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- PDB-4znc: Fc fragment of human IgG in complex with the C domain of staphylo... -

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Basic information

Entry
Database: PDB / ID: 4znc
TitleFc fragment of human IgG in complex with the C domain of staphylococcal protein A mutant - Q9W
Components
  • Ig gamma-3 chain C region
  • Immunoglobulin G-binding protein A
KeywordsPROTEIN BINDING / Staphylococcal protein A / SpA / three-helix-bundle / antibody / IgG / protein-binding domain
Function / homology
Function and homology information


IgG immunoglobulin complex / IgG binding / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding ...IgG immunoglobulin complex / IgG binding / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / 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 3 / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsDeis, L.N. / Oas, T.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Suppression of conformational heterogeneity at a protein-protein interface.
Authors: Deis, L.N. / Wu, Q. / Wang, Y. / Qi, Y. / Daniels, K.G. / Zhou, P. / Oas, T.G.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Derived calculations
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein A
B: Immunoglobulin G-binding protein A
C: Immunoglobulin G-binding protein A
D: Ig gamma-3 chain C region
E: Ig gamma-3 chain C region
F: Ig gamma-3 chain C region


Theoretical massNumber of molelcules
Total (without water)95,4596
Polymers95,4596
Non-polymers00
Water2,270126
1
A: Immunoglobulin G-binding protein A
D: Ig gamma-3 chain C region


Theoretical massNumber of molelcules
Total (without water)31,8202
Polymers31,8202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunoglobulin G-binding protein A
E: Ig gamma-3 chain C region


Theoretical massNumber of molelcules
Total (without water)31,8202
Polymers31,8202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Immunoglobulin G-binding protein A
F: Ig gamma-3 chain C region


Theoretical massNumber of molelcules
Total (without water)31,8202
Polymers31,8202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.951, 87.210, 103.248
Angle α, β, γ (deg.)90.00, 91.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A


Mass: 6695.434 Da / Num. of mol.: 3 / Fragment: UNP residues 270-327 / Mutation: Q9W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38507
#2: Protein Ig gamma-3 chain C region / HDC / Heavy chain disease protein


Mass: 25124.361 Da / Num. of mol.: 3 / Fragment: UNP residues 168-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettagami 2 / References: UniProt: P01860
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
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: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG 5000 MME, ammonium sulfate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 52943 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 19.9
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXdev_1664refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZMD, 4WWI

4zmd

4wwi


Resolution: 2.28→34.819 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 1914 3.62 %Random selection
Rwork0.1963 ---
obs0.1979 52860 94.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→34.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6177 0 0 126 6303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166363
X-RAY DIFFRACTIONf_angle_d1.5068642
X-RAY DIFFRACTIONf_dihedral_angle_d15.4222392
X-RAY DIFFRACTIONf_chiral_restr0.063946
X-RAY DIFFRACTIONf_plane_restr0.0081119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.3370.3803960.2852691X-RAY DIFFRACTION70
2.337-2.40020.30691250.26333366X-RAY DIFFRACTION88
2.4002-2.47080.31641280.24153464X-RAY DIFFRACTION90
2.4708-2.55050.32931270.25073549X-RAY DIFFRACTION92
2.5505-2.64170.30531390.25493582X-RAY DIFFRACTION94
2.6417-2.74740.28771470.25313627X-RAY DIFFRACTION96
2.7474-2.87240.31481290.25163748X-RAY DIFFRACTION97
2.8724-3.02370.37291440.25843786X-RAY DIFFRACTION98
3.0237-3.21310.31031480.24413783X-RAY DIFFRACTION99
3.2131-3.46090.23981380.23223838X-RAY DIFFRACTION100
3.4609-3.80880.26611450.20333847X-RAY DIFFRACTION100
3.8088-4.35910.19671460.17073864X-RAY DIFFRACTION100
4.3591-5.48850.18631450.14113883X-RAY DIFFRACTION100
5.4885-34.82350.19671570.16073918X-RAY DIFFRACTION100

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