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- PDB-2ice: CRIg bound to C3c -

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Basic information

Entry
Database: PDB / ID: 2ice
TitleCRIg bound to C3c
Components
  • (Complement C3 alpha ...) x 2
  • Complement C3 beta chain
  • V-set and immunoglobulin domain-containing protein 4
KeywordsIMMUNE SYSTEM / Alternative Pathway / Complement / C3 / CRIg / Complement Receptor
Function / homology
Function and homology information


negative regulation of complement activation, alternative pathway / negative regulation of macrophage activation / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement component C3b binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning ...negative regulation of complement activation, alternative pathway / negative regulation of macrophage activation / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement component C3b binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / 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 / negative regulation of interleukin-2 production / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / complement activation, classical pathway / negative regulation of T cell proliferation / Peptide ligand-binding receptors / fatty acid metabolic process / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / 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 / G alpha (i) signalling events / secretory granule lumen / blood microparticle / immune response / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
VSIG4, immunoglobulin variable (IgV)-like domain / V-set and immunoglobulin domain-containing protein 4 / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / S-adenosyl-L-methionine-dependent methyltransferases / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / N-terminal domain of TfIIb ...VSIG4, immunoglobulin variable (IgV)-like domain / V-set and immunoglobulin domain-containing protein 4 / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / S-adenosyl-L-methionine-dependent methyltransferases / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / N-terminal domain of TfIIb / : / : / Complement component 3, CUB domain 2 / Complement component 3, CUB domain 1 / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / 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 / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / 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 / Other non-globular / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin domain / Single Sheet / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Special / Immunoglobulin V-set domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Complement C3 / V-set and immunoglobulin domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWiesmann, C.
CitationJournal: Nature / Year: 2006
Title: Structure of C3b in complex with CRIg gives insights into regulation of complement activation.
Authors: Wiesmann, C. / Katschke, K.J. / Yin, J. / Helmy, K.Y. / Steffek, M. / Fairbrother, W.J. / McCallum, S.A. / Embuscado, L. / DeForge, L. / Hass, P.E. / van Lookeren Campagne, M.
History
DepositionSep 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Sep 5, 2012Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C3 beta chain
B: Complement C3 alpha chain
C: Complement C3 alpha chain
S: V-set and immunoglobulin domain-containing protein 4
D: Complement C3 beta chain
E: Complement C3 alpha chain
F: Complement C3 alpha chain
T: V-set and immunoglobulin domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,16411
Polymers295,6608
Non-polymers5053
Water0
1
A: Complement C3 beta chain
B: Complement C3 alpha chain
C: Complement C3 alpha chain
S: V-set and immunoglobulin domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,2946
Polymers147,8304
Non-polymers4642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Complement C3 beta chain
E: Complement C3 alpha chain
F: Complement C3 alpha chain
T: V-set and immunoglobulin domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,8705
Polymers147,8304
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)384.936, 65.213, 147.676
Angle α, β, γ (deg.)90.000, 102.910, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A D
21A D
31A D
41A D
51A D
12S T

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNLEULEUAA104 - 207104 - 207
121GLNGLNLEULEUDE104 - 207104 - 207
211PROPROSERSERAA208 - 329208 - 329
221PROPROSERSERDE208 - 329208 - 329
311PROPROTYRTYRAA330 - 424330 - 424
321PROPROTYRTYRDE330 - 424330 - 424
411SERSERASPASPAA425 - 535425 - 535
421SERSERASPASPDE425 - 535425 - 535
511SERSERGLNGLNAA536 - 642536 - 642
521SERSERGLNGLNDE536 - 642536 - 642
112PROPROLYSLYSSD2 - 1183 - 119
122PROPROLYSLYSTH2 - 1183 - 119

NCS ensembles :
IDDetails
1A D
2S T

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Components

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Protein , 2 types, 4 molecules ADST

#1: Protein Complement C3 beta chain


Mass: 71170.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#4: Protein V-set and immunoglobulin domain-containing protein 4 / Protein Z39Ig


Mass: 13501.173 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VSIG4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y279

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Complement C3 alpha ... , 2 types, 4 molecules BECF

#2: Protein Complement C3 alpha chain


Mass: 23621.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#3: Protein Complement C3 alpha chain


Mass: 39537.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024

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Sugars / Non-polymers , 2 types, 3 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 3.05 Å3/Da / Density % sol: 59.72 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 65139 / Num. obs: 62367 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.1→3.21 Å / % possible all: 93.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A74

2a74


Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.868 / SU B: 51.236 / SU ML: 0.422 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.544 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.295 3112 5 %RANDOM
Rwork0.236 ---
all0.239 65023 --
obs0.239 62022 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.56 Å2
Baniso -1Baniso -2Baniso -3
1-6.32 Å20 Å2-2.14 Å2
2---4.57 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19589 0 30 0 19619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02220030
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.96927183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.67752454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8424.796905
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.247153557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.83115109
X-RAY DIFFRACTIONr_chiral_restr0.0840.23097
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214978
X-RAY DIFFRACTIONr_nbd_refined0.2120.28328
X-RAY DIFFRACTIONr_nbtor_refined0.3080.213260
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2521
X-RAY DIFFRACTIONr_metal_ion_refined0.1930.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.23
X-RAY DIFFRACTIONr_mcbond_it2.8152.512594
X-RAY DIFFRACTIONr_mcangle_it4.704520115
X-RAY DIFFRACTIONr_scbond_it2.4932.58300
X-RAY DIFFRACTIONr_scangle_it4.09957068
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A4189TIGHT POSITIONAL0.040.05
1A4189TIGHT THERMAL0.090.5
2D935TIGHT POSITIONAL0.040.05
2D935TIGHT THERMAL0.080.5
LS refinement shellResolution: 3.1→3.162 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.374 148 -
Rwork0.291 2650 -
obs-2798 92.62 %
Refinement TLS params.Method: refined / Origin x: 42.8843 Å / Origin y: -18.923 Å / Origin z: 31.1684 Å
111213212223313233
T-0.1888 Å2-0.0612 Å2-0.1479 Å2--0.0306 Å2-0.0049 Å2--0.0025 Å2
L0.4937 °2-0.121 °20.1684 °2-1.0837 °2-0.038 °2--0.2063 °2
S0.0962 Å °-0.125 Å °-0.1135 Å °0.3676 Å °-0.1192 Å °-0.517 Å °0.0307 Å °0.3382 Å °0.0229 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL

IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA1 - 1031 - 103
2AA104 - 207104 - 207
3AA208 - 329208 - 329
4AA330 - 424330 - 424
5AA425 - 535425 - 535
6AA536 - 642536 - 642
7BB730 - 8054 - 79
8BB806 - 91280 - 186
9CC1335 - 148037 - 182
10CC1481 - 1641183 - 343
11SD0 - 1181 - 119
12DE1 - 1031 - 103
13DE104 - 207104 - 207
14DE208 - 329208 - 329
15DE330 - 424330 - 424
16DE425 - 535425 - 535
17DE536 - 642536 - 642
18EF730 - 8054 - 79
19EF806 - 91280 - 186
20FG1335 - 148037 - 182
21FG1481 - 1641183 - 343
22TH0 - 1181 - 119

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