[English] 日本語
Yorodumi
- PDB-8sm0: Crystal structure of human complement receptor 2 (CD21) in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sm0
TitleCrystal structure of human complement receptor 2 (CD21) in complex with Epstein-Barr virus major glycoprotein gp350
Components
  • Complement receptor type 2
  • Envelope glycoprotein gp350
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of complement activation, classical pathway / complement receptor activity / complement binding / T cell mediated immunity / complement activation, alternative pathway / immunoglobulin receptor binding / type I interferon-mediated signaling pathway / B cell activation / B cell proliferation / host cell membrane ...negative regulation of complement activation, classical pathway / complement receptor activity / complement binding / T cell mediated immunity / complement activation, alternative pathway / immunoglobulin receptor binding / type I interferon-mediated signaling pathway / B cell activation / B cell proliferation / host cell membrane / complement activation, classical pathway / Regulation of Complement cascade / B cell differentiation / transmembrane signaling receptor activity / virus receptor activity / receptor complex / immune response / receptor ligand activity / symbiont entry into host cell / virion membrane / protein homodimerization activity / extracellular space / DNA binding / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Herpesvirus major outer envelope glycoprotein / : / : / : / : / Herpes virus envelope glycoprotein gp350, N-terminal A domain / Herpesvirus envelope glycoprotein gp350, N-terminal B domain / Herpesvirus envelope glycoprotein gp350 N-terminal C domain / Herpesvirus Envelope glycoprotein GP350 C-terminal / : ...Herpesvirus major outer envelope glycoprotein / : / : / : / : / Herpes virus envelope glycoprotein gp350, N-terminal A domain / Herpesvirus envelope glycoprotein gp350, N-terminal B domain / Herpesvirus envelope glycoprotein gp350 N-terminal C domain / Herpesvirus Envelope glycoprotein GP350 C-terminal / : / 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
Envelope glycoprotein GP350 / Complement receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsChen, W.-H. / Bu, W. / Cohen, J.I. / Kanekiyo, M. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-18-2-0040 United States
CitationJournal: Immunity / Year: 2025
Title: Structural basis for complement receptor engagement and virus neutralization through Epstein-Barr virus gp350.
Authors: Joyce, M.G. / Bu, W. / Chen, W.H. / Gillespie, R.A. / Andrews, S.F. / Wheatley, A.K. / Tsybovsky, Y. / Jensen, J.L. / Stephens, T. / Prabhakaran, M. / Fisher, B.E. / Narpala, S.R. / Bagchi, ...Authors: Joyce, M.G. / Bu, W. / Chen, W.H. / Gillespie, R.A. / Andrews, S.F. / Wheatley, A.K. / Tsybovsky, Y. / Jensen, J.L. / Stephens, T. / Prabhakaran, M. / Fisher, B.E. / Narpala, S.R. / Bagchi, M. / McDermott, A.B. / Nabel, G.J. / Kwong, P.D. / Mascola, J.R. / Cohen, J.I. / Kanekiyo, M.
History
DepositionApr 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Feb 19, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Feb 26, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Complement receptor type 2
G: Envelope glycoprotein gp350
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,80115
Polymers61,0502
Non-polymers2,75113
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.584, 49.255, 78.323
Angle α, β, γ (deg.)90.00, 101.64, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Complement receptor type 2 / Cr2 / Complement C3d receptor / Epstein-Barr virus receptor / EBV receptor


Mass: 14155.256 Da / Num. of mol.: 1 / Fragment: first two amino-terminal domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CR2, C3DR / Production host: Homo sapiens (human) / References: UniProt: P20023
#2: Protein Envelope glycoprotein gp350 / Membrane antigen / MA


Mass: 46895.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Strain: B95-8 / Gene: BLLF1 / Production host: Homo sapiens (human) / References: UniProt: P03200
#3: 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.: 12
Source method: isolated from a genetically manipulated source
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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.60M AMMONIUM SULFATE, 2% PEG 400, 0.5% GLYCEROL, 0.1M SODIUM ACETATE PH5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 56365 / % possible obs: 84.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3
Reflection shellResolution: 1.684→1.75 Å / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1994

