HEADER REGULATOR OF COMPLEMENT PATHWAY 23-SEP-03 1UOT TITLE HUMAN CD55 DOMAINS 3 & 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT DECAY-ACCELERATING FACTOR; COMPND 3 CHAIN: P; COMPND 4 FRAGMENT: EXTRACELLULAR SCR DOMAINS 3 & 4, RESIDUES COMPND 5 161-285; COMPND 6 SYNONYM: CD55 ANTIGEN, DAF, CR, CD55; COMPND 7 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 REGULATOR OF COMPLEMENT PATHWAY, IMMUNE SYSTEM PROTEIN, KEYWDS 2 COMPLEMENT DECAY ACCELERATING FACTOR, ENTEROVIRAL KEYWDS 3 RECEPTOR, BACTERIAL RECEPTOR, LIGAND FOR CD97, COMPLEMENT KEYWDS 4 PATHWAY, ALTERNATIVE SPLICING, GPI-ANCHOR EXPDTA X-RAY DIFFRACTION AUTHOR P.WILLIAMS,Y.CHAUDHRY,I.G.GOODFELLOW,J.BILLINGTON,B.SPILLER, AUTHOR 2 D.J.EVANS,S.M.LEA REVDAT 2 24-FEB-09 1UOT 1 VERSN REVDAT 1 25-SEP-03 1UOT 0 JRNL AUTH P.WILLIAMS,Y.CHAUDHRY,I.G.GOODFELLOW,J.BILLINGTON, JRNL AUTH 2 R.POWELL,O.B.SPILLER,D.J.EVANS,S.M.LEA JRNL TITL MAPPING CD55 FUNCTION. THE STRUCTURE OF TWO JRNL TITL 2 PATHOGEN-BINDING DOMAINS AT 1.7 A JRNL REF J.BIOL.CHEM. V. 278 10691 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12499389 JRNL DOI 10.1074/JBC.M212561200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.M.LEA,R.POWELL,D.J.EVANS REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION REMARK 1 TITL 2 ANALYSIS OF A BIOLOGICALLY ACTIVE FRAGMENT OF CD55 REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 1198 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 10329784 REMARK 1 DOI 10.1107/S0907444999001638 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.M.LEA,R.POWELL,T.MCKEE,D.J.EVANS,D.J.BROWN, REMARK 1 AUTH 2 D.I.STUART,A.VAN DER MERWE REMARK 1 TITL DETERMINATION OF THE AFFINITY AND KINETIC REMARK 1 TITL 2 CONSTANTS FOR THE INTERACTION BETWEEN THE HUMAN REMARK 1 TITL 3 VIRUS ECHOVIRUS 11 AND ITS CELLULAR RECEPTOR, CD55 REMARK 1 REF J.BIOL.CHEM. V. 273 30443 1998 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 9804811 REMARK 1 DOI 10.1074/JBC.273.46.30443 REMARK 2 REMARK 2 RESOLUTION. 3.0 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5.6.1 REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.0 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.5 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 2642 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) : 0.223 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 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) : 0.224 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.223 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 118 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 2642 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 950 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 8 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 4.123 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.002 ; 2.0 ; 981 REMARK 3 BOND ANGLES (DEGREES) : 0.502 ; 3.0 ; 1325 REMARK 3 TORSION ANGLES (DEGREES) : 19.966; 0.0 ; 570 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.006 ; 2.000 ; 25 REMARK 3 GENERAL PLANES (A) : 0.011 ; 5.000 ; 144 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 0.755 ; 20.000; 981 REMARK 3 NON-BONDED CONTACTS (A) : 0.437 ; 5.000 ; 18 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 : 1.14 REMARK 3 BSOL : 28 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: DRIVEN BY BUSTER MAXIMUM LIKELIHOOD. REMARK 3 THIS IS A NEW REFINEMENT OF PDB ENTRY 1H2Q REMARK 4 REMARK 4 1UOT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-SEP-03. REMARK 100 THE PDBE ID CODE IS EBI-13574. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2432 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.3000 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) : 3.