HEADER REGULATOR OF COMPLEMENT PATHWAY 21-JUL-03 1OK9 TITLE DECAY ACCELERATING FACTOR (CD55): THE STRUCTURE OF AN INTACT HUMAN TITLE 2 COMPLEMENT REGULATOR. COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT DECAY-ACCELERATING FACTOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: FOUR EXTRACELLULAR SCR DOMAINS, RESIDUES 35-285; COMPND 5 SYNONYM: DAF, CR, CD55; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: SOAKED IN 2MM K2PTCL4 FOR 6 DAYS 2 PT(II) BINDING COMPND 8 SITES GLYCEROLS, ACETATES AND SULPHATES FROM CRYSTALLISATION BUFFER 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 B; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 37762; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: B834(DE3); SOURCE 8 OTHER_DETAILS: HUMAN SEQUENCE EXPRESSED IN E.COLI. KEYWDS REGULATOR OF COMPLEMENT PATHWAY, REGULATOR OF COMPLEMENT, DECAY KEYWDS 2 ACCELERATION OF C3/C5 CONVERTASES, PATHOGEN RECEPTOR, SHORT KEYWDS 3 CONSENSUS REPEAT DOMAINS, IMMUNE SYSTEM PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.LUKACIK,P.ROVERSI,J.WHITE,D.ESSER,G.P.SMITH,J.BILLINGTON, AUTHOR 2 P.A.WILLIAMS,P.M.RUDD,M.R.WORMALD,M.D.M.CRISPIN,C.M.RADCLIFFE, AUTHOR 3 R.A.DWEK,D.J.EVANS,B.P.MORGAN,R.A.G.SMITH,S.M.LEA REVDAT 6 13-DEC-23 1OK9 1 LINK REVDAT 5 10-APR-19 1OK9 1 SOURCE REVDAT 4 24-FEB-09 1OK9 1 VERSN REVDAT 3 26-AUG-04 1OK9 1 REMARK REVDAT 2 12-FEB-04 1OK9 1 AUTHOR JRNL REVDAT 1 07-JAN-04 1OK9 0 JRNL AUTH P.LUKACIK,P.ROVERSI,J.WHITE,D.ESSER,G.P.SMITH,J.BILLINGTON, JRNL AUTH 2 P.A.WILLIAMS,P.M.RUDD,M.R.WORMALD,D.J.HARVEY,M.D.M.CRISPIN, JRNL AUTH 3 C.M.RADCLIFFE,R.A.DWEK,D.J.EVANS,B.P.MORGAN,R.A.G.SMITH, JRNL AUTH 4 S.M.LEA JRNL TITL COMPLEMENT REGULATION AT THE MOLECULAR LEVEL: THE STRUCTURE JRNL TITL 2 OF DECAY-ACCELERATING FACTOR JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 1279 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 14734808 JRNL DOI 10.1073/PNAS.0307200101 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.WHITE,P.LUKACIK,D.ESSER,M.STEWARD,N.GIDDINGS,J.R.BRIGHT, REMARK 1 AUTH 2 S.FRITCHLEY,B.P.MORGAN,S.M.LEA,G.P.SMITH,R.A.G.SMITH REMARK 1 TITL BIOLOGICAL ACTIVITY, MEMBRANE-TARGETING MODIFICATION, AND REMARK 1 TITL 2 CRYSTALLIZATION OF SOLUBLE HUMAN DECAY ACCELERATING FACTOR REMARK 1 TITL 3 EXPRESSED IN E. COLI REMARK 1 REF PROTEIN SCI. V. 13 2406 2004 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 15322283 REMARK 1 DOI 10.1110/PS.03455604 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5F REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 10338 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.2400 