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H6O, 1LY2

2h6o

1ly2


Resolution: 1.68→30.68 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.54
RfactorNum. reflection% reflection
Rfree0.241 2796 4.96 %
Rwork0.212 --
obs0.214 56365 84.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.73 Å2
Refinement stepCycle: LAST / Resolution: 1.68→30.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4055 0 173 237 4465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.684-1.71280.3694490.3379683X-RAY DIFFRACTION22
1.7128-1.7440.3569610.3371201X-RAY DIFFRACTION38
1.744-1.77750.299860.31951640X-RAY DIFFRACTION52
1.7775-1.81380.37511080.32522073X-RAY DIFFRACTION66
1.8138-1.85320.38321120.31882341X-RAY DIFFRACTION74
1.8532-1.89630.31051320.2842634X-RAY DIFFRACTION83
1.8963-1.94370.32191610.25882776X-RAY DIFFRACTION89
1.9437-1.99630.28231450.25282907X-RAY DIFFRACTION92
1.9963-2.0550.24861430.24443015X-RAY DIFFRACTION94
2.055-2.12130.26411790.25563016X-RAY DIFFRACTION96
2.1213-2.19710.25261670.23763035X-RAY DIFFRACTION97
2.1971-2.28510.27451680.23833082X-RAY DIFFRACTION97
2.2851-2.3890.27491500.23753157X-RAY DIFFRACTION99
2.389-2.51490.28181640.24213151X-RAY DIFFRACTION99
2.5149-2.67240.27111570.23413161X-RAY DIFFRACTION99
2.6724-2.87860.26151740.23063168X-RAY DIFFRACTION99
2.8786-3.1680.23681660.2243181X-RAY DIFFRACTION99
3.168-3.62580.23081560.19493186X-RAY DIFFRACTION99
3.6258-4.56570.19371710.16413190X-RAY DIFFRACTION99
4.5657-30.680.20861470.18572972X-RAY DIFFRACTION89
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)
13.7834-0.4820.65196.923-1.25065.0847-0.0859-0.4439-0.0290.21550.00450.61190.0664-0.57020.06350.1713-0.08410.050.25380.0140.2902-49.7219-1.44118.5975
25.6824-3.16121.47448.1668-3.26275.14210.05170.3117-0.17360.1637-0.01410.19350.3396-0.2735-0.21380.2619-0.11120.0030.148-0.00890.2054-47.2658-6.656413.1255
31.38690.10170.54540.39380.46621.79180.0742-0.305-0.46610.45870.5462-0.1620.60630.5811-0.17080.67270.1903-0.1230.3652-0.16830.43-29.4284-18.041311.9411
46.79632.7328-5.93842.354-2.59445.5750.0287-0.9287-0.86310.8317-0.1441-1.28460.48191.53850.04610.60280.1081-0.17890.5335-0.04520.6741-27.0675-16.377115.9476
54.13930.91810.89895.50161.03984.39830.23910.4002-0.0699-0.2886-00.0867-0.5304-0.08730.40890.33710.061-0.07330.2139-0.16320.2852-33.7204-11.80840.5975
62.3519-0.1966-0.12393.7541-3.18453.45860.1196-0.2106-0.4411-0.11570.3585-0.05581.4914-0.2212-0.58170.49440.0457-0.1140.24-0.03430.4305-36.5486-19.37445.9833
72.83030.04270.68750.6295-0.1341.1794-0.17210.81520.145-0.07510.0303-0.03960.00730.22170.0470.1993-0.11010.01490.34690.07010.2185-17.47637.916213.1659
83.4265-0.1968-0.1892.9148-1.07692.62330.1338-0.3958-0.48320.403-0.1062-0.29110.63090.01140.15130.3919-0.0719-0.05870.1570.04560.2164-28.8296-1.974431.5685
92.10530.31580.30091.034-0.24771.3411-0.41310.78450.72810.0737-0.3152-0.3019-0.5190.6319-0.92990.204-0.31060.0010.50250.34930.312511.021314.258424.4904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'C' AND (RESID 1 THROUGH 31 )
2X-RAY DIFFRACTION2CHAIN 'C' AND (RESID 32 THROUGH 63 )
3X-RAY DIFFRACTION3CHAIN 'C' AND (RESID 64 THROUGH 83 )
4X-RAY DIFFRACTION4CHAIN 'C' AND (RESID 84 THROUGH 92 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 93 THROUGH 111 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 112 THROUGH 129 )
7X-RAY DIFFRACTION7CHAIN 'G' AND (RESID 7 THROUGH 187 )
8X-RAY DIFFRACTION8CHAIN 'G' AND (RESID 188 THROUGH 305 )
9X-RAY DIFFRACTION9CHAIN 'G' AND (RESID 306 THROUGH 425 )

+
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