HEADER IMMUNE SYSTEM 09-APR-09 3IY2 TITLE VARIABLE DOMAINS OF THE COMPUTER GENERATED MODEL (WAM) OF FAB 6 FITTED TITLE 2 INTO THE CRYOEM RECONSTRUCTION OF THE VIRUS-FAB 6 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIBODY 6, LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FRAGMENT OF ANTIBODY 6; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ANTIBODY 6, HEAVY CHAIN; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: FRAGMENT OF ANTIBODY 6 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 6 ORGANISM_TAXID: 10090 KEYWDS CRYOEM, NEUTRALIZING ANTIBODY, PARVOVIRUS, CANINE, FELINE, FAB KEYWDS 2 FOOTPRINT, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR S.HAFENSTEIN,V.D.BOWMAN,T.SUN,C.D.NELSON,L.M.PALERMO,P.R.CHIPMAN, AUTHOR 2 A.J.BATTISTI,C.R.PARRISH,M.G.ROSSMANN REVDAT 4 06-NOV-24 3IY2 1 REMARK REVDAT 3 18-JUL-18 3IY2 1 REMARK REVDAT 2 26-MAY-09 3IY2 1 JRNL REVDAT 1 12-MAY-09 3IY2 0 JRNL AUTH S.HAFENSTEIN,V.D.BOWMAN,T.SUN,C.D.NELSON,L.M.PALERMO, JRNL AUTH 2 P.R.CHIPMAN,A.J.BATTISTI,C.R.PARRISH,M.G.ROSSMANN JRNL TITL STRUCTURAL COMPARISON OF DIFFERENT ANTIBODIES INTERACTING JRNL TITL 2 WITH PARVOVIRUS CAPSIDS JRNL REF J.VIROL. V. 83 5556 2009 JRNL REFN ISSN 0022-538X JRNL PMID 19321620 JRNL DOI 10.1128/JVI.02532-08 REMARK 2 REMARK 2 RESOLUTION. 18.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EM3DR, EMPFT REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 18.00 REMARK 3 NUMBER OF PARTICLES : 2520 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 3IY2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000160008. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : FAB FRAGMENT FROM MAB B REMARK 245 INTERACTING WITH FELINE REMARK 245 PANLEUKOPENIA VIRUS (FPV); REMARK 245 FELINE PANLEUKOPENIA VIRUS REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 15-APR-05 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 93.00 REMARK 245 MICROSCOPE MODEL : FEI/PHILIPS CM300FEG/T REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 1.20 REMARK 245 MAXIMUM DEFOCUS (NM) : 4.20 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3700.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 45000 REMARK 245 CALIBRATED MAGNIFICATION : 47190 REMARK 245 SOURCE : TUNGSTEN HAIRPIN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 THR A 67 C THR A 67 O -0.213 REMARK 500 THR A 67 C GLN A 68 N 0.167 REMARK 500 PHE B 164 CZ PHE B 164 CE2 -0.136 REMARK 500 REMARK 500 REMARK: NULL 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 VAL A 17 CA - CB - CG2 ANGL. DEV. = -13.9 DEGREES REMARK 500 TYR A 30 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 GLU A 54 N - CA - CB ANGL. DEV. = -11.9 DEGREES REMARK 500 ARG A 59 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 GLN A 68 OE1 - CD - NE2 ANGL. DEV. = -18.6 DEGREES REMARK 500 GLN A 68 CG - CD - NE2 ANGL. DEV. = 18.1 DEGREES REMARK 500 HIS A 88 ND1 - CE1 - NE2 ANGL. DEV. = 9.3 DEGREES REMARK 500 HIS A 89 ND1 - CE1 - NE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 PRO A 93 CB - CA - C ANGL. DEV. = -25.9 DEGREES REMARK 500 HIS B 135 N - CA - CB ANGL. DEV. = -15.6 DEGREES REMARK 500 HIS B 135 CB - CG - CD2 ANGL. DEV. = -17.8 DEGREES REMARK 500 HIS B 135 CG - ND1 - CE1 ANGL. DEV. = -7.9 DEGREES REMARK 500 HIS B 135 ND1 - CE1 - NE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 TRP B 136 CD1 - NE1 - CE2 ANGL. DEV. = -5.5 DEGREES REMARK 500 GLU B 146 CG - CD - OE1 ANGL. DEV. = -21.3 DEGREES REMARK 500 GLU B 146 CG - CD - OE2 ANGL. DEV. = 17.9 DEGREES REMARK 500 TRP B 147 CD1 - NE1 - CE2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ILE B 148 CG1 - CB - CG2 ANGL. DEV. = -16.8 DEGREES REMARK 500 PHE B 164 CB - CG - CD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 PHE B 164 CD1 - CG - CD2 ANGL. DEV. = 9.0 DEGREES REMARK 500 PHE B 164 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES