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- PDB-1ly2: Crystal structure of unliganded human CD21 SCR1-SCR2 (Complement ... -

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Basic information

Entry
Database: PDB / ID: 1ly2
TitleCrystal structure of unliganded human CD21 SCR1-SCR2 (Complement receptor type 2)
Componentscomplement receptor type 2
KeywordsIMMUNE SYSTEM / Complement receptor / Epstein Barr virus / Regulator of complement activation / short consensus repeat / viral receptor / complement control protein
Function / homology
Function and homology information


negative regulation of complement activation, classical pathway / complement receptor activity / T cell mediated immunity / complement binding / complement activation, alternative pathway / immunoglobulin receptor binding / type I interferon-mediated signaling pathway / B cell activation / B cell proliferation / complement activation, classical pathway ...negative regulation of complement activation, classical pathway / complement receptor activity / T cell mediated immunity / complement binding / complement activation, alternative pathway / immunoglobulin receptor binding / type I interferon-mediated signaling pathway / B cell activation / B cell proliferation / complement activation, classical pathway / B cell differentiation / Regulation of Complement cascade / transmembrane signaling receptor activity / virus receptor activity / receptor complex / immune response / symbiont entry into host cell / protein homodimerization activity / DNA binding / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
: / 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
Complement receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsProta, A.E. / Sage, D.R. / Stehle, T. / Fingeroth, J.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The crystal structure of human CD21: Implications for Epstein-Barr virus and C3d binding.
Authors: Prota, A.E. / Sage, D.R. / Stehle, T. / Fingeroth, J.D.
History
DepositionJun 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: complement receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6993
Polymers14,2561
Non-polymers4422
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.6, 33.27, 42.11
Angle α, β, γ (deg.)91.51, 111.44, 117.81
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein complement receptor type 2 / CD21 / Epstein-Barr virus receptor


Mass: 14256.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CR2 / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P20023
#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.: 2
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
124 mg/mlprotein1drop
230 %PEG40001reservoir
3100 mM1reservoirMgCl2
4100 mM1reservoirCsCl
5100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.05 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 1, 2001 / Details: wiggler
RadiationMonochromator: wiggler / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 12743 / Num. obs: 11265 / % possible obs: 88.4 %
Reflection shellResolution: 1.8→1.9 Å / Rsym value: 0.1 / % possible all: 55.8
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Num. measured all: 42404 / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
% possible obs: 55.8 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 6.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Crystal structure of liganded CD21 (complex with C3d)

Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1127 10 %random
Rwork0.179 ---
all-12743 --
obs-11265 --
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 0 28 146 1170
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.34
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.306 / Rfactor Rwork: 0.294

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