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- PDB-8a47: IdeS in complex with IgG1 Fc -

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Basic information

Entry
Database: PDB / ID: 8a47
TitleIdeS in complex with IgG1 Fc
Components
  • IgG-degrading protease
  • IgG1 Fc
KeywordsIMMUNE SYSTEM / Antibody / protease / IgG / Fc / IdeS
Function / homologyIg protease IdeS / Mac 1 / Papain-like cysteine peptidase superfamily / peptidase activity / proteolysis / IgG-degrading protease
Function and homology information
Biological speciesHomo sapiens (human)
Streptococcus pyogenes serotype M59 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.338 Å
AuthorsSudol, A.S.L. / Tews, I. / Crispin, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Extensive substrate recognition by the streptococcal antibody-degrading enzymes IdeS and EndoS.
Authors: Sudol, A.S.L. / Butler, J. / Ivory, D.P. / Tews, I. / Crispin, M.
History
DepositionJun 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 11, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: IgG1 Fc
B: IgG1 Fc
C: IgG-degrading protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7876
Polymers86,0403
Non-polymers2,7463
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint14 kcal/mol
Surface area33370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.558, 108.448, 63.093
Angle α, β, γ (deg.)90.000, 90.059, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 230 - 443 / Label seq-ID: 10 - 223

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Antibody / Protein , 2 types, 3 molecules ABC

#1: Antibody IgG1 Fc


Mass: 25554.982 Da / Num. of mol.: 2 / Mutation: E382A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFUSE-hIgG1-Fc / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human)
#2: Protein IgG-degrading protease


Mass: 34930.137 Da / Num. of mol.: 1 / Mutation: C94A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M59 (bacteria)
Gene: mac, SAMEA1711581_00766 / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8B6IYA1

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-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: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(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)]beta-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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

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Non-polymers , 2 types, 201 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.08 Å3/Da / Density % sol: 69.86 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.12 M monosaccharides mix (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D- Xylose; 0.2M N-Acetyl-D-Glucosamine), 0.1 M buffer system 3 (Tris (base); BICINE; pH 8.5) ...Details: 0.12 M monosaccharides mix (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D- Xylose; 0.2M N-Acetyl-D-Glucosamine), 0.1 M buffer system 3 (Tris (base); BICINE; pH 8.5), 30 % v/v precipitant mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 23, 2021 / Details: Vertical CRL
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5068
pseudo-merohedral22-h,-k,l20.4932
ReflectionResolution: 2.338→48.53 Å / Num. obs: 60351 / % possible obs: 97.7 % / Redundancy: 4.96 % / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.112 / Rrim(I) all: 0.255 / Χ2: 0.954 / Net I/σ(I): 5.3
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 1 / Num. unique obs: 3005 / CC1/2: 0.335 / Rpim(I) all: 0.426 / Rrim(I) all: 0.978 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y08

1y08


Resolution: 2.338→48.529 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.18 / WRfactor Rwork: 0.153 / SU B: 2.221 / SU ML: 0.057 / Average fsc free: 0.986 / Average fsc work: 0.9914 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.034
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2031 3049 5.052 %
Rwork0.1712 57301 -
all0.173 --
obs-60350 97.398 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å2-0 Å2-1.549 Å2
2--8.708 Å20 Å2
3----9.478 Å2
Refinement stepCycle: LAST / Resolution: 2.338→48.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5791 0 185 200 6176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126157
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165486
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.6788391
X-RAY DIFFRACTIONr_angle_other_deg0.4991.60812904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6715728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.497521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.053101010
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.92410271
X-RAY DIFFRACTIONr_chiral_restr0.070.2960
X-RAY DIFFRACTIONr_chiral_restr_other0.0160.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026838
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021147
X-RAY DIFFRACTIONr_nbd_refined0.1970.21020
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.24998
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22952
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.23309
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0780.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3130.26
X-RAY DIFFRACTIONr_nbd_other0.1760.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.27
X-RAY DIFFRACTIONr_mcbond_it3.4343.6772918
X-RAY DIFFRACTIONr_mcbond_other3.4313.6772918
X-RAY DIFFRACTIONr_mcangle_it4.8765.5093644
X-RAY DIFFRACTIONr_mcangle_other4.8755.5113645
X-RAY DIFFRACTIONr_scbond_it3.5683.973239
X-RAY DIFFRACTIONr_scbond_other3.5683.9683238
X-RAY DIFFRACTIONr_scangle_it5.1955.8374747
X-RAY DIFFRACTIONr_scangle_other5.1955.8394748
X-RAY DIFFRACTIONr_lrange_it7.10845.2736491
X-RAY DIFFRACTIONr_lrange_other7.10845.2876492
X-RAY DIFFRACTIONr_ncsr_local_group_10.1310.056023
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.131450.05009
12AX-RAY DIFFRACTIONLocal ncs0.131450.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.338-2.3990.3632090.3484108X-RAY DIFFRACTION95.3612
2.399-2.4640.4041910.3054198X-RAY DIFFRACTION98.8514
2.464-2.5360.3122400.2644070X-RAY DIFFRACTION98.6044
2.536-2.6140.2951980.2413917X-RAY DIFFRACTION98.2804
2.614-2.6990.3111990.2143813X-RAY DIFFRACTION98.5265
2.699-2.7940.2851870.2183684X-RAY DIFFRACTION98.4486
2.794-2.90.2492160.1953537X-RAY DIFFRACTION98.4264
2.9-3.0180.2031490.1883450X-RAY DIFFRACTION97.7989
3.018-3.1520.211940.1743228X-RAY DIFFRACTION97.9674
3.152-3.3060.2021420.1663172X-RAY DIFFRACTION97.7293
3.306-3.4840.1711590.1612950X-RAY DIFFRACTION97.3083
3.484-3.6950.1871620.1552772X-RAY DIFFRACTION96.4497
3.695-3.950.1741310.1442609X-RAY DIFFRACTION96.5129
3.95-4.2660.1731520.1282423X-RAY DIFFRACTION97.2065
4.266-4.6730.1431180.1162244X-RAY DIFFRACTION96.6053
4.673-5.2230.1281220.1162021X-RAY DIFFRACTION96.4013
5.223-6.0290.1541060.1411778X-RAY DIFFRACTION96.2206
6.029-7.3780.172770.1431502X-RAY DIFFRACTION95.2352
7.378-10.410.131620.1281175X-RAY DIFFRACTION94.6442
10.41-48.5290.235350.206650X-RAY DIFFRACTION92.5676

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