HEADER IMMUNE SYSTEM 07-APR-09 3IY0 TITLE VARIABLE DOMAINS OF THE X-RAY STRUCTURE OF FAB 14 FITTED TITLE 2 INTO THE CRYOEM RECONSTRUCTION OF THE VIRUS-FAB 14 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB 14, LIGHT DOMAIN; COMPND 3 CHAIN: L; COMPND 4 FRAGMENT: FAB14; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB 14, HEAVY DOMAIN; COMPND 7 CHAIN: H 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, KEYWDS 2 FAB FOOTPRINT, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR S.HAFENSTEIN,V.D.BOWMAN,T.SUN,C.D.NELSON,L.M.PALERMO, AUTHOR 2 P.R.CHIPMAN,A.J.BATTISTI,C.R.PARRISH,M.G.ROSSMANN REVDAT 2 26-MAY-09 3IY0 1 JRNL REVDAT 1 12-MAY-09 3IY0 0 JRNL AUTH S.HAFENSTEIN,V.D.BOWMAN,T.SUN,C.D.NELSON, JRNL AUTH 2 L.M.PALERMO,P.R.CHIPMAN,A.J.BATTISTI,C.R.PARRISH, JRNL AUTH 3 M.G.ROSSMANN JRNL TITL STRUCTURAL COMPARISON OF DIFFERENT ANTIBODIES JRNL TITL 2 INTERACTING 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 1 REMARK 2 REMARK 2 RESOLUTION. 12.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : COMMON LINES 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) : 12.500 REMARK 3 NUMBER OF PARTICLES : 2059 REMARK 3 CTF CORRECTION METHOD : ROBEM REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 3IY0 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-09. REMARK 100 THE RCSB ID CODE IS RCSB160006. 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 : ICOSAHEDRAL REMARK 245 NAME OF SAMPLE : FAB FRAGMENT OF MAB14 REMARK 245 INTERACTING WITH CANINE REMARK 245 PARVOVIRUS 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 : 17-JUN-04 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 109 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) : 1.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3.80 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 37.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : 45000 REMARK 245 CALIBRATED MAGNIFICATION : 47190 REMARK 245 SOURCE : TUNGSTEN HAIRPIN REMARK 245 ACCELERATION VOLTAGE (KV) : 45 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 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H 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: 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 ASN L 30 -109.41 50.84 REMARK 500 ALA L 84 -163.33 -123.04 REMARK 500 PRO H 14 151.03 -45.87 REMARK 500 PRO H 41 -71.91 -39.67 REMARK 500 ALA H 43 -23.66 102.92 REMARK 500 ALA H 75 -10.66 71.57 REMARK 500 LEU H 86 117.21 -30.23 REMARK 500 PHE H 101 -157.17 -98.84 REMARK 500 ALA H 102 15.66 -143.