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- PDB-6krv: Crystal structure of mouse IgG2b Fc complexed with B domain of Pr... -

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Basic information

Entry
Database: PDB / ID: 6krv
TitleCrystal structure of mouse IgG2b Fc complexed with B domain of Protein A
Components
  • Ig gamma-2B chain C region
  • Immunoglobulin G-binding protein A
KeywordsIMMUNE SYSTEM / FC-FRAGMENT / IMMUNOGLOBULIN / PROTEIN A / B-DOMAIN
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 / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / 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 / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / IgG binding / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / positive regulation of immune response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 2B / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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_unobs_or_zero_occ_atoms / 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_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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.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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: Immunoglobulin G-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2397
Polymers80,1994
Non-polymers4,0413
Water00
1
A: Ig gamma-2B chain C region
B: Ig gamma-2B chain C region
D: Immunoglobulin G-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2455
Polymers55,6683
Non-polymers2,5772
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ig gamma-2B chain C region
hetero molecules

D: Immunoglobulin G-binding protein A

C: Ig gamma-2B chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5955
Polymers55,6683
Non-polymers2,9272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_455x-1/2,-y+1/2,-z+1/21
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)145.280, 145.280, 155.528
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 24530.783 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 7D7 / Plasmid details: hybridoma / References: UniProt: P01867
#2: Antibody Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A / SpA


Mass: 6606.237 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38507
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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: 1463.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-1-2-1-3/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 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]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpa1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2-2-1-2-1/a4-b1_b3-c1_b6-e1_c2-d1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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]{}}}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationY

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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: 5.12 Å3/Da / Density % sol: 75.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 60% (v/v) Tacsimate (pH 7.0)

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 25631 / % possible obs: 99.9 % / Redundancy: 14.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.1
Reflection shellResolution: 3.3→3.53 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4547 / CC1/2: 0.936 / % possible all: 99.9

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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: 3.3→19.98 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.64
RfactorNum. reflection% reflection
Rfree0.2503 1316 5.21 %
Rwork0.2079 --
obs0.2102 25260 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 304.91 Å2 / Biso mean: 150.8514 Å2 / Biso min: 76.54 Å2
Refinement stepCycle: final / Resolution: 3.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4950 0 273 0 5223
Biso mean--183.5 --
Num. residues----621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115362
X-RAY DIFFRACTIONf_angle_d1.3177322
X-RAY DIFFRACTIONf_chiral_restr0.064887
X-RAY DIFFRACTIONf_plane_restr0.008893
X-RAY DIFFRACTIONf_dihedral_angle_d9.8183263
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3-3.43350.37931550.3093260099
3.4335-3.58890.30751330.29522624100
3.5889-3.77690.40561450.3326253596
3.7769-4.01180.30121450.2467260198
4.0118-4.31870.24191320.1822648100
4.3187-4.7480.19911210.15912696100
4.748-5.4230.21541550.16192691100
5.423-6.78760.23881730.21832700100
6.7876-19.980.23291570.19552849100
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)
15.1427-1.04110.58866.9493-0.87984.0278-0.11460.0394-0.1925-0.07090.1802-0.4563-0.05010.3061-0.13731.014-0.6192-0.02561.2596-0.10631.1575-0.034964.797915.2657
27.3103-1.603-0.15697.8729-1.10356.31010.11470.1648-0.0546-0.59670.1479-0.36411.0006-0.39570.07011.0394-0.4795-0.11461.0705-0.25911.4321-2.634557.234810.1785
36.7882-0.8992.05331.87852.4824.99270.1957-1.1726-1.06420.51570.5109-0.27210.9222-0.721-0.19531.1626-1.0564-0.18760.92460.10891.3098-22.32952.322317.6058
49.587-3.6363-1.21256.7761.04484.4038-0.6673-0.40471.1171-0.39021.13740.4566-0.7225-0.7142-0.41040.8564-0.2337-0.22511.31870.10131.0611-26.105866.351936.2356
55.3301-1.3622-0.30365.49310.46118.738-0.3471-0.01420.3845-0.2370.93450.0293-0.5392-0.8939-0.58840.9039-0.2501-0.22050.99870.1651.0838-27.891465.317132.2628
65.0251-1.4007-1.09828.0802-2.28066.6070.30041.19520.4683-1.1113-0.3869-0.90440.85721.05050.06811.86020.76-0.41382.9353-0.41911.5391-0.699643.003952.8185
77.50227.0532-2.28159.1474-0.09172.5131-0.47751.2250.74890.4077-1.42530.826-0.5974-0.49921.78382.06690.2153-0.26862.6406-0.41690.8426-1.978856.995551.5563
87.4338-3.1815-2.19077.29570.398.1009-0.6955-1.6199-0.6570.94991.18410.07091.0522-0.7694-0.55511.0713-0.0509-0.22991.51040.24430.9347-26.245552.844844.2924
97.5869-4.84510.76246.8732-0.82527.5288-0.3127-3.0376-0.75820.49551.50690.45721.2755-0.3355-1.11011.63250.2254-0.29051.54160.14721.1038-23.449153.246855.3732
101.7463-0.7481-0.54227.13460.66062.3246-0.13761.09050.0608-0.48890.3050.6668-0.4758-0.3946-0.17441.2077-0.6296-0.14091.93740.36411.218-38.676361.0486-2.4371
115.09632.47911.92428.6023.07465.7725-0.50090.8064-0.1568-0.9770.5294-1.2302-0.71091.3848-0.1031.0843-0.6720.02211.4374-0.00851.3214-25.919739.5856-2.9823
129.64212.14233.49698.91743.48842.16570.97942.580.58831.608-0.32770.2484-0.5032-1.3514-0.41341.81390.7233-0.26341.8027-0.15681.222-13.262647.24365.3534
132.9555-0.26172.33498.58924.64658.75430.29092.114-0.2041-0.13670.00320.27490.89680.6533-0.23281.62790.4347-0.31171.7565-0.15161.3406-3.195543.913769.1074
148.23220.52225.18280.88791.80239.77650.97070.1693-0.11360.5538-0.256-0.02871.5566-0.5592-0.67011.58630.3664-0.24321.6260.1261.2854-8.591846.51176.2504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 237 through 307 )A237 - 307
2X-RAY DIFFRACTION2chain 'A' and (resid 308 through 336 )A308 - 336
3X-RAY DIFFRACTION3chain 'A' and (resid 337 through 346 )A337 - 346
4X-RAY DIFFRACTION4chain 'A' and (resid 347 through 393 )A347 - 393
5X-RAY DIFFRACTION5chain 'A' and (resid 394 through 443 )A394 - 443
6X-RAY DIFFRACTION6chain 'B' and (resid 242 through 319 )B242 - 319
7X-RAY DIFFRACTION7chain 'B' and (resid 335 through 344 )B335 - 344
8X-RAY DIFFRACTION8chain 'B' and (resid 345 through 428 )B345 - 428
9X-RAY DIFFRACTION9chain 'B' and (resid 429 through 444 )B429 - 444
10X-RAY DIFFRACTION10chain 'C' and (resid 237 through 361 )C237 - 361
11X-RAY DIFFRACTION11chain 'C' and (resid 362 through 444 )C362 - 444
12X-RAY DIFFRACTION12chain 'D' and (resid 6 through 18 )D6 - 18
13X-RAY DIFFRACTION13chain 'D' and (resid 19 through 37 )D19 - 37
14X-RAY DIFFRACTION14chain 'D' and (resid 38 through 57 )D38 - 57

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