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- PDB-2ux2: High resolution structure of human CD59 -

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Basic information

Entry
Database: PDB / ID: 2ux2
TitleHigh resolution structure of human CD59
ComponentsCD59 GLYCOPROTEIN
KeywordsIMMUNE SYSTEM / MAC / MIRL / CD59 / MEMBRANE / GPI-ANCHOR / LIPOPROTEIN / GLYCOPROTEIN / COMPLEMENT REGULATOR
Function / homology
Function and homology information


negative regulation of activation of membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Cargo concentration in the ER / COPII-mediated vesicle transport / tertiary granule membrane / specific granule membrane / transport vesicle / COPI-mediated anterograde transport ...negative regulation of activation of membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Cargo concentration in the ER / COPII-mediated vesicle transport / tertiary granule membrane / specific granule membrane / transport vesicle / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane / Regulation of Complement cascade / ER to Golgi transport vesicle membrane / blood coagulation / vesicle / cell surface receptor signaling pathway / Golgi membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / cell surface / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
: / CD59 glycoprotein / CD59 antigen, conserved site / Ly-6 / u-PAR domain signature. / u-PAR/Ly-6 domain / Ly-6 antigen / uPA receptor -like domain / Ly-6 antigen/uPA receptor-like / CD59 / CD59 / Snake toxin-like superfamily ...: / CD59 glycoprotein / CD59 antigen, conserved site / Ly-6 / u-PAR domain signature. / u-PAR/Ly-6 domain / Ly-6 antigen / uPA receptor -like domain / Ly-6 antigen/uPA receptor-like / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLeath, K.J. / Johnson, S. / Roversi, P. / Morgan, B.P. / Smith, R.A.G. / Lea, S.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: High-Resolution Structures of Bacterially Expressed Soluble Human Cd59.
Authors: Leath, K.J. / Johnson, S. / Roversi, P. / Hughes, T.R. / Smith, R.A.G. / Mackenzie, L. / Morgan, B.P. / Lea, S.M.
History
DepositionMar 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2007Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD59 GLYCOPROTEIN
B: CD59 GLYCOPROTEIN
C: CD59 GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)27,3043
Polymers27,3043
Non-polymers00
Water3,819212
1
A: CD59 GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)9,1011
Polymers9,1011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CD59 GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)9,1011
Polymers9,1011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: CD59 GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)9,1011
Polymers9,1011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.840, 60.840, 107.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.658, -0.753, -0.026), (0.75, 0.658, -0.066), (0.067, 0.024, 0.997)-1.3069, 1.55132, -18.74823
2given(-0.984, -0.18, 0.012), (0.181, -0.983, 0.03), (0.006, 0.031, 0.999)39.78791, 45.91266, -21.2548

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Components

#1: Protein CD59 GLYCOPROTEIN / MEMBRANE ATTACK COMPLEX INHIBITION FACTOR / MACIF / MAC-INHIBITORY PROTEIN / MAC-IP / PROTECTIN / ...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: 9101.303 Da / Num. of mol.: 3 / Fragment: RESIDUES 26-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET59-06 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): UT5600 DE3 / References: UniProt: P13987
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growDetails: 25% PEG8000, 0.03M POTASSIUM PHOSPHATE

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.24
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2006
RadiationMonochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 20934 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 0.65 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 29
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 7 / % possible all: 100

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Processing

Software
NameVersionClassification
TNT5.11.2.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J8C

2j8c


Resolution: 1.8→20 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTEGO
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1038 5 %RANDOM
Rwork0.185 ---
all0.187 20772 --
obs0.187 20772 --
Solvent computationSolvent model: BABINET SCALING / Bsol: 107 Å2 / ksol: 0.49 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 0 212 2099
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00419695
X-RAY DIFFRACTIONt_angle_deg0.82726705
X-RAY DIFFRACTIONt_dihedral_angle_d12.74141
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.01692
X-RAY DIFFRACTIONt_gen_planes0.0252745
X-RAY DIFFRACTIONt_it1.256196920
X-RAY DIFFRACTIONt_nbd0.193185
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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