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- PDB-2qej: Crystal structure of a Staphylococcus aureus protein (SSL7) in co... -

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Basic information

Entry
Database: PDB / ID: 2qej
TitleCrystal structure of a Staphylococcus aureus protein (SSL7) in complex with Fc of human IgA1
Components
  • IG ALPHA-1 C REGION
  • SUPERANTIGEN-LIKE MOLECULE 7
KeywordsIMMUNE SYSTEM / IGA1 / ANTIBODY / IMMUNOGLOBULIN / OB-FOLD / BETA-GRASP / SSL
Function / homology
Function and homology information


secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / IgA immunoglobulin complex / IgG immunoglobulin complex / immunoglobulin complex, circulating / positive regulation of respiratory burst / Scavenging of heme from plasma / complement activation, classical pathway ...secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / IgA immunoglobulin complex / IgG immunoglobulin complex / immunoglobulin complex, circulating / positive regulation of respiratory burst / Scavenging of heme from plasma / complement activation, classical pathway / antigen binding / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / antibacterial humoral response / blood microparticle / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Ubiquitin-like (UB roll) - #120 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Immunoglobulin / Immunoglobulin domain / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...Ubiquitin-like (UB roll) - #120 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Immunoglobulin / Immunoglobulin domain / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant alpha 1 / :
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRamsland, P.A. / Willoughby, N. / Trist, H.M. / Farrugia, W. / Hogarth, P.M. / Fraser, J.D. / Wines, B.D.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for evasion of IgA immunity by Staphylococcus aureus revealed in the complex of SSL7 with Fc of human IgA1
Authors: Ramsland, P.A. / Willoughby, N. / Trist, H.M. / Farrugia, W. / Hogarth, P.M. / Fraser, J.D. / Wines, B.D.
History
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IG ALPHA-1 C REGION
B: IG ALPHA-1 C REGION
C: SUPERANTIGEN-LIKE MOLECULE 7
D: SUPERANTIGEN-LIKE MOLECULE 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,38712
Polymers93,0374
Non-polymers1,3498
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.306, 109.263, 170.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody / Protein / Sugars , 3 types, 6 molecules ABCD

#1: Antibody IG ALPHA-1 C REGION


Mass: 23468.623 Da / Num. of mol.: 2 / Fragment: FC REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHA1 / Plasmid: pAPEX-3p derivative / Production host: Escherichia coli (E. coli) / Strain (production host): HEK293EBNA / References: UniProt: P01876
#2: Protein SUPERANTIGEN-LIKE MOLECULE 7 / SSL7


Mass: 23050.020 Da / Num. of mol.: 2 / Fragment: SET1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: STRAIN NUMBER 4427 (GL1 ISOLATE) / Gene: ssl7 / Plasmid: pET32a-3C / Production host: Escherichia coli (E. coli) / Strain (production host): AD494(DE3)pLysS / References: UniProt: Q2YVR9
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 50 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 3.58 Å3/Da / Density % sol: 65.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 12% PEG 8000, 66 mM sodium cacodylate pH 6.5, 130 mM calcium acetate, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 24, 2006 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→30.82 Å / Num. all: 22643 / Num. obs: 22643 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 68.9 Å2 / Rsym value: 0.103 / Net I/σ(I): 10
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 2164 / Rsym value: 0.362 / % possible all: 97

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1OW0 and 1V1P

1ow0

1v1p


Resolution: 3.2→30.82 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.312 2081 -RANDOM
Rwork0.229 ---
all-22643 --
obs-22643 92.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3.2→30.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6287 0 87 44 6418
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_improper_angle_d0.97
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.422 323 -
Rwork0.322 --
obs-3276 87.9 %

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