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- PDB-4wwi: Crystal structure of the C domain of staphylococcal protein A in ... -

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Basic information

Entry
Database: PDB / ID: 4wwi
TitleCrystal structure of the C domain of staphylococcal protein A in complex with the Fc fragment of human IgG at 2.3 Angstrom resolution
Components
  • Ig gamma-3 chain C region
  • Immunoglobulin G-binding protein A
KeywordsPROTEIN BINDING / three-helix bundle / conformational heterogeneity / S. aureus / antibody binding
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: 2.307 Å
AuthorsDeis, L.N. / Oas, T.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM081666 United States
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
DepositionNov 11, 2014Deposition 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 13, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)95,2856
Polymers95,2856
Non-polymers00
Water2,972165
1
A: Immunoglobulin G-binding protein A
D: Ig gamma-3 chain C region


Theoretical massNumber of molelcules
Total (without water)31,7622
Polymers31,7622
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)31,7622
Polymers31,7622
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)31,7622
Polymers31,7622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.918, 88.116, 101.038
Angle α, β, γ (deg.)90.00, 90.95, 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: 6637.353 Da / Num. of mol.: 3 / Fragment: UNP residues 270-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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): Origami Rosetta / References: UniProt: P01860
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: NaOAc, ammonium sulfate, PEG 5K MME, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.307→41.18 Å / Num. obs: 53496 / % possible obs: 99.47 % / Redundancy: 7.5 % / Net I/σ(I): 19.5
Reflection shellResolution: 2.307→2.389 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.5 / % possible all: 94.81

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(phenix.refine: dev_1664)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NPD, 1FC1

4npd

1fc1


Resolution: 2.307→41.177 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 1871 3.7 %Random selection
Rwork0.2098 ---
obs0.2113 50557 94.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.307→41.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6074 0 0 165 6239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036423
X-RAY DIFFRACTIONf_angle_d0.7128728
X-RAY DIFFRACTIONf_dihedral_angle_d13.2872453
X-RAY DIFFRACTIONf_chiral_restr0.029946
X-RAY DIFFRACTIONf_plane_restr0.0031144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3066-2.3690.32941060.28022945X-RAY DIFFRACTION74
2.369-2.43870.32691270.2673427X-RAY DIFFRACTION86
2.4387-2.51740.30291250.25833454X-RAY DIFFRACTION87
2.5174-2.60740.33841430.2583612X-RAY DIFFRACTION92
2.6074-2.71170.30231660.24773777X-RAY DIFFRACTION95
2.7117-2.83510.27691380.23393862X-RAY DIFFRACTION97
2.8351-2.98460.27981550.24553870X-RAY DIFFRACTION98
2.9846-3.17150.30081580.23373933X-RAY DIFFRACTION99
3.1715-3.41630.30261590.21443963X-RAY DIFFRACTION100
3.4163-3.75980.2641360.22613796X-RAY DIFFRACTION95
3.7598-4.30340.1931440.18673983X-RAY DIFFRACTION100
4.3034-5.41990.2061550.174011X-RAY DIFFRACTION100
5.4199-41.18390.23481590.20084053X-RAY DIFFRACTION99

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