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.2380 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.00 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 499 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 10338 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3938 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 9 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 2.100 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.004 ; 2.000 ; 4098 REMARK 3 BOND ANGLES (DEGREES) : 0.611 ; 3.000 ; 5520 REMARK 3 TORSION ANGLES (DEGREES) : 21.300; 0.000 ; 2386 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.005 ; 2.000 ; 110 REMARK 3 GENERAL PLANES (A) : 0.011 ; 5.000 ; 582 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 0.752 ; 20.000; 4094 REMARK 3 NON-BONDED CONTACTS (A) : 0.045 ; 5.000 ; 123 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : 0 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : BABINET SCALING REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 71.00 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BUSTER-TNT MAXIMUM LIKELIHOOD REMARK 3 REFINEMENT BETA11:-6.3 BETA12:4.0 BETA13:1.6 BETA22:11.2 BETA23: REMARK 3 5.9 BETA33:-4.5 REMARK 4 REMARK 4 1OK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1290013134. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.960 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10372 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 41.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.11400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1OJV REMARK 200 REMARK 200 REMARK: PT SITES FOUND WITH MOLREP PHASES FROM PDB ENTRY 1H03 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULPHATE, 20% M-PEG 5K, REMARK 280 0.1M SODIUM ACETATE PH 4.6, 16% GLYCEROL THEN SOAKED IN 2 MM REMARK 280 K2PTCL4 FOR 6 DAYS, PH 4.60 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS 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 CE MET A 227 ND1 HIS A 231 2.12 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 PRO A 99 C - N - CD ANGL. DEV. = -15.4 DEGREES REMARK 500 PRO B 99 C - N - CD ANGL. DEV. = -15.3 DEGREES REMARK 500 PRO B 105 C - N - CD ANGL. DEV. = -31.7 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 GLN A 2 27.30 -69.93 REMARK 500 GLU A 25 152.21 -49.78 REMARK 500 ARG A 64 50.95 87.74 REMARK 500 CYS A 66 -171.10 -66.88 REMARK 500 PRO A 69 133.78 -37.17 REMARK 500 PRO A 105 -53.35 -20.95 REMARK 500 PRO A 109 39.79 -94.23 REMARK 500 SER A 120 160.27 -47.09 REMARK 500 PRO A 132 163.57 -49.89 REMARK 500 ASN A 159 