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- PDB-8cjv: Structure of bovine CD46 ectodomain (SCR 1-4) -

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Basic information

Entry
Database: PDB / ID: 8cjv
TitleStructure of bovine CD46 ectodomain (SCR 1-4)
ComponentsMembrane cofactor protein
KeywordsIMMUNE SYSTEM / Host cell receptor
Function / homology
Function and homology information


inner acrosomal membrane / negative regulation of complement activation, classical pathway / T cell mediated immunity / complement activation, classical pathway / single fertilization / innate immune response / cell surface / extracellular space / plasma membrane
Similarity search - Function
Membrane cofactor protein CD46 / 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
Membrane cofactor protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsAitkenhead, H. / 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 13, 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
Revision 1.2Nov 6, 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)64,5017
Polymers63,3952
Non-polymers1,1065
Water00
1
A: Membrane cofactor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1403
Polymers31,6971
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Membrane cofactor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3614
Polymers31,6971
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.731, 129.731, 120.193
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

#1: Protein Membrane cofactor protein


Mass: 31697.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CD46, MCP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q6VE48
#2: 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.: 5 / 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
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: 3.99 Å3/Da / Density % sol: 69.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 10.5mg/ml in 0.1M sodium cacodylate tetrahydrate pH 6.4, 14% PEG smear broad, 0.2M CaCl2, 5% glycerol .

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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 EIGER2 X 16M / Detector: PIXEL / Date: Dec 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.84→91.73 Å / Num. obs: 10884 / % possible obs: 93.3 % / Redundancy: 25.6 % / Biso Wilson estimate: 50.37 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.487 / Rpim(I) all: 0.097 / Rrim(I) all: 0.497 / Net I/σ(I): 7.1
Reflection shellResolution: 2.84→3.24 Å / Redundancy: 20.5 % / Rmerge(I) obs: 2.225 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 544 / CC1/2: 0.63 / Rpim(I) all: 0.473 / Rrim(I) all: 2.278

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→88.17 Å / SU ML: 0.4001 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3918
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2855 528 4.86 %
Rwork0.2527 10343 -
obs0.2543 10871 43.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.48 Å2
Refinement stepCycle: LAST / Resolution: 2.84→88.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 70 0 3505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01493597
X-RAY DIFFRACTIONf_angle_d1.84014913
X-RAY DIFFRACTIONf_chiral_restr0.0985542
X-RAY DIFFRACTIONf_plane_restr0.0133648
X-RAY DIFFRACTIONf_dihedral_angle_d12.05591329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-3.130.4328170.3067309X-RAY DIFFRACTION5.39
3.13-3.580.3192390.32181015X-RAY DIFFRACTION17.27
3.58-4.510.29511550.24622966X-RAY DIFFRACTION50.9
4.51-88.170.27623170.24816053X-RAY DIFFRACTION99.04
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)
10.5896619523440.4188634880270.6784780783610.3641453271190.4176204185110.867994891960.0123294060306-0.4125982963160.5756868177290.568862222111-0.02994605173331.45479315707-0.64308354985-1.071780308542.650759934870.7257582576890.6113324698340.3959093934240.8687097459160.03673442552290.954902992287-86.940771755612.1575671994-7.48469328806
20.475587083567-0.067213621911-0.07973727095170.155797059175-0.05748173367440.4373281981340.1760159332190.1530351313990.168603148169-0.0885651254567-0.0762906633042-0.0642548971629-0.1238296931760.07214362771310.141358055573-0.008980222832420.0420423131380.1881885390680.07026724767830.0179321294755-0.223050890854-56.000237828-1.37974437251-17.5864603753
31.548147307360.1481372300820.249675695920.1597661551980.09997739051270.07949945744710.08046819230960.4373252523830.388064805823-0.264967218712-0.300359049171-1.105309508670.2417455100550.6335347246040.1250837033680.5923398385070.55361698124-0.02188031019231.06738242509-0.04102763534761.12592484106-23.6449499599-22.817552877-16.4753188406
40.957695029477-0.0568494857553-0.1076522151032.1659081676-0.3690693976142.650211026260.182860856889-0.2236695082230.8182128402150.552879753441-0.0793664551483-1.43280244002-0.5865283560421.178646109591.911778030640.304650599196-0.23608392838-0.160144569430.942009171974-0.1054249811220.765365144555-40.65234695527.337264214336.69659909777
51.417815992870.808455487584-0.01695904977961.13011824466-0.1097959433921.231501825230.1703973340890.187913107597-0.272956334977-0.09556989505690.00416150892415-0.06700015268220.421546927224-0.0504546220253-0.3342102720990.19674461882-0.0485694844423-0.1036906992230.366140428873-0.001662166157280.0605762126-72.0888803675-5.44875311024-2.36931362302
6-0.0003607557490330.00193872031479-0.000887741012710.00113548677361-0.000959638130816-0.0009947851587290.195655546678-0.389186252355-0.7984720785140.478950523135-0.04944724468851.086369176660.129953798819-1.213577148650.2908205654760.7187134726620.1498535134590.2543909298522.223742118520.1789395194332.48516247497-109.670549532-13.78410339850.632806095491
70.482847164689-0.06573462935850.4146208269090.0268764130392-0.1508742384622.83106080045-0.0460347767134-0.19617102708-0.613287832531-0.01576402561250.4287006343790.02555015477540.9167283146160.255094896170.2243805990160.6138947645360.33432308403-0.0238283345680.642881390571-0.1166987747270.795323805834-22.5509935162-52.2874461443-3.43441641244
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 104 )AA41 - 1041 - 64
22chain 'A' and (resid 105 through 168 )AA105 - 16865 - 128
33chain 'A' and (resid 169 through 235 )AA169 - 235129 - 195
44chain 'B' and (resid 41 through 104 )BD41 - 1041 - 64
55chain 'B' and (resid 105 through 168 )BD105 - 16865 - 128
66chain 'B' and (resid 169 through 234 )BD169 - 234129 - 194
77chain 'A' and (resid 236 through 294 )AA236 - 294196 - 254

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