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- PDB-3oed: The structure of the complex between complement receptor CR2 and ... -

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Basic information

Entry
Database: PDB / ID: 3oed
TitleThe structure of the complex between complement receptor CR2 and its ligand complement fragment C3d
Components
  • Complement C3
  • Complement receptor type 2
KeywordsIMMUNE SYSTEM / Complement Receptor / Complement fragment C3d / B Cell
Function / homology
Function and homology information


complement receptor activity / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement binding / negative regulation of complement activation, classical pathway / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning ...complement receptor activity / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement binding / negative regulation of complement activation, classical pathway / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / T cell mediated immunity / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / B cell proliferation / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / immunoglobulin receptor binding / Peptide ligand-binding receptors / B cell differentiation / fatty acid metabolic process / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / transmembrane signaling receptor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / virus receptor activity / G alpha (i) signalling events / secretory granule lumen / blood microparticle / receptor complex / inflammatory response / positive regulation of protein phosphorylation / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein homodimerization activity / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
: / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement Module, domain 1 / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 ...: / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement Module, domain 1 / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Complement Module; domain 1 / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Glycosyltransferase - #20 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Ribbon / Immunoglobulin-like fold / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Complement C3 / Complement receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsIsenman, D.E. / van den Elsen, J.M.H.
CitationJournal: Science / Year: 2011
Title: A crystal structure of the complex between human complement receptor 2 and its ligand C3d.
Authors: van den Elsen, J.M. / Isenman, D.E.
History
DepositionAug 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C3
C: Complement receptor type 2
B: Complement C3
D: Complement receptor type 2


Theoretical massNumber of molelcules
Total (without water)99,1544
Polymers99,1544
Non-polymers00
Water28816
1
A: Complement C3
C: Complement receptor type 2


Theoretical massNumber of molelcules
Total (without water)49,5772
Polymers49,5772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C3
D: Complement receptor type 2


Theoretical massNumber of molelcules
Total (without water)49,5772
Polymers49,5772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.120, 146.120, 253.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


Mass: 34746.750 Da / Num. of mol.: 2 / Fragment: C3 (unp residues 996-1303) / Mutation: C1010A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3, CPAMD1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01024
#2: Protein Complement receptor type 2 / Cr2 / Complement C3d receptor / Epstein-Barr virus receptor / EBV receptor


Mass: 14830.066 Da / Num. of mol.: 2 / Fragment: CR2 (unp residues 20-153)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3DR, CR2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P20023
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, 20% Poly Ethylene Glycol 6000, 200 mM CaCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 19280 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 10.2 / Num. unique all: 19280 / Rsym value: 0.91 / % possible all: 99.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1c3D

1c3d


Resolution: 3.16→47 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.886 / SU B: 52.607 / SU ML: 0.408 / Cross valid method: THROUGHOUT / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25866 919 5.1 %RANDOM
Rwork0.18917 ---
obs-17131 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 3.16→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6612 0 0 16 6628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226780
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.9639204
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53824.406286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.348151146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0441532
X-RAY DIFFRACTIONr_chiral_restr0.0930.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215118
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.162→3.244 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 69 -
Rwork0.251 1236 -
obs--100 %
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)
10.6733-0.1087-0.3751.19470.16211.59790.064-0.02240.04240.01120.0169-0.0768-0.04710.0299-0.0810.0356-0.02490.00580.0374-0.01010.0706-8.5485-21.6283-57.6528
20.99140.4032-0.07630.95210.13670.86440.015-0.02180.06440.036-0.01780.0016-0.0673-0.03430.00280.0663-0.0124-0.00810.0778-0.02230.0424-28.9277-30.7946-64.3885
30.7974-0.03670.02441.34340.00981.24720.0613-0.1234-0.03230.0968-0.0475-0.10510.0135-0.03-0.01380.0343-0.0558-0.0160.10260.01470.0466-44.2294-71.6467-68.5768
41.7430.10860.33262.26270.48610.65280.1756-0.1093-0.36490.01610.0865-0.25450.1116-0.0646-0.2620.0368-0.0388-0.04430.0657-0.00870.177-23.4993-60.3752-69.7465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 294
2X-RAY DIFFRACTION2C0 - 129
3X-RAY DIFFRACTION3B1 - 294
4X-RAY DIFFRACTION4D0 - 129

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