155.28 -46.44 REMARK 500 SER A 178 -157.20 -118.93 REMARK 500 TYR A 213 136.77 -37.98 REMARK 500 ASN A 239 92.54 -30.17 REMARK 500 GLU B 25 152.21 -49.76 REMARK 500 LYS B 78 -178.57 -60.79 REMARK 500 GLU B 104 79.35 -100.72 REMARK 500 PRO B 105 -49.21 -23.79 REMARK 500 PRO B 109 39.91 -94.27 REMARK 500 SER B 120 160.33 -47.22 REMARK 500 ASN B 159 155.25 -46.40 REMARK 500 SER B 178 -160.34 -115.79 REMARK 500 TYR B 213 135.52 -38.02 REMARK 500 ILE B 228 82.59 -150.87 REMARK 500 VAL B 237 -61.22 -161.75 REMARK 500 ASN B 238 -85.79 62.33 REMARK 500 PRO B 249 -173.18 -52.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 CYS B 62 -10.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PT A1257 PT REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 227 SD REMARK 620 2 HIS A 231 ND1 97.8 REMARK 620 3 HIS A 231 NE2 133.6 44.8 REMARK 620 4 CL A1258 CL 150.9 111.1 71.2 REMARK 620 5 CL A1259 CL 81.5 117.2 134.9 87.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PT B1257 PT REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B 227 SD REMARK 620 2 HIS B 231 N 100.7 REMARK 620 3 HIS B 231 ND1 69.7 90.9 REMARK 620 4 CL B1258 CL 126.2 76.7 161.0 REMARK 620 5 CL B1259 CL 129.8 121.3 82.6 91.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PT A1257 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B1255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PT B1257 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1258 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1259 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1260 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1261 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1262 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H03 RELATED DB: PDB REMARK 900 HUMAN CD55 DOMAINS 3 & 4 REMARK 900 RELATED ID: 1H04 RELATED DB: PDB REMARK 900 HUMAN CD55 DOMAINS 3 & 4 REMARK 900 RELATED ID: 1H2P RELATED DB: PDB REMARK 900 HUMAN CD55 DOMAINS 3 & 4 REMARK 900 RELATED ID: 1H2Q RELATED DB: PDB REMARK 900 HUMAN CD55 DOMAINS 3 & 4 REMARK 900 RELATED ID: 1M11 RELATED DB: PDB REMARK 900 STRUCTURAL MODEL OF HUMAN DECAY-ACCELERATING FACTOR BOUNDTO REMARK 900 ECHOVIRUS 7 FROM CRYO- ELECTRON MICROSCOPY REMARK 900 RELATED ID: 1NWV RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A FUNCTIONALLY ACTIVE COMPONENT OFDECAY REMARK 900 ACCELERATING FACTOR REMARK 900 RELATED ID: 1OJV RELATED DB: PDB REMARK 900 DECAY ACCELERATING FACTOR: THE STRUCTURE OF AN INTACT HUMAN REMARK 900 COMPLEMENT REGULATOR. REMARK 900 RELATED ID: 1OJW RELATED DB: PDB REMARK 900 DECAY ACCELERATING FACTOR: THE