REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.A.LUFTIG,M.MATTU,P.DI GIOVINE,R.GELEZIUNAS,R.HRIN, REMARK 1 AUTH 2 G.BARBATO,E.BIANCHI,M.D.MILLER,A.PESSI,A.CARFI REMARK 1 TITL STRUCTURAL BASIS FOR HIV-1 NEUTRALIZATION BY A GP41 FUSION REMARK 1 TITL 2 INTERMEDIATE-DIRECTED ANTIBODY. REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 13 740 2006 REMARK 1 REFN ISSN 1545-9993 REMARK 1 PMID 16862157 REMARK 1 DOI 10.1038/NSMB1127 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 93.16 REMARK 3 NUMBER OF REFLECTIONS : 28253 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.23913 REMARK 3 R VALUE (WORKING SET) : 0.23693 REMARK 3 FREE R VALUE : 0.27943 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1509 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.300 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.360 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1961 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.284 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.336 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4962 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 118 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.977 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.25 REMARK 3 B22 (A**2) : 0.06 REMARK 3 B33 (A**2) : -0.36 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : -0.20 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.454 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.284 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.215 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.729 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.887 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5057 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6862 ; 1.183 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 634 ; 5.420 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 223 ;37.443 ;25.426 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 872 ;15.175 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;15.243 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 781 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3780 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3179 ; 0.622 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5131 ; 1.190 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1878 ; 1.649 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1731 ; 2.898 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. DISORDERED LOOPS REGIONS OF GP41-5HB WERE REMARK 3 NOT MODELED. REMARK 4 REMARK 4 2XRA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-SEP-10. REMARK 100 THE PDBE ID CODE IS EBI-44580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : 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) : 0.9765 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28254 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.30 REMARK 200 RESOLUTION RANGE LOW (A) : 37.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 3.2 REMARK 200 R MERGE (I) : 0.12 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.00 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) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.4 REMARK 200 R MERGE FOR SHELL (I) : 0.35 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.10 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 2CMR REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 0.2 M REMARK 280 AMMONIUM SULPHATE, 25% PEG 3350 (W/V) REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 31.35500 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L 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 MET A 542 REMARK 465 SER A 585 REMARK 465 GLY A 586 REMARK 465 GLY A 587 REMARK 465 HIS A 1625 REMARK 465 SER A 1665 REMARK 465 ALA A 2582 REMARK 465 GLY A 3620 REMARK 465 GLY A 3621 REMARK 465 SER A 3622 REMARK 465 GLY A 3623 REMARK 465 SER A 3665 REMARK 465 GLY A 3666 REMARK 465 GLY A 3667 REMARK 465 LEU A 4583 REMARK 465 GLU A 4584 REMARK 465 GLY A 4585 REMARK 465 GLY A 4586 REMARK 465 HIS A 4587 REMARK 465 HIS A 4588 REMARK 465 HIS A 4589 REMARK 465 HIS A 4590 REMARK 465 HIS A 4591 REMARK 465 HIS A 4592 REMARK 465 GLY A 4593 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 PRO H 14 O LEU H 82C 2.13 REMARK 500 O ARG L 30 O SER L 67 2.17 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 SER H 84 1.82 -58.68 REMARK 500 PRO H 100B 34.95 -84.50 REMARK 500 SER H 112 -77.50 -119.78 REMARK 500 SER H 113 -20.82 108.53 REMARK 500 SER H 127 125.19 113.70 REMARK 500 LYS H 129 -0.23 111.82 REMARK 500 SER H 130 17.28 -144.32 REMARK 500 ASP H 144 70.12 65.59 REMARK 500 ARG L 30 -136.00 37.24 REMARK 500 ALA L 51 -45.86 76.04 REMARK 500 SER L 67 -67.13 -129.35 REMARK 500 ASN L 138 72.91 48.00 REMARK 500 ASN L 152 28.70 32.58 REMARK 500 ASN L 158 55.03 -151.68 REMARK 500 SER L 182 160.91 113.79 REMARK 500 ARG L 211 168.01 157.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DF4 RELATED DB: PDB REMARK 900 INTERACTIONS BETWEEN HIV-1 GP41 CORE AND REMARK 900 DETERGENTS AND THEIR IMPLICATIONS FOR MEMBRANE REMARK 900 FUSION REMARK 900 RELATED ID: 1DF5 RELATED DB: PDB REMARK 900 INTERACTIONS BETWEEN HIV-1 GP41 CORE AND REMARK 900 DETERGENTS AND THEIR IMPLICATIONS FOR MEMBRANE REMARK 900 FUSION REMARK 900 RELATED ID: 1DLB RELATED DB: PDB REMARK 900 HELICAL INTERACTIONS IN THE HIV-1 GP41 REMARK 900 CORE REVEALS STRUCTURAL BASIS FOR THE REMARK 900 INHIBITORY ACTIVITY OF GP41 PEPTIDES REMARK 900 RELATED ID: 1OPN RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF CCR5 RECEPTOR IN REMARK 900 COMPLEX WITH HIVGP120 ENVELOPE GLYCOPROTEIN REMARK 900 AND CD4 RECEPTOR REMARK 900 RELATED ID: 1OPW RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF CCR5 RECEPTOR IN REMARK 900 COMPLEX WITH HIVGP120 ENVELOPE GLYCOPROTEIN REMARK 900 AND CD4 RECEPTOR REMARK 900 RELATED ID: 1GC1 RELATED DB: PDB REMARK 900 HIV-1 GP120 CORE COMPLEXED WITH CD4 AND REMARK 900 A NEUTRALIZING HUMAN ANTIBODY REMARK 900 RELATED ID: 1OPT RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF CCR5 RECEPTOR IN REMARK 900 COMPLEX WITH HIVGP120 ENVELOPE GLYCOPROTEIN REMARK 900 AND CD4 RECEPTOR REMARK 900 RELATED ID: 1K33 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF THE GP41 CORE REMARK 900 MUTANT REMARK 900 RELATED ID: 1RZJ RELATED DB: PDB REMARK 900 HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN REMARK 900 COMPLEXED WITH CD4AND INDUCED NEUTRALIZING REMARK 900 ANTIBODY 17B REMARK 900 RELATED ID: 1G9M RELATED DB: PDB REMARK 900 HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN REMARK 900 COMPLEXED WITH CD4AND INDUCED NEUTRALIZING REMARK 900 ANTIBODY 17B REMARK 900 RELATED ID: 1K34 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF GP41 CORE REMARK 900 MUTANT REMARK 900 RELATED ID: 1AIK RELATED DB: PDB REMARK 900 HIV GP41 CORE STRUCTURE REMARK 900 RELATED ID: 2CMR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HIV-1 NEUTRALIZING REMARK 900 ANTIBODY D5 FAB BOUND TO THE GP41 INNER REMARK 900 -CORE MIMETIC 5-HELIX REMARK 900 RELATED ID: 1GZL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF C14LINKMID/IQN17: A REMARK 900 CROSS-LINKED INHIBITOR OF HIV-1 ENTRY REMARK 900 BOUND TO THE GP41 HYDROPHOBIC POCKET REMARK 900 RELATED ID: 1MZI RELATED DB: PDB REMARK 900 SOLUTION ENSEMBLE STRUCTURES OF HIV-1 GP41 REMARK 900 2F5 MAB EPITOPE