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- PDB-2j8b: High resolution structure of human CD59 -

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Basic information

Entry
Database: PDB / ID: 2j8b
TitleHigh resolution structure of human CD59
ComponentsCD59 GLYCOPROTEIN
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING PROTEIN / GLYCOPROTEIN / LIPID-BINDING PROTEIN MAC / MEMBRANE / GPI-ANCHOR / COMPLEMENT / LIPOPROTEIN
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: 1.15 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
DepositionOct 24, 2006Deposition 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 1.3Oct 18, 2017Group: Data collection / Category: diffrn / diffrn_source
Revision 1.4Dec 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 1.5Oct 23, 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


Theoretical massNumber of molelcules
Total (without water)9,1581
Polymers9,1581
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.948, 45.918, 46.033
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 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 / CD59


Mass: 9158.354 Da / Num. of mol.: 1 / Fragment: MATURE POLYPEPTIDE, RESIDUES 26-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: PURIFIED FROM INCLUSION BODIES AFTER EXPRESSION IN ESCHERICHIA COLI
Cell: LYMPHOCYTES, ERYTHROCYTES, PLATELETS, ENDOTHELIA, EPITHELIA
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.: 117 / 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: 1.84 Å3/Da / Density % sol: 33 % / Description: NONE
Crystal growDetails: 28 % PEG 4000 0.25M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.92, 1.24
DetectorType: ADSC CCD / Detector: CCD / Date: May 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
21.241
ReflectionResolution: 1.1→26.2 Å / Num. obs: 27724 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.7
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.7 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CDQ

1cdq


Resolution: 1.15→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.043 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 78 WAS NOT MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1238 5 %RANDOM
Rwork0.164 ---
obs0.165 23463 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2---0.66 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms629 0 0 117 746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022698
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.411.931950
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.145584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17425.52638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34215126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.596153
X-RAY DIFFRACTIONr_chiral_restr0.0990.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02538
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.3281
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.5486
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.5123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.347
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4280.552
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.72427
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4353677
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0692308
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7283273
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.202 80
Rwork0.203 1709

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