HEADER IMMUNE SYSTEM 09-APR-09 3IY5 TITLE VARIABLE DOMAINS OF THE MOUSE FAB (1AIF) FITTED INTO THE CRYOEM TITLE 2 RECONSTRUCTION OF THE VIRUS-FAB 16 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIBODY FRAGMENT IGG2A (LIGHT CHAIN); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FAB; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ANTIBODY FRAGMENT IGG2A (HEAVY CHAIN); COMPND 7 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 3IY5 1 REMARK REVDAT 2 26-MAY-09 3IY5 1 JRNL REVDAT 1 12-MAY-09 3IY5 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 : 1AIF REMARK 3 REFINEMENT SPACE : REAL 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 : 2084 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 3IY5 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_1000160011. 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 15 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 : 03-JUN-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) : 0.40 REMARK 245 MAXIMUM DEFOCUS (NM) : 4.80 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) : 37.70 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: 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 OD1 ASN B 139 O ASN B 162 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 GLU B 172 CB GLU B 172 CG 0.125 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 LEU A 34 CA - CB - CG ANGL. DEV. = 15.4 DEGREES REMARK 500 THR B 136 N - CA - C ANGL. DEV. = -20.4 DEGREES REMARK 500 LEU B 211 CA - CB - CG ANGL. DEV. = -14.1 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 SER A 28 99.34 -59.07 REMARK 500 SER A 31 -62.40 -27.98 REMARK 500 SER A 32 40.83 -68.18 REMARK 500 ASN A 33 25.43 -159.31 REMARK 500 SER A 41 136.95 -22.13 REMARK 500 PRO A 47 108.39 -42.26 REMARK 500 TRP A 48 -63.21 -97.09 REMARK 500 SER A 57 103.56 -36.57 REMARK 500 SER A 68 123.62 -175.40 REMARK 500 SER A 77 -81.99 -47.40 REMARK 500 ALA A 84 22.88 -59.67 REMARK 500 ASN A 93 -70.82 -78.95 REMARK 500 LYS B 111 98.68 -165.76 REMARK 500 LYS B 127 81.13 -162.49 REMARK 500 CYS B 130 140.59 178.43 REMARK 500 THR B 136 74.32 -160.35 REMARK 500 ASN B 138 -64.70 -0.79 REMARK 500 TYR B 140 -159.75 -131.46 REMARK 500 VAL B 156 -70.63 -86.91 REMARK 500 ALA B 157 -164.92 -125.41 REMARK 500 GLU B 158 113.62 170.95 REMARK 500 ASN B 162 -29.54 -18.68 REMARK 500 SER B 163 -25.84 151.88 REMARK 500 ASN B 165 -74.81 -36.02 REMARK 500 TYR B 170 -158.50 -122.03 REMARK 500 GLU B 172 -54.10 -15.02 REMARK 500 VAL B 174 -37.19 -158.71 REMARK 500 ARG B 182 129.47 -171.63 REMARK 500 SER B 187 -3.91 78.62 REMARK 500 GLU B 199 -46.77 -27.74 REMARK 500 LEU B 211 47.33 -88.87 REMARK 500 ALA B 215 -154.10 178.53 REMARK 500 THR B 223 143.89 -170.26 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 TYR B 140 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-5110 