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- PDB-8ci3: Structure of bovine CD46 ectodomain (SCR 1-2) -

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Basic information

Entry
Database: PDB / ID: 8ci3
TitleStructure of bovine CD46 ectodomain (SCR 1-2)
ComponentsMembrane cofactor protein
KeywordsIMMUNE SYSTEM / Host cell receptor type one transmembrane protein
Function / homology
Function and homology information


inner acrosomal membrane / negative regulation of complement activation, classical pathway / T cell mediated immunity / single fertilization / complement activation, classical pathway / innate immune response / cell surface / extracellular space / plasma membrane
Similarity search - Function
Membrane cofactor protein CD46 / : / 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
Similarity search - Domain/homology
Membrane cofactor protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsAitkenhead, H. / David I Stuart, D.I. / El Omari, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011224/1 United Kingdom
CitationJournal: Viruses / Year: 2023
Title: Structure of Bovine CD46 Ectodomain.
Authors: Aitkenhead, H. / Stuart, D.I. / El Omari, K.
History
DepositionFeb 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
A: Membrane cofactor protein
B: Membrane cofactor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6598
Polymers29,9312
Non-polymers1,7276
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint8 kcal/mol
Surface area15790 Å2
Unit cell
Length a, b, c (Å)91.090, 91.090, 121.123
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Membrane cofactor protein


Mass: 14965.661 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CD46, MCP / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q6VE48

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Sugars , 3 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 64 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 4.2 Å3/Da / Density % sol: 70.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH8.5, 20% PEG 8000, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.33→72.8 Å / Num. obs: 22417 / % possible obs: 99.4 % / Redundancy: 25.4 % / Biso Wilson estimate: 52.05 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.2336 / Rpim(I) all: 0.04699 / Rrim(I) all: 0.2383 / Net I/σ(I): 10.19
Reflection shellResolution: 2.33→2.413 Å / Redundancy: 25.8 % / Rmerge(I) obs: 3.599 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 2168 / CC1/2: 0.736 / Rpim(I) all: 0.7181 / Rrim(I) all: 3.671 / % possible all: 99.45

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Processing

Software
NameVersionClassification
PHASER1.18.2_3874phasing
PHENIX1.18.2_3874refinement
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→72.8 Å / SU ML: 0.3274 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7773
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2557 1123 5.04 %
Rwork0.2268 21178 -
obs0.2283 22301 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.12 Å2
Refinement stepCycle: LAST / Resolution: 2.33→72.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 111 62 2129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092113
X-RAY DIFFRACTIONf_angle_d0.892884
X-RAY DIFFRACTIONf_chiral_restr0.052340
X-RAY DIFFRACTIONf_plane_restr0.007371
X-RAY DIFFRACTIONf_dihedral_angle_d13.1723786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.440.38141420.34872542X-RAY DIFFRACTION98.5
2.44-2.560.3261480.32882582X-RAY DIFFRACTION99.02
2.56-2.720.32611500.28272575X-RAY DIFFRACTION98.62
2.72-2.930.30121440.27152620X-RAY DIFFRACTION99.68
2.93-3.230.28511170.23592644X-RAY DIFFRACTION99.39
3.23-3.70.25461320.22972677X-RAY DIFFRACTION100
3.7-4.660.2181400.18512700X-RAY DIFFRACTION99.89
4.66-72.80.22921500.20942838X-RAY DIFFRACTION99.47
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.419991589781.74719541008-0.8489693047371.6653800774-1.043508389320.822021520142-0.247998467797-0.0252340361844-0.253667869438-0.0969266236424-0.0917720218242-0.7294933416960.002507141066530.3102922028520.3425808238290.710389157459-0.1832333974390.05357481574160.8106999130360.1560204534020.8014493861166.643138551814.70305711580.796213081703
23.295614981590.0463914104974-0.4348945950761.754215140060.3548218678132.521203098620.05117114281120.03427190099190.03963482854340.118428228475-0.1520100584410.1645141496920.0773738745396-0.2130635740090.1008218553790.530236567659-0.0569533627016-0.002778090470460.507917092076-0.01272748702360.44805512038937.5979400276-1.9939049782811.6065724224
30.609361190197-0.4576624973041.025421728291.32582926164-0.2599470729931.98543750249-0.2584727628941.483118305530.799590157185-0.4779659070160.3017043242041.21932045564-0.751076935459-0.830332266948-0.05660645816340.7916405356070.0731789974187-0.2904082376221.53352504560.321548446351.1859868107620.06093902414.69843606898-13.8922943664
42.6233853255-0.160785984681-0.2851294070882.54096680457-0.6918449695072.6423297167-0.0303075414501-0.142536248823-0.1660916650760.0835323664338-0.097743561063-0.167965217970.3288476891780.2081672593420.05035839591720.4971718057140.0395962832799-0.02107311522680.55035628147-0.001234927058050.47950689669752.5495003617-4.43243868115-3.58933908811
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 41 through 101 )AA41 - 1011 - 61
22chain 'A' and (resid 102 through 169 )AA102 - 16962 - 129
33chain 'B' and (resid 41 through 101 )BF41 - 1011 - 61
44chain 'B' and (resid 102 through 169 )BF102 - 16962 - 129

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