STRUCTURE OF AN INTACT HUMAN REMARK 900 COMPLEMENT REGULATOR. REMARK 900 RELATED ID: 1OJY RELATED DB: PDB REMARK 900 DECAY ACCELERATING FACTOR: THE STRUCTURE OF AN INTACT HUMAN REMARK 900 COMPLEMENT REGULATOR. REMARK 900 RELATED ID: 1OK1 RELATED DB: PDB REMARK 900 DECAY ACCELERATING FACTOR: THE STRUCTURE OF AN INTACT HUMAN REMARK 900 COMPLEMENT REGULATOR. REMARK 900 RELATED ID: 1OK2 RELATED DB: PDB REMARK 900 DECAY ACCELERATING FACTOR: THE STRUCTURE OF AN INTACT HUMAN REMARK 900 COMPLEMENT REGULATOR. REMARK 900 RELATED ID: 1OK3 RELATED DB: PDB REMARK 900 DECAY ACCELERATING FACTOR: THE STRUCTURE OF AN INTACT HUMAN REMARK 900 COMPLEMENT REGULATOR. REMARK 900 RELATED ID: 1UOT RELATED DB: PDB REMARK 900 HUMAN CD55 DOMAINS 3 & 4 REMARK 900 RELATED ID: 1UPN RELATED DB: PDB REMARK 900 COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR REMARK 900 DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A REMARK 999 REMARK 999 SEQUENCE REMARK 999 MET AND GLN ADDED AT N-TERMINUS, CYS ADDED AT C-TERMINUS REMARK 999 RESIDUES A48 B48 MAP TO RESIDUE 80 OF SWISSPROT ENTRY REMARK 999 P08174. RESIDUE 80 IN THE SWISSPROT ENTRY IS GIVEN AS THR, REMARK 999 BUT SOME REFERENCES FOR SWS P08174 SHOW RESIDUE 80 AS ILE. REMARK 999 THE RESIDUE IS ANNOTATED AS A CONFLICT IN THE SWS ENTRY AS REMARK 999 OF 16-07-2003 DBREF 1OK9 A 1 2 PDB 1OK9 1OK9 1 2 DBREF 1OK9 A 3 253 UNP P08174 DAF_HUMAN 35 285 DBREF 1OK9 A 254 254 PDB 1OK9 1OK9 254 254 DBREF 1OK9 B 1 2 PDB 1OK9 1OK9 1 2 DBREF 1OK9 B 3 253 UNP P08174 DAF_HUMAN 35 285 DBREF 1OK9 B 254 254 PDB 1OK9 1OK9 254 254 SEQADV 1OK9 ILE A 48 UNP P08174 THR 80 CONFLICT SEQADV 1OK9 ILE B 48 UNP P08174 THR 80 CONFLICT SEQRES 1 A 254 MET GLN ASP CYS GLY LEU PRO PRO ASP VAL PRO ASN ALA SEQRES 2 A 254 GLN PRO ALA LEU GLU GLY ARG THR SER PHE PRO GLU ASP SEQRES 3 A 254 THR VAL ILE THR TYR LYS CYS GLU GLU SER PHE VAL LYS SEQRES 4 A 254 ILE PRO GLY GLU LYS ASP SER VAL ILE CYS LEU LYS GLY SEQRES 5 A 254 SER GLN TRP SER ASP ILE GLU GLU PHE CYS ASN ARG SER SEQRES 6 A 254 CYS GLU VAL PRO THR ARG LEU ASN SER ALA SER LEU LYS SEQRES 7 A 254 GLN PRO TYR ILE THR GLN ASN TYR PHE PRO VAL GLY THR SEQRES 8 A 254 VAL VAL GLU TYR GLU CYS ARG PRO GLY TYR ARG ARG GLU SEQRES 9 A 254 PRO SER LEU SER PRO LYS LEU THR CYS LEU GLN ASN LEU SEQRES 10 A 254 LYS TRP SER THR ALA VAL GLU PHE CYS LYS LYS LYS SER SEQRES 11 A 254 CYS PRO ASN PRO GLY GLU ILE ARG ASN GLY GLN ILE ASP SEQRES 12 A 254 VAL PRO GLY GLY ILE LEU PHE GLY ALA THR ILE SER PHE SEQRES 13 A 254 SER CYS ASN THR GLY TYR LYS LEU PHE GLY SER THR SER SEQRES 14 A 254 SER PHE CYS LEU ILE SER GLY SER SER VAL GLN TRP