RELATED DB: EMDB REMARK 900 THE CRYOEM RECONSTRUCTION OF THE VIRUS-FAB 16 COMPLEX DBREF 3IY5 A 1 108 PDB 3IY5 3IY5 1 108 DBREF 3IY5 B 109 230 PDB 3IY5 3IY5 109 230 SEQRES 1 A 108 ASP ILE GLN LEU THR GLN SER PRO ALA PHE MET ALA ALA SEQRES 2 A 108 SER PRO GLY GLU LYS VAL THR ILE THR CYS SER VAL SER SEQRES 3 A 108 SER SER ILE SER SER SER ASN LEU HIS TRP TYR GLN GLN SEQRES 4 A 108 LYS SER GLU THR SER PRO LYS PRO TRP ILE TYR GLY THR SEQRES 5 A 108 SER ASN LEU ALA SER GLY VAL PRO VAL ARG PHE SER GLY SEQRES 6 A 108 SER GLY SER GLY THR SER TYR SER LEU THR ILE SER SER SEQRES 7 A 108 MET GLU ALA GLU ASP ALA ALA THR TYR TYR CYS GLN GLN SEQRES 8 A 108 TRP ASN SER TYR PRO TYR THR PHE GLY GLY GLY THR LYS SEQRES 9 A 108 LEU GLU ILE LYS SEQRES 1 B 122 GLU VAL LYS LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 122 PRO GLY GLY SER MET LYS LEU SER CYS VAL ALA SER GLY SEQRES 3 B 122 PHE THR PHE ASN ASN TYR TRP MET SER TRP VAL ARG GLN SEQRES 4 B 122 SER PRO GLU LYS GLY LEU GLU TRP VAL ALA GLU ILE ARG SEQRES 5 B 122 LEU ASN SER ASP ASN PHE ALA THR HIS TYR ALA GLU SER SEQRES 6 B 122 VAL LYS GLY LYS PHE ILE ILE SER ARG ASP ASP SER LYS SEQRES 7 B 122 SER ARG LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU SEQRES 8 B 122 ASP THR GLY ILE TYR TYR CYS VAL LEU ARG PRO LEU PHE SEQRES 9 B 122 TYR TYR ALA VAL ASP TYR TRP GLY GLN GLY THR SER VAL SEQRES 10 B 122 THR VAL SER SER ALA HELIX 1 1 SER A 30 SER A 32 5 3 HELIX 2 2 ASP B 183 SER B 187 5 5 HELIX 3 3 ARG B 197 THR B 201 5 5 SHEET 1 A 3 VAL A 19 SER A 24 0 SHEET 2 A 3 SER A 71 ILE A 76 -1 O TYR A 72 N CYS A 23 SHEET 3 A 3 PHE A 63 GLY A 67 -1 N SER A 64 O THR A 75 SHEET 1 B 5 ASN A 54 LEU A 55 0 SHEET 2 B 5 LYS A 46 TYR A 50 -1 N TYR A 50 O ASN A 54 SHEET 3 B 5 LEU A 34 GLN A 39 -1 N TRP A 36 O ILE A 49 SHEET 4 B 5 THR A 86 GLN A 91 -1 O TYR A 88 N TYR A 37 SHEET 5 B 5 THR A 103 LYS A 104 -1 O THR A 103 N TYR A 87 SHEET 1 C 2 LYS B 111 GLN B 113 0 SHEET 2 C 2 VAL B 131 SER B 133 -1 O VAL B 131 N GLN B 113 SHEET 1 D 5 GLY B 118 VAL B 120 0 SHEET 2 D 5 SER B 224 VAL B 227 1 O THR B 226 N VAL B 120 SHEET 3 D 5 GLY B 202 PRO B 210 -1 N GLY B 202 O VAL B 225 SHEET 4 D 5 TYR B 140 SER B 148 -1 N VAL B 145 O TYR B 205 SHEET 5 D 5 GLY B 152 TRP B 155 -1 O GLY B 152 N SER B 148 SHEET 1 E 5 GLY B 118 VAL B 120 0 SHEET 2 E 5 SER B 224 VAL B 227 1 O THR B 226 N VAL B 120 SHEET 3 E 5 GLY B 202 PRO B 210 -1 N GLY B 202 O VAL B 225 SHEET 4 E 5 TYR B 140 SER B 148 -1 N VAL B 145 O TYR B 205 SHEET 5 E 5 ILE B 159 ARG B 160 -1 O ILE B 159 N MET B 142 SHEET 1 F 2 PHE B 178 SER B 181 0 SHEET 2 F 2 TYR B 190 MET B 193 -1 O GLN B 192 N ILE B 179 SSBOND 1 CYS A 23 CYS A 89 1555 1555 2.07 SSBOND 2 CYS B 130 CYS B 206 1555 1555 2.04 CISPEP 1 SER A 7 PRO A 8 0 -0.05 CISPEP 2 TYR A 95 PRO A 96 0 -0.03 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