REMARK 500 PHE B 164 CG - CD1 - CE1 ANGL. DEV. = -6.9 DEGREES REMARK 500 PHE B 164 CG - CD2 - CE2 ANGL. DEV. = -11.0 DEGREES REMARK 500 PHE B 164 CD1 - CE1 - CZ ANGL. DEV. = -33.7 DEGREES REMARK 500 PHE B 164 CZ - CE2 - CD2 ANGL. DEV. = -26.2 DEGREES REMARK 500 LEU B 170 CB - CA - C ANGL. DEV. = -12.8 DEGREES REMARK 500 LEU B 170 N - CA - CB ANGL. DEV. = -20.1 DEGREES REMARK 500 LEU B 170 CB - CG - CD2 ANGL. DEV. = -15.3 DEGREES REMARK 500 VAL B 205 CA - CB - CG2 ANGL. DEV. = -16.0 DEGREES REMARK 500 TYR B 208 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES 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 TYR A 28 -114.08 55.55 REMARK 500 LEU A 45 -59.25 -122.24 REMARK 500 ALA A 49 -51.67 61.48 REMARK 500 ALA A 91 153.16 66.26 REMARK 500 VAL B 111 -169.09 123.04 REMARK 500 ASN B 155 -17.30 -177.35 REMARK 500 ALA B 192 172.49 169.85 REMARK 500 GLU B 204 -104.97 -81.42 REMARK 500 TYR B 208 151.10 -31.22 REMARK 500 TRP B 209 2.24 -178.38 REMARK 500 THR B 213 103.72 163.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLN A 68 0.10 SIDE CHAIN REMARK 500 HIS B 135 0.19 SIDE CHAIN REMARK 500 PHE B 164 0.18 SIDE CHAIN REMARK 500 PHE B 206 0.11 SIDE CHAIN REMARK 500 TYR B 208 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-5107 RELATED DB: EMDB REMARK 900 THE CRYOEM RECONSTRUCTION OF THE VIRUS-FAB 6 COMPLEX DBREF 3IY2 A 1 107 PDB 3IY2 3IY2 1 107 DBREF 3IY2 B 108 218 PDB 3IY2 3IY2 108 218 SEQRES 1 A 107 LEU MET THR GLN ILE PRO ALA SER LEU SER ALA SER VAL SEQRES 2 A 107 GLY GLU THR VAL THR ILE THR CYS ARG ALA THR LYS ASN SEQRES 3 A 107 ILE TYR SER TYR LEU ALA TRP TYR GLN GLN LYS GLN GLY SEQRES 4 A 107 LYS SER PRO GLN VAL LEU VAL HIS ASN ALA LYS THR LEU SEQRES 5 A 107 THR GLU GLY VAL PRO SER ARG PHE SER GLY SER GLY SER SEQRES 6 A 107 GLY THR GLN PHE SER LEU LYS ILE ASN SER LEU GLN PRO SEQRES 7 A 107 GLU ASP PHE GLY SER TYR TYR CYS GLN HIS HIS TYR ALA SEQRES 8 A 107 THR PRO TYR THR PHE GLY GLY GLY THR LYS LEU GLU ILE SEQRES 9 A 107 LYS ARG ALA SEQRES 1 B 111 SER GLY THR VAL LEU ALA ARG PRO GLY ALA SER VAL LYS SEQRES 2 B 111 MET SER CYS LYS ALA SER GLY TYR THR PHE THR TYR TRP SEQRES 3 B 111 MET HIS TRP VAL LYS GLN ARG PRO GLY GLN GLY LEU GLU SEQRES 4 B 111 TRP ILE GLY ALA ILE PHE PRO GLY ASN SER ASP SER ASP SEQRES 5 B 111 TYR ASN GLN LYS PHE LYS GLY LYS ALA LYS LEU THR ALA SEQRES 6 B 111 VAL THR SER THR SER ASN GLU THR ALA TYR MET ASP LEU SEQRES 7 B 111 SER SER LEU THR ASP SER ALA VAL TYR TYR CYS THR ARG SEQRES 8 B 111 LYS ASP TYR GLY THR GLU VAL PHE VAL TYR TRP GLY GLN SEQRES 9 B 111 GLY THR LEU VAL THR VAL SER HELIX 1 1 GLN A 77 PHE A 81 5 5 HELIX 2 2 GLN B 162 LYS B 165 5 4 HELIX 3 3 SER B 187 SER B 191 5 5 SHEET 1 A 4 MET A 2 ILE A 5 0 SHEET 2 A 4 VAL A 17 ALA A 23 -1 O THR A 20 N ILE A 5 SHEET 3 A 4 GLN A 68 ILE A 73 -1 O LEU A 71 N ILE A 19 SHEET 4 A 4 PHE A 60 SER A 65 -1 N SER A 63 O SER A 70 SHEET 1 B 6 SER A 8 SER A 12 0 SHEET 2 B 6 THR A 100 LYS A 105 1 O LYS A 105 N ALA A 11 SHEET 3 B 6 GLY A 82 HIS A 88 -1 N GLY A 82 O LEU A 102 SHEET 4 B 6 LEU A 31 GLN A 36 -1 N TYR A 34 O TYR A 85 SHEET 5 B 6 GLN A 43 HIS A 47 -1 O VAL A 46 N TRP A 33 SHEET 6 B 6 THR A 51 LEU A 52 -1 O THR A 51 N HIS A 47 SHEET 1 C 6 VAL B 111 ALA B 113 0 SHEET 2 C 6 LEU B 214 VAL B 217 1 O THR B 216 N VAL B 111 SHEET 3 C 6 ALA B 192 LYS B 199 -1 N ALA B 192 O VAL B 215 SHEET 4 C 6 TRP B 133 GLN B 139 -1 N GLN B 139 O VAL B 193 SHEET 5 C 6 LEU B 145 PHE B 152 -1 O GLU B 146 N LYS B 138 SHEET 6 C 6 ASP B 157 TYR B 160 -1 O ASP B 159 N ALA B 150 SHEET 1 D 3 SER B 118 LYS B 124 0 SHEET 2 D 3 ASN B 178 ASP B 184 -1 O ALA B 181 N MET B 121 SHEET 3 D 3 ALA B 168 VAL B 173 -1 N THR B 171 O THR B 180 SSBOND 1 CYS A 21 CYS A 86 1555 1555 2.59 SSBOND 2 CYS B 123 CYS B 196 1555 1555 2.58 CISPEP 1 ILE A 5 PRO A 6 0 3.97 CISPEP 2 THR A 92 PRO A 93 0 -2.95 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000