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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 1H03 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 15.70850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.39700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.44000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.39700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.70850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.44000 REMARK 290 SMTRY3 4 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 GENERATING THE BIOMOLECULE 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: P 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 400 REMARK 400 COMPOUND REMARK 400 FUNCTION: THIS PROTEIN RECOGNIZES C4B AND C3B FRAGMENTS THAT REMARK 400 CONDENSE WITH CELL-SURFACE HYDROXYL OR AMINO GROUPS WHEN NASCENT REMARK 400 C4B AND C3B ARE LOCALLY GENERATED DURING C4 AND C3 ACTIVATION. 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 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 SER P 45 148.80 176.94 REMARK 500 ARG P 90 -29.65 74.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): 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 REMARK 900 FACTOR BOUNDTO ECHOVIRUS 7 FROM CRYO- REMARK 900 ELECTRON MICROSCOPY REMARK 900 RELATED ID: 1NWV RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A FUNCTIONALLY ACTIVE REMARK 900 COMPONENT OFDECAY ACCELERATING FACTOR REMARK 900 RELATED ID: 1OJV RELATED DB: PDB REMARK 900 DECAY ACCELERATING FACTOR: THE STRUCTURE OF REMARK 900 AN INTACT HUMAN COMPLEMENT REGULATOR. REMARK 900 RELATED ID: 1OJW RELATED DB: PDB REMARK 900 DECAY ACCELERATING FACTOR: THE STRUCTURE OF REMARK 900 AN INTACT HUMAN COMPLEMENT REGULATOR. REMARK 900 RELATED ID: 1OJY RELATED DB: PDB REMARK 900 DECAY ACCELERATING FACTOR: THE STRUCTURE OF REMARK 900 AN INTACT HUMAN COMPLEMENT REGULATOR. REMARK 900 RELATED ID: 1OK1 RELATED DB: PDB REMARK 900 DECAY ACCELERATING FACTOR: THE STRUCTURE OF REMARK 900 AN INTACT HUMAN COMPLEMENT REGULATOR. REMARK 900 RELATED ID: 1OK2 RELATED DB: PDB REMARK 900 DECAY ACCELERATING FACTOR: THE STRUCTURE OF REMARK 900 AN INTACT HUMAN COMPLEMENT REGULATOR. REMARK 900 RELATED ID: 1OK3 RELATED DB: PDB REMARK 900 DECAY ACCELERATING FACTOR: THE STRUCTURE OF REMARK 900 AN INTACT HUMAN COMPLEMENT REGULATOR. REMARK 900 RELATED ID: 1OK9 RELATED DB: PDB REMARK 900 DECAY ACCELERATING FACTOR: THE STRUCTURE OF REMARK 900 AN INTACT HUMAN COMPLEMENT REGULATOR. DBREF 1UOT P 5 129 UNP P08174 DAF_HUMAN 161 285 SEQRES 1 P 125 LYS SER CYS PRO ASN PRO GLY GLU ILE ARG ASN GLY GLN SEQRES 2 P 125 ILE ASP VAL PRO GLY GLY ILE LEU PHE GLY ALA THR ILE SEQRES 3 P 125 SER PHE SER CYS ASN THR GLY TYR LYS LEU PHE GLY SER SEQRES 4 P 125 THR SER SER PHE CYS LEU ILE SER GLY SER SER VAL GLN SEQRES 5 P 125 TRP SER ASP PRO LEU PRO GLU CYS ARG GLU ILE TYR CYS SEQRES 6 P 125 PRO ALA PRO PRO GLN ILE ASP ASN GLY ILE ILE GLN GLY SEQRES 7 P 125 GLU ARG ASP HIS TYR GLY TYR ARG GLN SER VAL THR TYR SEQRES 8 P 125 ALA CYS ASN LYS GLY PHE THR MET ILE GLY GLU HIS SER SEQRES 9 P 125 ILE TYR CYS THR VAL ASN ASN ASP GLU GLY GLU TRP SER SEQRES 10 P 125 GLY PRO PRO PRO GLU CYS ARG GLY FORMUL 2 HOH *8(H2 O1) SHEET 1 PA 4 GLY P 16 ASP P 19 0 SHEET 2 PA 4 THR P 29 CYS P 34 -1 O SER P 31 N ASP P 19 SHEET 3 PA 4 SER P 45 LEU P 49 -1 O SER P 46 N ILE P 30 SHEET 4 PA 4 GLN P 56 TRP P 57 -1 O GLN P 56 N LEU P 49 SHEET 1 PB 2 TYR P 38 PHE P 41 0 SHEET 2 PB 2 GLU P 63 GLU P 66 -1 O GLU P 63 N PHE P 41 SHEET 1 PC 4 GLY P 78 ILE P 80 0 SHEET 2 PC 4 SER P 92 CYS P 97 -1 O ALA P 96 N ILE P 79 SHEET 3 PC 4 SER P 108 VAL P 113 -1 O ILE P 109 N VAL P 93 SHEET 4 PC 4 GLY P 118 TRP P 120 -1 O GLU P 119 N THR P 112 SHEET 1 PD 2 THR P 102 ILE P 104 0 SHEET 2 PD 2 GLU P 126 ARG P 128 -1 O GLU P 126 N ILE P 104 SSBOND 1 CYS P 7 CYS P 48 1555 1555 2.03 SSBOND 2 CYS P 34 CYS P 64 1555 1555 2.03 SSBOND 3 CYS P 69 CYS P 111 1555 1555 2.03 SSBOND 4 CYS P 97 CYS P 127 1555 1555 2.03 CISPEP 1 SER P 51 GLY P 52 0 -4.88 CRYST1 31.417 36.880 106.794 90.00 90.00 90.00 P 21 21 21 4 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 0.031830 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027115 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009364 0.00000 MASTER 266 0 0 0 12 0 0 6 0 0 0 10 END