HEADER IMMUNE SYSTEM 09-APR-09 3IY3 TITLE VARIABLE DOMAINS OF THE COMPUTER GENERATED MODEL (WAM) OF FAB 8 FITTED TITLE 2 INTO THE CRYOEM RECONSTRUCTION OF THE VIRUS-FAB 8 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIBODY FRAGMENT FROM NEUTRALIZING ANTIBODY 8 (LIGHT COMPND 3 CHAIN); COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: FAB 8; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ANTIBODY FRAGMENT FROM NEUTRALIZING ANTIBODY 8 (HEAVY COMPND 8 CHAIN); COMPND 9 CHAIN: B 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 3 18-JUL-18 3IY3 1 REMARK REVDAT 2 26-MAY-09 3IY3 1 JRNL REVDAT 1 12-MAY-09 3IY3 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. 11.10 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) : 11.10 REMARK 3 NUMBER OF PARTICLES : 4344 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 3IY3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000160009. 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 8 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 : 23-JAN-04 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) : 1.80 REMARK 245 MAXIMUM DEFOCUS (NM) : 3.10 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) : 25.44 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 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 MET A 37 CG - SD - CE ANGL. DEV. = -9.9 DEGREES REMARK 500 HIS B 168 ND1 - CE1 - NE2 ANGL. DEV. = 8.8 DEGREES REMARK 500 VAL B 210 CA - CB - CG1 ANGL. DEV. = 9.3 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 PRO A 8 -159.37 -87.78 REMARK 500 TYR A 31 110.74 -167.62 REMARK 500 TYR A 36 57.65 -97.20 REMARK 500 ALA A 55 -45.05 84.28 REMARK 500 SER A 56 10.29 -141.80 REMARK 500 ALA A 88 -172.41 -179.14 REMARK 500 SER A 95 34.80 -140.75 REMARK 500 PRO B 127 155.39 -47.91 REMARK 500 ALA B 129 -160.59 -102.01 REMARK 500 LYS B 132 69.37 -152.00 REMARK 500 CYS B 135 103.69 -173.30 REMARK 500 SER B 138 146.71 -175.99 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 PHE B 193 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-5108 RELATED DB: EMDB REMARK 900 THE CRYOEM RECONSTRUCTION OF THE VIRUS-FAB 8 COMPLEX DBREF 3IY3 A 1 113 PDB 3IY3 3IY3 1 113 DBREF 3IY3 B 114 232 PDB 3IY3 3IY3 114 232 SEQRES 1 A 113 ASP ILE VAL LEU THR GLN PHE PRO GLY SER LEU ALA VAL SEQRES 2 A 113 SER LEU GLY GLN ARG ALA THR ILE SER CYS LYS ALA SER SEQRES 3 A 113 GLN ARG VAL ASP TYR ASP GLY VAL SER TYR MET ASN TRP SEQRES 4 A 113 TYR GLN GLN LYS PRO GLY GLN PRO PRO LYS LEU LEU ILE SEQRES 5 A 113 ASN ALA ALA SER ASP LEU GLU SER GLY ILE PRO ALA ARG SEQRES 6 A 113 PHE SER GLY THR GLY SER GLY THR ASP PHE THR LEU ASN SEQRES 7 A 113 ILE HIS PRO VAL GLU GLU GLU ASP ALA ALA THR TYR TYR SEQRES 8 A 113 CYS GLN