HEADER IMMUNE SYSTEM 16-AUG-07 2QZF
TITLE SCR1 OF DAF FROM 1OJV FITTED INTO CRYOEM DENSITY
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: COMPLEMENT DECAY-ACCELERATING FACTOR;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: SCR1 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS SCR1 OF DAF FROM STRUCTURE 1OJV FITTED INTO CRYOEM DENSITY, BLOOD
KEYWDS 2 GROUP 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 5 18-JUL-18 2QZF 1 REMARK
REVDAT 4 30-MAY-12 2QZF 1 REMARK VERSN
REVDAT 3 24-FEB-09 2QZF 1 VERSN
REVDAT 2 04-DEC-07 2QZF 1 JRNL AUTHOR
REVDAT 1 30-OCT-07 2QZF 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 : 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 2QZF 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_1000044237.
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) : 24.00
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 GLN A1002 32.14 -58.71
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: EMD-1412 RELATED DB: EMDB
DBREF 2QZF A 1003 1062 UNP P08174 DAF_HUMAN 35 94
SEQADV 2QZF MET A 1001 UNP P08174 INSERTION
SEQADV 2QZF GLN A 1002 UNP P08174 INSERTION
SEQRES 1 A 62 MET GLN ASP CYS GLY LEU PRO PRO ASP VAL PRO ASN ALA
SEQRES 2 A 62 GLN PRO ALA LEU GLU GLY ARG THR SER PHE PRO GLU ASP
SEQRES 3 A 62 THR VAL ILE THR TYR LYS CYS GLU GLU SER PHE VAL LYS
SEQRES 4 A 62 ILE PRO GLY GLU LYS ASP SER VAL ILE CYS LEU LYS GLY
SEQRES 5 A 62 SER GLN TRP SER ASP ILE GLU GLU PHE CYS
SHEET 1 A 2 ASP A1003 CYS A1004 0
SHEET 2 A 2 PHE A1023 PRO A1024 -1 O PHE A1023 N CYS A1004
SHEET 1 B 4 ALA A1013 PRO A1015 0
SHEET 2 B 4 VAL A1028 CYS A1033 -1 O LYS A1032 N GLN A1014
SHEET 3 B 4 SER A1046 LEU A1050 -1 O VAL A1047 N ILE A1029
SHEET 4 B 4 GLN A1054 TRP A1055 -1 O GLN A1054 N LEU A1050
SSBOND 1 CYS A 1004 CYS A 1049 1555 1555 2.03
SSBOND 2 CYS A 1033 CYS A 1062 1555 1555 2.04
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
(ATOM LINES ARE NOT SHOWN.)
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