[English] 日本語
Yorodumi
- PDB-8cjv: Structure of bovine CD46 ectodomain (SCR 1-4) -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 2.84 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 (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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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 .

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more