GLN SER ASN TYR ASP PRO TRP THR PHE GLY GLY SEQRES 9 A 113 GLY THR LYS LEU GLU ILE LYS ARG ALA SEQRES 1 B 119 GLU ILE GLN LEU GLN GLN THR GLY PRO GLU LEU VAL GLN SEQRES 2 B 119 PRO GLY ALA SER VAL LYS ILE SER CYS LYS ALA SER GLY SEQRES 3 B 119 TYR SER PHE THR ASP TYR ILE MET VAL TRP VAL LYS GLN SEQRES 4 B 119 SER HIS GLY LYS GLY LEU GLU TRP ILE GLY ASN ILE ASN SEQRES 5 B 119 PRO TYR HIS GLY ARG THR ALA TYR ASN LEU LYS PHE LYS SEQRES 6 B 119 GLY LYS ALA THR LEU THR VAL ASP LYS SER SER SER THR SEQRES 7 B 119 ALA PHE MET GLN LEU ASN SER LEU ILE SER GLU ASP SER SEQRES 8 B 119 ALA VAL PHE TYR CYS VAL ARG LYS GLY TYR VAL GLU GLY SEQRES 9 B 119 GLY GLY LEU ASP TYR TRP GLY GLN GLY THR SER VAL ILE SEQRES 10 B 119 VAL SER HELIX 1 1 GLU A 83 ALA A 87 5 5 HELIX 2 2 SER B 141 TYR B 145 5 5 HELIX 3 3 LEU B 175 LYS B 178 5 4 HELIX 4 4 LYS B 187 SER B 190 5 4 HELIX 5 5 ILE B 200 SER B 204 5 5 SHEET 1 A 4 LEU A 4 PHE A 7 0 SHEET 2 A 4 ALA A 19 ALA A 25 -1 O LYS A 24 N THR A 5 SHEET 3 A 4 ASP A 74 ILE A 79 -1 O LEU A 77 N ILE A 21 SHEET 4 A 4 PHE A 66 SER A 71 -1 N SER A 67 O ASN A 78 SHEET 1 B 6 SER A 10 SER A 14 0 SHEET 2 B 6 THR A 106 LYS A 111 1 O GLU A 109 N LEU A 11 SHEET 3 B 6 ALA A 88 GLN A 94 -1 N ALA A 88 O LEU A 108 SHEET 4 B 6 MET A 37 GLN A 42 -1 N ASN A 38 O GLN A 93 SHEET 5 B 6 LYS A 49 ASN A 53 -1 O LEU A 51 N TRP A 39 SHEET 6 B 6 ASP A 57 LEU A 58 -1 O ASP A 57 N ASN A 53 SHEET 1 C 4 SER A 10 SER A 14 0 SHEET 2 C 4 THR A 106 LYS A 111 1 O GLU A 109 N LEU A 11 SHEET 3 C 4 ALA A 88 GLN A 94 -1 N ALA A 88 O LEU A 108 SHEET 4 C 4 THR A 101 PHE A 102 -1 O THR A 101 N GLN A 94 SHEET 1 D 2 ASP A 30 TYR A 31 0 SHEET 2 D 2 VAL A 34 SER A 35 -1 O VAL A 34 N TYR A 31 SHEET 1 E 2 GLN B 116 GLN B 119 0 SHEET 2 E 2 CYS B 135 SER B 138 -1 O SER B 138 N GLN B 116 SHEET 1 F 6 GLU B 123 VAL B 125 0 SHEET 2 F 6 THR B 227 VAL B 231 1 O ILE B 230 N VAL B 125 SHEET 3 F 6 ALA B 205 LYS B 212 -1 N PHE B 207 O THR B 227 SHEET 4 F 6 ILE B 146 GLN B 152 -1 N VAL B 148 O VAL B 210 SHEET 5 F 6 LEU B 158 ASN B 165 -1 O GLU B 159 N LYS B 151 SHEET 6 F 6 ARG B 170 TYR B 173 -1 O ALA B 172 N ASN B 163 SHEET 1 G 4 GLU B 123 VAL B 125 0 SHEET 2 G 4 THR B 227 VAL B 231 1 O ILE B 230 N VAL B 125 SHEET 3 G 4 ALA B 205 LYS B 212 -1 N PHE B 207 O THR B 227 SHEET 4 G 4 LEU B 220 TRP B 223 -1 O TYR B 222 N ARG B 211 SHEET 1 H 3 VAL B 131 ILE B 133 0 SHEET 2 H 3 THR B 191 LEU B 196 -1 O MET B 194 N ILE B 133 SHEET 3 H 3 ALA B 181 ASP B 186 -1 N THR B 184 O PHE B 193 SSBOND 1 CYS A 23 CYS A 92 1555 1555 2.59 SSBOND 2 CYS B 135 CYS B 209 1555 1555 2.59 CISPEP 1 PHE A 7 PRO A 8 0 -3.84 CISPEP 2 HIS A 80 PRO A 81 0 3.68 CISPEP 3 ASP A 98 PRO A 99 0 5.02 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