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- PDB-6kru: Crystal structure of mouse IgG2b Fc -

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Basic information

Entry
Database: PDB / ID: 6kru
TitleCrystal structure of mouse IgG2b Fc
ComponentsIg gamma-2B chain C region
KeywordsIMMUNE SYSTEM / FC-FRAGMENT / IMMUNOGLOBULIN / GLYCOSYLATION
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTaniguchi, Y. / Satoh, T. / Yagi, H. / Kato, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP19H01017 Japan
CitationJournal: Int J Mol Sci / Year: 2019
Title: On-Membrane Dynamic Interplay between Anti-GM1 IgG Antibodies and Complement Component C1q.
Authors: Yanaka, S. / Yogo, R. / Watanabe, H. / Taniguchi, Y. / Satoh, T. / Komura, N. / Ando, H. / Yagi, H. / Yuki, N. / Uchihashi, T. / Kato, K.
History
DepositionAug 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ig gamma-2B chain C region
B: Ig gamma-2B chain C region
C: Ig gamma-2B chain C region
D: Ig gamma-2B chain C region
E: Ig gamma-2B chain C region
F: Ig gamma-2B chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,79112
Polymers147,1856
Non-polymers9,6076
Water6,143341
1
A: Ig gamma-2B chain C region
B: Ig gamma-2B chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3134
Polymers49,0622
Non-polymers3,2512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint49 kcal/mol
Surface area22830 Å2
MethodPISA
2
C: Ig gamma-2B chain C region
D: Ig gamma-2B chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3134
Polymers49,0622
Non-polymers3,2512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint43 kcal/mol
Surface area21500 Å2
MethodPISA
3
E: Ig gamma-2B chain C region
F: Ig gamma-2B chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1664
Polymers49,0622
Non-polymers3,1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint41 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.550, 130.165, 134.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ig gamma-2B chain C region


Mass: 24530.783 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: GB2 / Plasmid details: hybridoma / References: UniProt: P01867
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-2-1-2-1-3-4/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1479.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-2-1-2-1-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.57 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG3350, 0.2 M lithium chloride, and 0.1 M Bis-Tris (pH 6.5)

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 88009 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 18.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.015 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4370 / CC1/2: 0.795 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RGS

2rgs


Resolution: 2.3→19.98 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.34
RfactorNum. reflection% reflection
Rfree0.2367 4487 5.11 %
Rwork0.1981 --
obs0.2001 87753 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.04 Å2 / Biso mean: 59.6822 Å2 / Biso min: 30.65 Å2
Refinement stepCycle: final / Resolution: 2.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9687 0 650 341 10678
Biso mean--75.48 55.25 -
Num. residues----1215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110632
X-RAY DIFFRACTIONf_angle_d1.18814553
X-RAY DIFFRACTIONf_chiral_restr0.0581806
X-RAY DIFFRACTIONf_plane_restr0.0061737
X-RAY DIFFRACTIONf_dihedral_angle_d8.6676454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3001-2.32620.32041360.3161268997
2.3262-2.35350.36221670.29372709100
2.3535-2.38210.32251390.28562737100
2.3821-2.41230.32681440.27562758100
2.4123-2.44390.32641690.26942736100
2.4439-2.47740.35021390.25812750100
2.4774-2.51270.31931590.24852731100
2.5127-2.55010.30341400.25582792100
2.5501-2.58990.31351410.25192735100
2.5899-2.63230.3551430.24932767100
2.6323-2.67750.32181310.2572779100
2.6775-2.72610.27111280.24132776100
2.7261-2.77840.28181580.23222733100
2.7784-2.8350.29461700.24172753100
2.835-2.89640.33491220.24172777100
2.8964-2.96360.29281510.24852779100
2.9636-3.03750.26731470.24012755100
3.0375-3.11930.29481570.23152782100
3.1193-3.21070.28311670.22012716100
3.2107-3.31390.28291580.22972796100
3.3139-3.43180.26091450.21122767100
3.4318-3.56840.23071350.20592786100
3.5684-3.72990.20861410.19862822100
3.7299-3.92510.22571620.1812749100
3.9251-4.16890.19551400.15642828100
4.1689-4.48750.1831820.14972780100
4.4875-4.93290.1561490.1442815100
4.9329-5.63270.19121430.15122851100
5.6327-7.04450.20991430.19412875100
7.0445-19.980.21281810.1772943100

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