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- PDB-1ojy: Decay accelerating factor (cd55): the structure of an intact huma... -

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Basic information

Entry
Database: PDB / ID: 1ojy
TitleDecay accelerating factor (cd55): the structure of an intact human complement regulator.
ComponentsCOMPLEMENT DECAY-ACCELERATING FACTOR
KeywordsREGULATOR OF COMPLEMENT PATHWAY / REGULATOR OF COMPLEMENT / DECAY ACCELERATION OF C3/C5 CONVERTASES / PATHOGEN RECEPTOR / SHORT CONSENSUS REPEAT DOMAINS / PLASMA / GLYCOPROTEIN / MEMBRANE / GPI-ANCHOR
Function / homology
Function and homology information


regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / complement activation, classical pathway ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / complement activation, classical pathway / transport vesicle / side of membrane / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / Regulation of Complement cascade / positive regulation of T cell cytokine production / positive regulation of cytosolic calcium ion concentration / virus receptor activity / membrane raft / Golgi membrane / innate immune response / lipid binding / Neutrophil degranulation / cell surface / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Complement decay-accelerating factor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLukacik, P. / Roversi, P. / White, J. / Esser, D. / Smith, G.P. / Billington, J. / Williams, P.A. / Rudd, P.M. / Wormald, M.R. / Crispin, M.D.M. ...Lukacik, P. / Roversi, P. / White, J. / Esser, D. / Smith, G.P. / Billington, J. / Williams, P.A. / Rudd, P.M. / Wormald, M.R. / Crispin, M.D.M. / Radcliffe, C.M. / Dwek, R.A. / Evans, D.J. / Morgan, B.P. / Smith, R.A.G. / Lea, S.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Complement Regulation at the Molecular Level: The Structure of Decay-Accelerating Factor
Authors: Lukacik, P. / Roversi, P. / White, J. / Esser, D. / Smith, G.P. / Billington, J. / Williams, P.A. / Rudd, P.M. / Wormald, M.R. / Harvey, D.J. / Crispin, M.D.M. / Radcliffe, C.M. / Dwek, R.A. ...Authors: Lukacik, P. / Roversi, P. / White, J. / Esser, D. / Smith, G.P. / Billington, J. / Williams, P.A. / Rudd, P.M. / Wormald, M.R. / Harvey, D.J. / Crispin, M.D.M. / Radcliffe, C.M. / Dwek, R.A. / Evans, D.J. / Morgan, B.P. / Smith, R.A.G. / Lea, S.M.
#1: Journal: Protein Sci. / Year: 2004
Title: Biological Activity, Membrane-Targeting Modification, and Crystallization of Soluble Human Decay Accelerating Factor Expressed in E. Coli
Authors: White, J. / Lukacik, P. / Esser, D. / Steward, M. / Giddings, N. / Bright, J.R. / Fritchley, S. / Morgan, B.P. / Lea, S.M. / Smith, G.P. / Smith, R.A.G.
History
DepositionJul 16, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 7, 2004Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMPLEMENT DECAY-ACCELERATING FACTOR
B: COMPLEMENT DECAY-ACCELERATING FACTOR
C: COMPLEMENT DECAY-ACCELERATING FACTOR
D: COMPLEMENT DECAY-ACCELERATING FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,77617
Polymers112,6994
Non-polymers1,07713
Water2,576143
1
A: COMPLEMENT DECAY-ACCELERATING FACTOR
C: COMPLEMENT DECAY-ACCELERATING FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8448
Polymers56,3492
Non-polymers4946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: COMPLEMENT DECAY-ACCELERATING FACTOR
D: COMPLEMENT DECAY-ACCELERATING FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9329
Polymers56,3492
Non-polymers5837
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.829, 78.694, 80.903
Angle α, β, γ (deg.)72.70, 79.38, 81.70
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9972, 0.05653, -0.04897), (-0.06148, 0.99244, -0.10626), (0.0426, 0.10897, 0.99313)23.12275, 33.8668, -44.666
2given(0.99986, 0.01449, 0.00827), (-0.01428, 0.99959, -0.02493), (-0.00862, 0.0248, 0.99966)21.76586, 30.78671, -40.29158
3given(0.99816, 0.05645, -0.02203), (-0.05757, 0.99689, -0.05389), (0.01892, 0.05506, 0.9983)22.83537, 33.23575, -41.09311
4given(0.99883, 0.03428, -0.03403), (-0.03452, 0.99938, -0.0066), (0.03378, 0.00777, 0.9994)24.96305, 28.68526, -38.57953
5given(0.99936, 0.03481, -0.00771), (-0.03521, 0.99763, -0.05907), (0.00563, 0.0593, 0.99822)23.04648, 32.30637, -40.61421
6given(0.99942, 0.03055, -0.01524), (-0.03104, 0.99897, -0.0332), (0.01421, 0.03365, 0.99933)23.70138, 30.58217, -39.88476
7given(0.99994, 0.01049, 0.00361), (-0.01042, 0.99978, -0.0184), (-0.0038, 0.01836, 0.99982)23.07942, 29.40554, -39.37451
8given(0.9982, 0.04536, -0.03931), (-0.04827, 0.99589, -0.07659), (0.03567, 0.07835, 0.99629)24.37737, 33.72336, -42.5662