SER SEQRES 15 A 254 ASP PRO LEU PRO GLU CYS ARG GLU ILE TYR CYS PRO ALA SEQRES 16 A 254 PRO PRO GLN ILE ASP ASN GLY ILE ILE GLN GLY GLU ARG SEQRES 17 A 254 ASP HIS TYR GLY TYR ARG GLN SER VAL THR TYR ALA CYS SEQRES 18 A 254 ASN LYS GLY PHE THR MET ILE GLY GLU HIS SER ILE TYR SEQRES 19 A 254 CYS THR VAL ASN ASN ASP GLU GLY GLU TRP SER GLY PRO SEQRES 20 A 254 PRO PRO GLU CYS ARG GLY CYS SEQRES 1 B 254 MET GLN ASP CYS GLY LEU PRO PRO ASP VAL PRO ASN ALA SEQRES 2 B 254 GLN PRO ALA LEU GLU GLY ARG THR SER PHE PRO GLU ASP SEQRES 3 B 254 THR VAL ILE THR TYR LYS CYS GLU GLU SER PHE VAL LYS SEQRES 4 B 254 ILE PRO GLY GLU LYS ASP SER VAL ILE CYS LEU LYS GLY SEQRES 5 B 254 SER GLN TRP SER ASP ILE GLU GLU PHE CYS ASN ARG SER SEQRES 6 B 254 CYS GLU VAL PRO THR ARG LEU ASN SER ALA SER LEU LYS SEQRES 7 B 254 GLN PRO TYR ILE THR GLN ASN TYR PHE PRO VAL GLY THR SEQRES 8 B 254 VAL VAL GLU TYR GLU CYS ARG PRO GLY TYR ARG ARG GLU SEQRES 9 B 254 PRO SER LEU SER PRO LYS LEU THR CYS LEU GLN ASN LEU SEQRES 10 B 254 LYS TRP SER THR ALA VAL GLU PHE CYS LYS LYS LYS SER SEQRES 11 B 254 CYS PRO ASN PRO GLY GLU ILE ARG ASN GLY GLN ILE ASP SEQRES 12 B 254 VAL PRO GLY GLY ILE LEU PHE GLY ALA THR ILE SER PHE SEQRES 13 B 254 SER CYS ASN THR GLY TYR LYS LEU PHE GLY SER THR SER SEQRES 14 B 254 SER PHE CYS LEU ILE SER GLY SER SER VAL GLN TRP SER SEQRES 15 B 254 ASP PRO LEU PRO GLU CYS ARG GLU ILE TYR CYS PRO ALA SEQRES 16 B 254 PRO PRO GLN ILE ASP ASN GLY ILE ILE GLN GLY GLU ARG SEQRES 17 B 254 ASP HIS TYR GLY TYR ARG GLN SER VAL THR TYR ALA CYS SEQRES 18 B 254 ASN LYS GLY PHE THR MET ILE GLY GLU HIS SER ILE TYR SEQRES 19 B 254 CYS THR VAL ASN ASN ASP GLU GLY GLU TRP SER GLY PRO SEQRES 20 B 254 PRO PRO GLU CYS ARG GLY CYS HET ACT A1255 4 HET ACT A1256 4 HET PT A1257 1 HET CL A1258 1 HET CL A1259 1 HET SO4 A1260 5 HET ACT B1255 4 HET ACT B1256 4 HET PT B1257 1 HET CL B1258 1 HET CL B1259 1 HET SO4 B1260 5 HET GOL B1261 6 HET GOL B1262 6 HETNAM ACT ACETATE ION HETNAM PT PLATINUM (II) ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ACT 4(C2 H3 O2 1-) FORMUL 5 PT 2(PT 2+) FORMUL 6 CL 4(CL 1-) FORMUL 8 SO4 2(O4 S 2-) FORMUL 15 GOL 2(C3 H8 O3) FORMUL 17 HOH *9(H2 O) HELIX 1 1 PRO A 80 GLN A 84 5 5 HELIX 2 2 PRO B 80 GLN B 84 5 5 SHEET 1 AA 2 ASP A 3 CYS A 4 0 SHEET 2 AA 2 PHE A 23 PRO A 24 -1 O PHE A 23 N CYS A 4 SHEET 1 AB 4 ALA A 13 PRO A 15 0 SHEET 2 AB 4 VAL A 28 CYS A 33 -1 O LYS A 32 N GLN A 14 SHEET 3 AB 4 SER A 46 LEU A 50 -1 O VAL A 47 N ILE A 29 SHEET 4 AB 4 GLN A 54 TRP A 55 -1 O GLN A 54 N LEU A 50 SHEET 1 AC 2 PHE A 37 LYS A 39 0 SHEET 2 AC 2 CYS A 62 ARG A 64 -1 O ASN