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-5105 RELATED DB: EMDB REMARK 900 CRYOEM RECONSTRUCTION OF THE CANINE PARVOVIRUS-FAB 14 REMARK 900 COMPLEX DBREF 3IY0 L 1 108 PDB 3IY0 3IY0 1 108 DBREF 3IY0 H 1 120 PDB 3IY0 3IY0 1 120 SEQRES 1 L 108 ASP ILE VAL MET THR GLN SER HIS LYS PHE MET SER THR SEQRES 2 L 108 SER VAL GLY ASP ARG VAL SER ILE THR CYS LYS GLY SER SEQRES 3 L 108 GLN ASP VAL ASN SER ALA LEU ALA TRP TYR GLN GLN VAL SEQRES 4 L 108 PRO GLY GLN SER PRO ALA LEU LEU ILE TYR SER GLY SER SEQRES 5 L 108 ASN ARG TYR SER GLY VAL PRO GLY ARG PHE THR ALA SER SEQRES 6 L 108 GLY GLY GLY THR ASP PHE SER PHE THR ILE SER SER VAL SEQRES 7 L 108 GLN GLY GLU ASP LEU ALA LEU TYR TYR CYS GLN GLN HIS SEQRES 8 L 108 TYR THR THR PRO TRP THR PHE GLY GLY GLY THR LYS LEU SEQRES 9 L 108 GLU ILE LYS ARG SEQRES 1 H 120 ALA VAL HIS LEU GLN GLN SER GLY THR GLU LEU VAL ALA SEQRES 2 H 120 PRO GLY GLY GLY VAL LYS LEU SER CYS GLY ALA SER GLY SEQRES 3 H 120 TYR THR PHE THR ASN TYR ASP MET ASN TRP VAL ARG GLN SEQRES 4 H 120 ARG PRO GLY ALA GLY LEU GLU TRP ILE GLY TRP ILE PHE SEQRES 5 H 120 PRO GLY ASP GLY SER ALA ARG GLY ASN GLU LYS PHE GLY SEQRES 6 H 120 GLY ALA ALA ALA LEU ALA ALA ALA ALA ALA GLY GLY THR SEQRES 7 H 120 ALA TYR MET GLY LEU GLY GLY LEU SER SER GLU ASP SER SEQRES 8 H 120 GLY VAL TYR PHE CYS ALA ARG ARG GLY PHE ALA GLY ALA SEQRES 9 H 120 ALA SER PHE ALA TYR TRP GLY GLN GLY THR LEU VAL THR SEQRES 10 H 120 ALA GLY GLY HELIX 1 1 GLN L 79 LEU L 83 5 5 HELIX 2 2 THR H 28 TYR H 32 5 5 HELIX 3 3 GLU H 62 GLY H 65 5 4 HELIX 4 4 SER H 87 SER H 91 5 5 SHEET 1 A 4 MET L 4 THR L 5 0 SHEET 2 A 4 VAL L 19 GLY L 25 -1 O LYS L 24 N THR L 5 SHEET 3 A 4 ASP L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 A 4 PHE L 62 GLY L 66 -1 N SER L 65 O SER L 72 SHEET 1 B 6 PHE L 10 THR L 13 0 SHEET 2 B 6 THR L 102 ILE L 106 1 O GLU L 105 N MET L 11 SHEET 3 B 6 LEU L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 B 6 LEU L 33 GLN L 38 -1 N ALA L 34 O GLN L 89 SHEET 5 B 6 ALA L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 B 6 ASN L 53 ARG L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 C 4 PHE L 10 THR L 13 0 SHEET 2 C 4 THR L 102 ILE L 106 1 O GLU L 105 N MET L 11 SHEET 3 C 4 LEU L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 C 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 D 4 HIS H 3 GLN H 6 0 SHEET 2 D 4 VAL H 18 SER H 25 -1 O SER H 25 N HIS H 3 SHEET 3 D 4 THR H 78 LEU H 83 -1 O LEU H 83 N VAL H 18 SHEET 4 D 4 ALA H 68 ALA H 73 -1 N ALA H 69 O GLY H 82 SHEET 1 E 6 GLU H 10 VAL H 12 0 SHEET 2 E 6 THR H 114 ALA H 118 1 O LEU H 115 N GLU H 10 SHEET 3 E 6 GLY H 92 ARG H 99 -1 N GLY H 92 O VAL H 116 SHEET 4 E 6 MET H 34 ARG H 40 -1 N VAL H 37 O PHE H 95 SHEET 5 E 6 GLY H 44 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 E 6 ALA H 58 GLY H 60 -1 O ARG H 59 N TRP H 50 SHEET 1 F 4 GLU H 10 VAL H 12 0 SHEET 2 F 4 THR H 114 ALA H 118 1 O LEU H 115 N GLU H 10 SHEET 3 F 4 GLY H 92 ARG H 99 -1 N GLY H 92 O VAL H 116 SHEET 4 F 4 PHE H 107 TRP H 110 -1 O TYR H 109 N ARG H 98 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.03 SSBOND 2 CYS H 22 CYS H 96 1555 1555 2.03 CISPEP 1 THR L 94 PRO L 95 0 -0.14 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