HEADER IMMUNE SYSTEM 29-MAR-10 2XA3 TITLE CRYSTAL STRUCTURE OF THE BROADLY NEUTRALIZING LLAMA VHH D7 AND ITS TITLE 2 MODE OF HIV-1 GP120 INTERACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LLAMA HEAVY CHAIN ANTIBODY D7; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: VARIABLE DOMAIN OF A HEAVY CHAIN ANTIBODY SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_COMMON: LLAMA; SOURCE 4 ORGANISM_TAXID: 9844; SOURCE 5 TISSUE: BLOOD; SOURCE 6 CELL: LYMPHOCYTE; SOURCE 7 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 8 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 10 EXPRESSION_SYSTEM_VARIANT: VWK18GAL1 KEYWDS IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.HINZ,D.LUTJE HULSIK,A.FORSMAN,W.KOH,H.BELRHALI,A.GORLANI,H.DE AUTHOR 2 HAARD,R.A.WEISS,T.VERRIPS,W.WEISSENHORN REVDAT 3 20-DEC-23 2XA3 1 REMARK REVDAT 2 07-FEB-18 2XA3 1 SOURCE AUTHOR JRNL REVDAT 1 26-MAY-10 2XA3 0 JRNL AUTH A.HINZ,D.LUTJE HULSIK,A.FORSMAN,W.W.KOH,H.BELRHALI, JRNL AUTH 2 A.GORLANI,H.DE HAARD,R.A.WEISS,T.VERRIPS,W.WEISSENHORN JRNL TITL CRYSTAL STRUCTURE OF THE NEUTRALIZING LLAMA V(HH) D7 AND ITS JRNL TITL 2 MODE OF HIV-1 GP120 INTERACTION. JRNL REF PLOS ONE V. 5 10482 2010 JRNL REFN ESSN 1932-6203 JRNL PMID 20463957 JRNL DOI 10.1371/JOURNAL.PONE.0010482 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.FORSMAN,E.BEIRNAERT,M.M.I.AASA-CHAPMAN,B.HOORELBEKE, REMARK 1 AUTH 2 K.HIJAZI,W.KOH,V.TACK,A.SZYNOL,C.KELLY,A.MCKNIGHT,T.VERRIPS, REMARK 1 AUTH 3 H.DE HAARD,R.A.WEISS REMARK 1 TITL LLAMA ANTIBODY FRAGMENTS WITH CROSS-SUBTYPE HUMAN REMARK 1 TITL 2 IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1)-NEUTRALIZING REMARK 1 TITL 3 PROPERTIES AND HIGH AFFINITY FOR HIV-1 GP120. REMARK 1 REF J.VIROL. V. 82 12069 2008 REMARK 1 REFN ISSN 0022-538X REMARK 1 PMID 18842738 REMARK 1 DOI 10.1128/JVI.01379-08 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 22364 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1135 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 24.0298 - 2.9985 1.00 3044 140 0.1618 0.1616 REMARK 3 2 2.9985 - 2.3807 1.00 2881 150 0.1662 0.2215 REMARK 3 3 2.3807 - 2.0800 1.00 2836 147 0.1591 0.1773 REMARK 3 4 2.0800 - 1.8899 0.99 2816 168 0.1558 0.1765 REMARK 3 5 1.8899 - 1.7545 0.99 2788 162 0.1627 0.2099 REMARK 3 6 1.7545 - 1.6511 0.98 2737 149 0.1629 0.1929 REMARK 3 7 1.6511 - 1.5684 0.82 2311 125 0.1617 0.1996 REMARK 3 8 1.5684 - 1.5001 0.65 1816 94 0.1812 0.2226 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 : 0.36 REMARK 3 B_SOL : 51.49 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.22550 REMARK 3 B22 (A**2) : -0.41920 REMARK 3 B33 (A**2) : 1.64470 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.006 1199 REMARK 3 ANGLE : 1.065 1652 REMARK 3 CHIRALITY : 0.071 167 REMARK 3 PLANARITY : 0.005 225 REMARK 3 DIHEDRAL : 16.816 434 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: DISORDERED REGIONS FOR THE CDR3 LOOP REMARK 3 FROM RESIDUE 98 TO RESIDUE 100C. REMARK 4 REMARK 4 2XA3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1290043400. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.974 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22695 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 44.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 68.