A 63 N VAL A 38 SHEET 1 AD 3 ALA A 75 LEU A 77 0 SHEET 2 AD 3 VAL A 92 CYS A 97 -1 O GLU A 96 N SER A 76 SHEET 3 AD 3 LYS A 110 THR A 112 -1 O LEU A 111 N VAL A 93 SHEET 1 AE 2 TYR A 101 ARG A 103 0 SHEET 2 AE 2 CYS A 126 LYS A 128 -1 O LYS A 127 N ARG A 102 SHEET 1 AF 4 GLY A 140 ASP A 143 0 SHEET 2 AF 4 THR A 153 CYS A 158 -1 O SER A 155 N ASP A 143 SHEET 3 AF 4 SER A 169 SER A 175 -1 O SER A 170 N ILE A 154 SHEET 4 AF 4 SER A 178 TRP A 181 -1 O SER A 178 N SER A 175 SHEET 1 AG 2 TYR A 162 PHE A 165 0 SHEET 2 AG 2 GLU A 187 GLU A 190 -1 O GLU A 187 N PHE A 165 SHEET 1 AH 4 GLY A 202 ILE A 204 0 SHEET 2 AH 4 SER A 216 CYS A 221 -1 O ALA A 220 N ILE A 203 SHEET 3 AH 4 SER A 232 ASN A 238 -1 O ILE A 233 N VAL A 217 SHEET 4 AH 4 GLU A 241 TRP A 244 -1 O GLU A 241 N ASN A 238 SHEET 1 AI 6 GLU A 250 ARG A 252 0 SHEET 2 AI 6 THR A 226 GLU A 230 -1 O THR A 226 N ARG A 252 SHEET 3 AI 6 GLY B 140 VAL B 144 -1 O VAL B 144 N GLY A 229 SHEET 4 AI 6 THR B 153 CYS B 158 -1 O SER B 155 N ASP B 143 SHEET 5 AI 6 SER B 169 SER B 175 -1 O SER B 170 N ILE B 154 SHEET 6 AI 6 SER B 178 TRP B 181 -1 O SER B 178 N SER B 175 SHEET 1 BA 4 ALA B 13 PRO B 15 0 SHEET 2 BA 4 VAL B 28 CYS B 33 -1 O LYS B 32 N GLN B 14 SHEET 3 BA 4 SER B 46 LEU B 50 -1 O VAL B 47 N ILE B 29 SHEET 4 BA 4 GLN B 54 TRP B 55 -1 O GLN B 54 N LEU B 50 SHEET 1 BB 2 PHE B 37 LYS B 39 0 SHEET 2 BB 2 CYS B 62 ARG B 64 -1 O ASN B 63 N VAL B 38 SHEET 1 BC 3 ALA B 75 LEU B 77 0 SHEET 2 BC 3 VAL B 92 CYS B 97 -1 O GLU B 96 N SER B 76 SHEET 3 BC 3 LYS B 110 THR B 112 -1 O LEU B 111 N VAL B 93 SHEET 1 BD 2 TYR B 101 ARG B 103 0 SHEET 2 BD 2 CYS B 126 LYS B 128 -1 O LYS B 127 N ARG B 102 SHEET 1 BE 2 TYR B 162 PHE B 165 0 SHEET 2 BE 2 GLU B 187 GLU B 190 -1 O GLU B 187 N PHE B 165 SHEET 1 BF 4 GLY B 202 ILE B 204 0 SHEET 2 BF 4 SER B 216 CYS B 221 -1 O ALA B 220 N ILE B 203 SHEET 3 BF 4 SER B 232 THR B 236 -1 O ILE B 233 N VAL B 217 SHEET 4 BF 4 GLU B 243 TRP B 244 -1 O GLU B 243 N THR B 236 SSBOND 1 CYS A 4 CYS A 49 1555 1555 2.03 SSBOND 2 CYS A 33 CYS A 62 1555 1555 2.03 SSBOND 3 CYS A 66 CYS A 113 1555 1555 2.03 SSBOND 4 CYS A 97 CYS A 126 1555 1555 2.03 SSBOND 5 CYS A 131 CYS A 172 1555 1555 2.03 SSBOND 6 CYS A 158 CYS A 188 1555 1555 2.03 SSBOND 7 CYS A 193 CYS A 235 1555 1555 2.03 SSBOND 8 CYS A 221 CYS A 251 1555 1555 2.03 SSBOND 9 CYS B 4 CYS B 49 1555 1555 2.03 SSBOND 10 CYS B 33 CYS B 62 1555 1555 2.03 SSBOND 11 CYS B 66 CYS B 113 1555 1555 2.03 SSBOND 12 CYS B 97 CYS B 126 1555 1555 2.03 SSBOND 13 CYS B 131 CYS B 172 1555 1555 2.03 SSBOND 14 CYS B 158 CYS B 188 1555 1555 2.03 SSBOND 15 CYS B 193 CYS