[English] 日本語
Yorodumi
- PDB-6krv: Crystal structure of mouse IgG2b Fc complexed with B domain of Pr... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / IgG binding / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / 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 / Immunoglobulins / Immunoglobulin-like fold / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more