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- PDB-1uot: HUMAN CD55 DOMAINS 3 & 4 -

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Basic information

Entry
Database: PDB / ID: 1uot
TitleHUMAN CD55 DOMAINS 3 & 4
ComponentsCOMPLEMENT DECAY-ACCELERATING FACTOR
KeywordsREGULATOR OF COMPLEMENT PATHWAY / IMMUNE 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: 3 Å
AuthorsWilliams, P. / Chaudhry, Y. / Goodfellow, I.G. / 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.G. / Billington, J. / Powell, R. / Spiller, O.B. / 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
DepositionSep 23, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 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 ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 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

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Assembly

Deposited unit
P: COMPLEMENT DECAY-ACCELERATING FACTOR


Theoretical massNumber of molelcules
Total (without water)13,5861
Polymers13,5861
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.417, 36.880, 106.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 13586.049 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: THIS PROTEIN RECOGNIZES C4B AND C3B FRAGMENTS THAT CONDENSE WITH CELL-SURFACE HYDROXYL OR ...FUNCTION: THIS PROTEIN RECOGNIZES C4B AND C3B FRAGMENTS THAT CONDENSE WITH CELL-SURFACE HYDROXYL OR AMINO GROUPS WHEN NASCENT C4B AND C3B ARE LOCALLY GENERATED DURING C4 AND C3 ACTIVATION.
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: 2.28 Å3/Da / Density % sol: 45 %
Crystal growpH: 5.6 / Details: pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 2432 / % possible obs: 88 % / Redundancy: 4.8 % / Biso Wilson estimate: 4.123 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 2.3
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 1 / % possible all: 82

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Processing

Software
NameVersionClassification
TNT5.6.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H03

1h03


Resolution: 3→18.5 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: DRIVEN BY BUSTER MAXIMUM LIKELIHOOD. THIS IS A NEW REFINEMENT OF PDB ENTRY 1H2Q
RfactorNum. reflection% reflectionSelection details
Rwork0.223 ---
all0.224 2642 --
obs-2642 95.7 %-
Rfree--5 %RANDOM
Solvent computationSolvent model: BABINET SCALING / Bsol: 28 Å2 / ksol: 1.14 e/Å3
Refinement stepCycle: LAST / Resolution: 3→18.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 0 0 8 958
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0029812
X-RAY DIFFRACTIONt_angle_deg0.50213253
X-RAY DIFFRACTIONt_dihedral_angle_d19.9665700
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006252
X-RAY DIFFRACTIONt_gen_planes0.0111445
X-RAY DIFFRACTIONt_it0.75598120
X-RAY DIFFRACTIONt_nbd0.437185
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

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