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.500 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: PDB ENTRY 1HCV REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5 MG/ML OF D7 PROTEIN IN A SOLUTION OF REMARK 280 20MM HEPES PH 7, 0.1 M NACL MIXED WITH AN EQUAL VOLUME OF 100MM REMARK 280 SODIUM CACODYLATE PH 6, 20 MM MAGNESIUM ACETATE, 1.7M AMMONIUM REMARK 280 SULFATE AND 19 % GLYCEROL WELL CONDITION 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 18.68500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.37000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.09000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.37000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.68500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.09000 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 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 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 ARG A 100 CA - C - O ANGL. DEV. = 13.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1114 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1115 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1116 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1117 REMARK 999 REMARK 999 SEQUENCE REMARK 999 MUTATIONS DONE V5Q, A11V, G24A, A61V, A69D, S80Y. DBREF 2XA3 A 1 113 PDB 2XA3 2XA3 1 113 SEQRES 1 A 127 ALA VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 127 ALA GLY GLY SER LEU ARG LEU SER CYS THR VAL SER ALA SEQRES 3 A 127 ARG THR SER SER SER HIS ASP MET GLY TRP PHE ARG GLN SEQRES 4 A 127 ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ALA ILE SER SEQRES 5 A 127 TRP SER GLY GLY THR THR ASN TYR VAL ASP SER VAL LYS SEQRES 6 A 127 GLY ARG PHE ASP ILE SER LYS ASP ASN ALA LYS ASN ALA SEQRES 7 A 127 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 A 127 ALA VAL TYR TYR CYS ALA ALA LYS TRP ARG PRO LEU ARG SEQRES 9 A 127 TYR SER ASP ASN PRO SER ASN SER ASP TYR ASN TYR TRP SEQRES 10 A 127 GLY GLN GLY THR GLN VAL THR VAL SER SER HET SO4 A1114 5 HET SO4 A1115 5 HET SO4 A1116 5 HET SO4 A1117 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 4(O4 S 2-) FORMUL 6 HOH *172(H2 O) HELIX 1 1 ASP A 61 LYS A 64 5 4 HELIX 2 2 ASN A 73 LYS A 75 5 3 HELIX 3 3 LYS A 83 THR A 87 5 5 SHEET 1 AA 4 LEU A 4 SER A 7 0 SHEET 2 AA 4 LEU A 18 VAL A 24 -1 O SER A 21 N SER A 7 SHEET 3 AA 4 ALA A 77 MET A 82 -1 O VAL A 78 N CYS A 22 SHEET 4 AA 4 PHE A 67 ASP A 72 -1 O ASP A 68 N GLN A 81 SHEET 1 AB 4 GLY A 10 GLN A 13 0 SHEET 2 AB 4 THR A 107 SER A 112 1 O GLN A 108 N GLY A 10 SHEET 3 AB 4 ALA A 88 TRP A 96 -1 O ALA A 88 N VAL A 109 SHEET 4 AB 4 TYR A 102 TRP A 103 -1 O TYR A 102 N ALA A 94 SHEET 1 AC 6 GLY A 10 GLN A 13 0 SHEET 2 AC 6 THR A 107 SER A 112 1 O GLN A 108 N GLY A 10 SHEET 3 AC 6 ALA A 88 TRP A 96 -1 O ALA A 88 N VAL A 109 SHEET 4 AC 6 HIS A 32 GLN A 39 -1 O ASP A 33 N LYS A 95 SHEET 5 AC 6 GLU A 46 SER A 52 -1 O GLU A 46 N ARG A 38 SHEET 6 AC 6 THR A 57 TYR A 59 -1 O ASN A 58 N ALA A 50 SHEET 1 AD 2 TYR A 102 TRP A 103 0 SHEET 2 AD 2 ALA A 88 TRP A 96 -1 O ALA A 94 N TYR A 102 SSBOND 1 CYS A 22 CYS A 92 1555 1555 2.02 SITE 1 AC1 6 SER A 29 LYS A 83 TRP A 96 HOH A2165 SITE 2 AC1 6 HOH A2166 HOH A2167 SITE 1 AC2 6 GLY A 15 ARG A 97 PRO A 98 HOH A2020 SITE 2 AC2 6 HOH A2144 HOH A2168 SITE 1 AC3 7 PHE A 37 ARG A 45 SER A 100H ASP A 100I SITE 2 AC3 7 HOH A2135 HOH A2169 HOH A2170 SITE 1 AC4 7 ARG A 19 LYS A 75 TYR A 79 GLY A 106 SITE 2 AC4 7 HOH A2157 HOH A2171 HOH A2172 CRYST1 37.370 62.180 62.740 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 0.026759 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015939 0.00000