B 235 1555 1555 2.03 SSBOND 16 CYS B 221 CYS B 251 1555 1555 2.03 LINK SD MET A 227 PT A PT A1257 1555 1555 2.40 LINK ND1 HIS A 231 PT A PT A1257 1555 1555 1.89 LINK NE2 HIS A 231 PT A PT A1257 1555 1555 3.02 LINK PT A PT A1257 CL A CL A1258 1555 1555 2.27 LINK PT A PT A1257 CL A CL A1259 1555 1555 2.28 LINK SD MET B 227 PT A PT B1257 1555 1555 2.25 LINK N HIS B 231 PT A PT B1257 1555 1555 3.52 LINK ND1 HIS B 231 PT A PT B1257 1555 1555 2.04 LINK PT A PT B1257 CL A CL B1258 1555 1555 2.26 LINK PT A PT B1257 CL A CL B1259 1555 1555 2.33 CISPEP 1 ASN A 63 ARG A 64 0 10.30 CISPEP 2 GLN A 79 PRO A 80 0 3.77 CISPEP 3 PRO A 99 GLY A 100 0 1.43 CISPEP 4 ASN A 239 ASP A 240 0 0.40 CISPEP 5 ARG A 252 GLY A 253 0 1.59 CISPEP 6 GLY A 253 CYS A 254 0 1.32 CISPEP 7 GLN B 79 PRO B 80 0 3.04 CISPEP 8 PRO B 99 GLY B 100 0 1.40 CISPEP 9 ASN B 239 ASP B 240 0 0.38 CISPEP 10 ARG B 252 GLY B 253 0 1.04 SITE 1 AC1 8 PRO A 134 ILE A 154 PHE A 156 SER A 170 SITE 2 AC1 8 TRP A 181 ASP A 183 PRO A 184 LEU A 185 SITE 1 AC2 3 ARG A 208 ASP A 209 HIS A 210 SITE 1 AC3 5 TYR A 219 MET A 227 HIS A 231 CL A1258 SITE 2 AC3 5 CL A1259 SITE 1 AC4 5 HIS A 231 PT A1257 CL A1259 ASN B 133 SITE 2 AC4 5 PRO B 134 SITE 1 AC5 5 MET A 227 HIS A 231 PT A1257 CL A1258 SITE 2 AC5 5 VAL B 144 SITE 1 AC6 6 TYR A 213 ARG A 214 THR A 236 VAL A 237 SITE 2 AC6 6 TYR B 213 ARG B 214 SITE 1 AC7 8 PRO B 134 ILE B 154 PHE B 156 SER B 170 SITE 2 AC7 8 TRP B 181 ASP B 183 PRO B 184 LEU B 185 SITE 1 AC8 3 LEU B 72 ASN B 73 SER B 74 SITE 1 AC9 4 MET B 227 HIS B 231 CL B1258 CL B1259 SITE 1 BC1 4 MET B 227 GLY B 229 PT B1257 CL B1259 SITE 1 BC2 3 HIS B 231 PT B1257 CL B1258 SITE 1 BC3 5 SER B 36 PHE B 37 VAL B 38 SER B 65 SITE 2 BC3 5 GLU B 67 SITE 1 BC4 2 GLU B 136 ARG B 138 SITE 1 BC5 3 ASP B 9 PRO B 11 ILE B 58 CRYST1 46.130 54.600 62.770 87.19 85.61 65.74 P 1 2 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 0.021678 -0.009770 -0.001476 0.00000 SCALE2 0.000000 0.020089 -0.000388 0.00000 SCALE3 0.000000 0.000000 0.015981 0.00000 MTRIX1 1 0.999100 0.001130 -0.042350 2.49582 1 MTRIX2 1 -0.001760 -0.997670 -0.068270 50.17564 1 MTRIX3 1 -0.042320 0.068280 -0.996770 66.84209 1 MTRIX1 2 0.996050 0.067450 0.057810 5.36279 1 MTRIX2 2 0.067110 -0.997710 0.007900 48.08324 1 MTRIX3 2 0.058210 -0.003990 -0.998300 60.10329 1 MTRIX1 3 0.981770 -0.074540 0.174850 2.70388 1 MTRIX2 3 -0.074770 -0.997190 -0.005270 53.37027 1 MTRIX3 3 0.174750 -0.007900 -0.984580 55.48820 1 MTRIX1 4 0.921230 -0.116790 0.371070 0.94325 1 MTRIX2 4 -0.106110 -0.993140 -0.049150 55.19082 1 MTRIX3 4 0.374260 0.005910 -0.927310 47.21286 1