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Components

#1: Protein
COMPLEMENT DECAY-ACCELERATING FACTOR / DAF / CR / CD55


Mass: 28174.666 Da / Num. of mol.: 4 / Fragment: FOUR EXTRACELLULAR SCR DOMAINS, RESIDUES 35-285
Source method: isolated from a genetically manipulated source
Details: MODELLED GLYCEROLS, ACETATES AND SULPHATES FROM CRYSTALLISATION BUFFER
Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMAN SEQUENCE EXPRESSED IN E.COLI. / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P08174
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsMQ ADDED AT N-TERMINUS, C ADDED AT C-TERMINUS RESIDUES A48 B48 C48 D48MAP TO RESIDUE 80 OF ...MQ ADDED AT N-TERMINUS, C ADDED AT C-TERMINUS RESIDUES A48 B48 C48 D48MAP TO RESIDUE 80 OF SWISSPROT ENTRY P08174. RESIDUE 80 IN THE SWISSPROT ENTRY IS GIVEN AS THR, BUT SOME REFERENCES FOR SWS P08174 SHOW RESIDUE 80 AS ILE. THE RESIDUE IS ANNOTATED AS A CONFLICT IN THE SWS ENTRY AS OF 16-07-2003

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 53 %
Crystal growpH: 4.6
Details: 0.2 M AMMONIUM SULPHATE 20% M-PEG 5K, 0.1M SODIUM ACETATE PH 4.6, 10% GLYCEROL
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Mammonium sulfate1reservoir
220 %(w/v)MPEG50001reservoir
30.1 Msodium acetate1reservoirpH4.6
410 %(w/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 34638 / % possible obs: 94.4 % / Redundancy: 2.44 % / Biso Wilson estimate: -8.25 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.9
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 1.9 / % possible all: 94.2
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 38.6 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.7 Å / % possible obs: 94.2 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
TNT5Frefinement
DENZOV. 1.96)data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OJV

1ojv


Resolution: 2.6→16 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: BUSTER-TNT MAXIMUM LIKELIHOOD REFINEMENT ANISOTROPIC SCALING BETAIJS: BETA11:5.45 BETA12:- 25.10 BETA13:-5.29 BETA22:93.3 BETA23:-3.78 BETA33:-15.4
RfactorNum. reflection% reflectionSelection details
all0.254 32792 --
obs-34514 94.3 %-
Rfree---RANDOM
Solvent computationSolvent model: BABINET SCALING / Bsol: 53 Å2 / ksol: 0.35 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7840 0 67 143 8050
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00581412
X-RAY DIFFRACTIONt_angle_deg0.65109853
X-RAY DIFFRACTIONt_dihedral_angle_d20.647460
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0062172
X-RAY DIFFRACTIONt_gen_planes0.01411595
X-RAY DIFFRACTIONt_it0.885814120
X-RAY DIFFRACTIONt_nbd0.2062182
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
Refinement
*PLUS
Lowest resolution: 25 Å / Num. reflection obs: 32792 / Num. reflection Rfree: 1722 / % reflection Rfree: 5 % / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg0.7
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.60
X-RAY DIFFRACTIONt_planar_d0.0062
X-RAY DIFFRACTIONt_plane_restr0.0145
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.67 Å / Rfactor Rfree: 0.303 / Rfactor Rwork: 0.27

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