HEADER IMMUNE SYSTEM 16-AUG-07 2QZD TITLE FITTED STRUCTURE OF SCR4 OF DAF INTO CRYOEM DENSITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT DECAY-ACCELERATING FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SCR4 DOMAIN; 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 GENE: CD55, CR, DAF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SCR4 OF DAF FROM 1OJV FITTED INTO CRYOEM DENSITY, BLOOD GROUP KEYWDS 2 ANTIGEN, COMPLEMENT PATHWAY, GLYCOPROTEIN, GPI-ANCHOR, IMMUNE KEYWDS 3 RESPONSE, INNATE IMMUNITY, LIPOPROTEIN, MEMBRANE, SUSHI, IMMUNE KEYWDS 4 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 6 16-OCT-24 2QZD 1 REMARK SEQADV REVDAT 5 18-JUL-18 2QZD 1 REMARK REVDAT 4 30-MAY-12 2QZD 1 REMARK VERSN REVDAT 3 24-FEB-09 2QZD 1 VERSN REVDAT 2 04-DEC-07 2QZD 1 JRNL AUTHOR REVDAT 1 30-OCT-07 2QZD 0 JRNL AUTH S.HAFENSTEIN,V.D.BOWMAN,P.R.CHIPMAN,C.M.BATOR 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 : 1OJV 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 2QZD 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_1000044235. 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 : 50MM MES 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 A1214 -5.08 73.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-1412 RELATED DB: EMDB DBREF 2QZD A 1190 1253 UNP P08174 DAF_HUMAN 222 285 SEQADV 2QZD CYS A 1254 UNP P08174 INSERTION SEQRES 1 A 65 GLU ILE TYR CYS PRO ALA PRO PRO GLN ILE ASP ASN GLY SEQRES 2 A 65 ILE ILE GLN GLY GLU ARG ASP HIS TYR GLY TYR ARG GLN SEQRES 3 A 65 SER VAL THR TYR ALA CYS ASN LYS GLY PHE THR MET ILE SEQRES 4 A 65 GLY GLU HIS SER ILE TYR CYS THR VAL ASN ASN ASP GLU SEQRES 5 A 65 GLY GLU TRP SER GLY PRO PRO PRO GLU CYS ARG GLY CYS SHEET 1 A 4 GLY A1202 ILE A1204 0 SHEET 2 A 4 SER A1216 CYS A1221 -1 O ALA A1220 N ILE A1203 SHEET 3 A 4 SER A1232 ASN A1238 -1 O ILE A1233 N VAL A1217 SHEET 4 A 4 GLU A1241 TRP A1244 -1 O GLU A1243 N THR A1236 SHEET 1 B 2 THR A1226 ILE A1228 0 SHEET 2 B 2 GLU A1250 ARG A1252 -1 O ARG A1252 N THR A1226 SSBOND 1 CYS A 1193 CYS A 1235 1555 1555 2.03 SSBOND 2 CYS A 1221 CYS A 1251 1555 1555 2.03 CISPEP 1 GLY A 1253 CYS A 1254 0 29.05 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