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- PDB-2ofs: Crystal structure of human CD59 -

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Basic information

Entry
Database: PDB / ID: 2ofs
TitleCrystal structure of human CD59
ComponentsCD59 glycoprotein
KeywordsSIGNALING PROTEIN / complement inhibitor
Function / homology
Function and homology information


COPII-mediated vesicle transport / Cargo concentration in the ER / Neutrophil degranulation / Regulation of Complement cascade / COPI-mediated anterograde transport / negative regulation of activation of membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / anchored component of external side of plasma membrane / COPII vesicle coating ...COPII-mediated vesicle transport / Cargo concentration in the ER / Neutrophil degranulation / Regulation of Complement cascade / COPI-mediated anterograde transport / negative regulation of activation of membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / anchored component of external side of plasma membrane / COPII vesicle coating / tertiary granule membrane / specific granule membrane / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / ER to Golgi transport vesicle membrane / regulation of complement activation / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle / cell surface receptor signaling pathway / blood coagulation / Golgi membrane / focal adhesion / endoplasmic reticulum membrane / neutrophil degranulation / cell surface / extracellular space / extracellular exosome / membrane / plasma membrane
Ly-6 antigen/uPA receptor-like / CD59 glycoprotein / u-PAR/Ly-6 domain / CD59 antigen, conserved site / Ly-6 / u-PAR domain signature.
CD59 glycoprotein
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsDavies, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Crystal structure of CD59: implications for molecular recognition of the complement proteins C8 and C9 in the membrane-attack complex.
Authors: Huang, Y. / Fedarovich, A. / Tomlinson, S. / Davies, C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 4, 2007 / Release: May 29, 2007
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 29, 2007Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelAdvisory / Version format compliance
1.3Oct 18, 2017Structure modelRefinement descriptionsoftware_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD59 glycoprotein


Theoretical massNumber of molelcules
Total (without water)8,7751
Polymers8,7751
Non-polymers00
Water1,31573
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)56.400, 56.400, 39.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein/peptide CD59 glycoprotein / Membrane attack complex inhibition factor / MACIF / MAC-inhibitory protein / MAC-IP / Protectin / MEM43 antigen / Membrane inhibitor of reactive lysis / MIRL / 20 kDa homologous restriction factor / HRF-20 / HRF20 / 1F5 antigen


Mass: 8774.933 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD59 / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1168H / References: UniProt: P13987
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1 M sodium citrate, 16 % polyethylene glycol 6000, 5% isopropanol, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.75 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Dec 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.75 Å / Relative weight: 1
ReflectionResolution: 2.12→28.2 Å / Num. all: 4118 / Num. obs: 4118 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 52.9
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 12.5 / Num. unique all: 386 / Rsym value: 0.141 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345softwaredata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CDQ
Resolution: 2.12→28.2 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.557 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.287 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.254 189 4.6 %RANDOM
Rwork0.177 ---
All0.18 4115 --
Obs0.18 4115 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.672 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.48 Å20 Å2
2---0.95 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.12→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms608 0 0 73 681
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.010.022626
r_angle_refined_deg1.441.927850
r_dihedral_angle_1_deg7.224574
r_dihedral_angle_2_deg40.23725.58834
r_dihedral_angle_3_deg15.53315105
r_dihedral_angle_4_deg16.183152
r_chiral_restr0.0970.290
r_gen_planes_refined0.0040.02481
r_nbd_refined0.2170.2256
r_nbtor_refined0.30.2432
r_xyhbond_nbd_refined0.180.245
r_symmetry_vdw_refined0.1840.236
r_symmetry_hbond_refined0.2050.216
r_mcbond_it0.5051.5381
r_mcangle_it0.9962606
r_scbond_it1.6943275
r_scangle_it2.774.5244
LS refinement shellResolution: 2.121→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 16 -
Rwork0.21 270 -
Obs-286 92.26 %
Refinement TLS params.Method: refined / Origin x: -4.7948 Å / Origin y: 18.5089 Å / Origin z: -1.2395 Å
111213212223313233
T-0.02 Å2-0.0042 Å20.0366 Å2--0.03 Å20.0192 Å2--0.0183 Å2
L1.3566 °20.1653 °2-0.5707 °2-0.8915 °2-0.0496 °2--1.1218 °2
S-0.039 Å °-0.0224 Å °-0.1648 Å °0.0072 Å °-0.0402 Å °-0.0164 Å °-0.044 Å °0.0002 Å °0.0793 Å °

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