HEADER IMMUNE SYSTEM 16-AUG-07 2QZH TITLE SCR2/3 OF DAF FROM THE NMR STRUCTURE 1NWV FITTED INTO A CRYOEM TITLE 2 RECONSTRUCTION OF CVB3-RD COMPLEXED WITH DAF COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT DECAY-ACCELERATING FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SCR2/3 DOMAINS; COMPND 5 SYNONYM: CD55 ANTIGEN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS SCR2-3 OF DAF FITTED INTO CRYOEM DENSITY OF CVB3-RD COMPLEXED WITH KEYWDS 2 DAF, ALTERNATIVE SPLICING, BLOOD GROUP ANTIGEN, COMPLEMENT PATHWAY, KEYWDS 3 GLYCOPROTEIN, GPI-ANCHOR, IMMUNE RESPONSE, INNATE IMMUNITY, KEYWDS 4 LIPOPROTEIN, MEMBRANE, POLYMORPHISM, SUSHI, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR S.HAFENSTEIN,V.D.BOWMAN,P.R.CHIPMAN,C.M.BATOR KELLY,F.LIN,M.E.MEDOF, AUTHOR 2 M.G.ROSSMANN REVDAT 5 21-FEB-24 2QZH 1 REMARK SEQADV REVDAT 4 18-JUL-18 2QZH 1 REMARK REVDAT 3 24-FEB-09 2QZH 1 VERSN REVDAT 2 04-DEC-07 2QZH 1 JRNL AUTHOR REVDAT 1 30-OCT-07 2QZH 0 JRNL AUTH S.HAFENSTEIN,V.D.BOWMAN,P.R.CHIPMAN,C.M.KELLY,F.LIN, JRNL AUTH 2 M.E.MEDOF,M.G.ROSSMANN JRNL TITL INTERACTION OF DECAY-ACCELERATING FACTOR WITH COXSACKIEVIRUS JRNL TITL 2 B3. JRNL REF J.VIROL. V. 81 12927 2007 JRNL REFN ISSN 0022-538X JRNL PMID 17804498 JRNL DOI 10.1128/JVI.00931-07 REMARK 2 REMARK 2 RESOLUTION. 14.00 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 : 1NVW 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) : 14.00 REMARK 3 NUMBER OF PARTICLES : 2269 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 2QZH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000044239. 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 : COXSACKIEVIRUS B3, RD STRAIN, REMARK 245 COMPLEXED WITH DECAY- REMARK 245 ACCELERATING FACTOR; COMPLEMENT REMARK 245 DECAY-ACCELERATING FACTOR REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.00 REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOILS REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT BEFORE PLUNGING REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.00 REMARK 245 SAMPLE DETAILS : ONE DAF BINDS EACH BINDING REMARK 245 SITE, ONE PER EACH PROTOMER REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 06-AUG-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) : 1.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4.60 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2400.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 45000 REMARK 245 CALIBRATED MAGNIFICATION : NULL 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 ARG A1062 -81.14 -123.21 REMARK 500 SER A1063 157.80 63.49 REMARK 500 VAL A1066 110.29 -36.47 REMARK 500 PRO A1067 172.33 -57.55 REMARK 500 SER A1072 15.62 -156.69 REMARK 500 PRO A1078 36.28 -66.53 REMARK 500 ILE A1080 -81.66 -64.19 REMARK 500 THR A1081 -32.47 72.05 REMARK 500 ASN A1083 -75.17 -117.57 REMARK 500 GLU A1102 -179.38 -46.57 REMARK 500 PRO A1103 21.78 -54.34 REMARK 500 SER A1104 71.15 73.11 REMARK 500 LEU A1105 -166.42 -127.17 REMARK 500 SER A1106 100.91 -41.41 REMARK 500 PRO A1107 56.42 -94.05 REMARK 500 LEU A1112 -103.90 -82.73 REMARK 500 ASN A1114 50.28 -118.01 REMARK 500 LEU A1115 45.86 18.60 REMARK 500 TRP A1117 151.89 -42.69 REMARK 500 SER A1118 -130.00 -68.67 REMARK 500 VAL A1121 -82.57 -103.83 REMARK 500 GLU A1122 67.09 -176.68 REMARK 500 LYS A1125 -93.00 -148.59 REMARK 500 LYS A1126 144.24 178.67 REMARK 500 ASN A1131 126.08 64.43 REMARK 500 PRO A1132 9.93 -68.72 REMARK 500 ILE A1135 -136.15 -67.14 REMARK 500 GLN A1139 174.72 171.99 REMARK 500 PRO A1143 18.60 -68.80 REMARK 500 ALA A1150 -162.64 -110.27 REMARK 500 THR A1151 163.78 177.65 REMARK 500 PHE A1163 71.40 -118.00 REMARK 500 SER A1167 160.17 169.71 REMARK 500 SER A1176 -179.87 69.63 REMARK 500 VAL A1177 104.08 -51.89 REMARK 500 PRO A1182 -153.68 -66.36 REMARK 500 PRO A1184 -147.80 -67.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-1412 RELATED DB: EMDB DBREF 2QZH A 1062 1188 UNP P08174 DAF_HUMAN 96 222 SEQADV 2QZH PHE A 1061 UNP P08174 INSERTION SEQADV 2QZH HIS A 1189 UNP P08174 INSERTION SEQRES 1 A 129 PHE ARG SER CYS GLU VAL PRO THR ARG LEU ASN SER ALA SEQRES 2 A 129 SER LEU LYS GLN PRO TYR ILE THR GLN ASN TYR PHE PRO SEQRES 3 A 129 VAL GLY THR VAL VAL GLU TYR GLU CYS ARG PRO GLY TYR SEQRES 4 A 129 ARG ARG GLU PRO SER LEU SER PRO LYS LEU THR CYS LEU SEQRES 5 A 129 GLN ASN LEU LYS TRP SER THR ALA VAL GLU PHE CYS LYS SEQRES 6 A 129 LYS LYS SER CYS PRO ASN PRO GLY GLU ILE ARG ASN GLY SEQRES 7 A 129 GLN ILE ASP VAL PRO GLY GLY ILE LEU PHE GLY ALA THR SEQRES 8 A 129 ILE SER PHE SER CYS ASN THR GLY TYR LYS LEU PHE GLY SEQRES 9 A 129 SER THR SER SER PHE CYS LEU ILE SER GLY SER SER VAL SEQRES 10 A 129 GLN TRP SER ASP PRO LEU PRO GLU CYS ARG GLU HIS SHEET 1 A 2 ALA A1073 LEU A1075 0 SHEET 2 A 2 TYR A1093 CYS A1095 -1 O GLU A1094 N SER A1074 SHEET 1 B 2 THR A1089 VAL A1091 0 SHEET 2 B 2 LEU A1109 CYS A1111 -1 O LEU A1109 N VAL A1091 SHEET 1 C 4 GLY A1138 ASP A1141 0 SHEET 2 C 4 THR A1151 CYS A1156 -1 O SER A1155 N GLN A1139 SHEET 3 C 4 SER A1168 LEU A1171 -1 O SER A1168 N ILE A1152 SHEET 4 C 4 GLN A1178 TRP A1179 -1 O GLN A1178 N LEU A1171 SHEET 1 D 2 TYR A1160 LEU A1162 0 SHEET 2 D 2 CYS A1186 GLU A1188 -1 O ARG A1187 N LYS A1161 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