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- PDB-1h2p: Human CD55 domains 3 & 4 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1h2p
TitleHuman CD55 domains 3 & 4
ComponentsCOMPLEMENT DECAY-ACCELERATING FACTOR
KeywordsIMMUNE SYSTEM PROTEIN / COMPLEMENT DECAY ACCELERATING FACTOR / ENTEROVIRAL RECEPTOR / BACTERIAL RECEPTOR / LIGAND FOR CD97 / COMPLEMENT PATHWAY / ALTERNATIVE SPLICING / 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
Complement decay-accelerating factor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWilliams, P. / Chaudhry, Y. / Goodfellow, I. / Billington, J. / Spiller, B. / Evans, D.J. / Lea, S.M.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Mapping Cd55 Function. The Structure of Two Pathogen-Binding Domains at 1.7 A
Authors: Williams, P. / Chaudhry, Y. / Goodfellow, I. / Billington, J. / Powell, R. / Spiller, O. / Evans, D.J. / Lea, S.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of a Biologically Active Fragment of Cd55
Authors: Lea, S.M. / Powell, R. / Evans, D.J.
#2: Journal: J.Biol.Chem. / Year: 1998
Title: Determination of the Affinity and Kinetic Constants for the Interaction between the Human Virus Echovirus 11 and its Cellular Receptor, Cd55
Authors: Lea, S.M. / Powell, R. / Mckee, T. / Evans, D.J. / Brown, D.J. / Stuart, D.I. / Van Der Merwe, A.
History
DepositionAug 13, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 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
P: COMPLEMENT DECAY-ACCELERATING FACTOR


Theoretical massNumber of molelcules
Total (without water)13,5851
Polymers13,5851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.900, 20.700, 41.800
Angle α, β, γ (deg.)90.00, 99.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13585.064 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR SCR DOMAINS 3 & 4, RESIDUES 161-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P08174
Compound detailsRECOGNIZES C4B AND C3B FRAGMENTS GENERATED DURING C4 AND C3 ACTIVATION. PART OF THE COMPLEMENT ...RECOGNIZES C4B AND C3B FRAGMENTS GENERATED DURING C4 AND C3 ACTIVATION. PART OF THE COMPLEMENT CASCADE IN IMMNUNITY.
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growpH: 4.5 / Details: pH 4.50
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, sitting drop
Details: Lea, S.M., (1999) Acta Crystallogr.,Sect.D, D55, 1198.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %PEG40001reservoir
20.2 Msodium acetate1reservoir
30.1 Msodium acetate trihydrate1reservoirpH4.6
48-12 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.96
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 2726 / % possible obs: 99 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 2.5
Reflection shellResolution: 2.8→3 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 1.2 / % possible all: 97
Reflection
*PLUS
Lowest resolution: 40 Å / Redundancy: 4.8 % / Num. measured all: 13095 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.2

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H03

1h03


Resolution: 2.8→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: GROUPED B'S USED - ONE MAIN CHAIN AND ONE SIDE CHAIN GROUP PER RESIDUE
RfactorNum. reflection% reflectionSelection details
Rfree0.304 -5 %RANDOM
Rwork0.258 ---
obs0.258 2726 99 %-
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 0 0 933
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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