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- PDB-8sm0: Crystal structure of human complement receptor 2 (CD21) in comple... -

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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


complement receptor activity / complement binding / negative regulation of complement activation, classical pathway / T cell mediated immunity / complement activation, alternative pathway / B cell proliferation / host cell membrane / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway ...complement receptor activity / complement binding / negative regulation of complement activation, classical pathway / T cell mediated immunity / complement activation, alternative pathway / B cell proliferation / host cell membrane / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / Regulation of Complement cascade / transmembrane signaling receptor activity / virus receptor activity / receptor complex / immune response / virion membrane / protein homodimerization activity / DNA binding / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
: / : / : / : / 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 / Sushi repeat (SCR repeat) ...: / : / : / : / 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 / 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: To Be Published
Title: Structural Basis For Receptor Engagement And Virus Neutralization Through Epstein-Barr Virus Gp350
Authors: Chen, W.-H. / Bu, W. / Cohen, J.I. / Kanekiyo, M. / Joyce, G.M.
History
DepositionApr 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 3.03 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

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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

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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 )

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