYS SER ILE CYS VAL GLN LEU SEQRES 8 A 181 ALA THR SER VAL GLU ILE ALA CYS THR GLY ALA GLY HIS SEQRES 9 A 181 CYS ALA ILE SER ARG ALA LYS TRP ALA ASN THR LEU LYS SEQRES 10 A 181 GLN ILE ALA SER LYS LEU ARG GLU GLN TYR GLY ALA LYS SEQRES 11 A 181 THR ILE ILE PHE LYS PRO SER SER GLY GLY ASP PRO GLU SEQRES 12 A 181 PHE VAL ASN HIS SER PHE ASN CYS GLY GLY GLU PHE PHE SEQRES 13 A 181 TYR CYS ALA SER THR GLN LEU PHE ALA SER THR TRP PHE SEQRES 14 A 181 ALA SER THR GLY THR LYS HIS HIS HIS HIS HIS HIS HET NAG A 201 14 HET NAG A 202 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 2(C8 H15 N O6) HELIX 1 AA1 PRO A 12 SER A 16 5 5 HELIX 2 AA2 ASP A 44 ARG A 50 1 7 HELIX 3 AA3 ARG A 109 GLY A 128 1 20 HELIX 4 AA4 PRO A 142 ASN A 146 1 5 SHEET 1 AA1 7 LEU A 62 LEU A 64 0 SHEET 2 AA1 7 SER A 17 ARG A 26 -1 N GLY A 21 O PHE A 63 SHEET 3 AA1 7 ILE A 87 CYS A 99 -1 O VAL A 95 N ILE A 19 SHEET 4 AA1 7 HIS A 104 SER A 108 -1 O ALA A 106 N ALA A 98 SHEET 5 AA1 7 THR A 2 ARG A 8 -1 N ILE A 3 O ILE A 107 SHEET 6 AA1 7 GLU A 154 CYS A 158 -1 O TYR A 157 N ARG A 8 SHEET 7 AA1 7 HIS A 147 CYS A 151 -1 N CYS A 151 O GLU A 154 SHEET 1 AA2 6 VAL A 74 ARG A 76 0 SHEET 2 AA2 6 ILE A 87 CYS A 99 -1 O GLN A 90 N VAL A 74 SHEET 3 AA2 6 SER A 17 ARG A 26 -1 N ILE A 19 O VAL A 95 SHEET 4 AA2 6 THR A 35 PRO A 40 -1 O ARG A 39 N THR A 25 SHEET 5 AA2 6 THR A 131 PHE A 134 1 O ILE A 133 N PHE A 38 SHEET 6 AA2 6 SER A 166 TRP A 168 -1 O TRP A 168 N ILE A 132 SSBOND 1 CYS A 7 CYS A 158 1555 1555 2.03 SSBOND 2 CYS A 15 CYS A 151 1555 1555 2.03 SSBOND 3 CYS A 51 CYS A 88 1555 1555 2.03 SSBOND 4 CYS A 99 CYS A 105 1555 1555 2.03 LINK ND2 ASN A 18 C1 NAG A 201 1555 1555 1.44 LINK ND2 ASN A 65 C1 NAG A 202 1555 1555 1.44 CISPEP 1 ARG A 8 PRO A 9 0 -2.09 CRYST1 34.330 53.060 77.990 90.00 90.00 90.00 P 21 21 21 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 0.029129 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018847 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012822 0.00000