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- PDB-5u66: Modified single helix from the B-domain of protein A bound to IgG1 Fc -

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Entry
Database: PDB / ID: 5u66
TitleModified single helix from the B-domain of protein A bound to IgG1 Fc
Components
  • IgG1 fc derived from CD4-fc fusion
  • STAPLED PEPTIDE FROM DOMAIN B OF PROTEIN A
Keywordsimmune system/inhibitor / IgG1 Fc / staple peptide / Protein A / B-domain / immune system-inhibitor complex
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex / FCGR activation ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
STAPLED PEPTIDE FROM DOMAIN B OF PROTEIN A / Immunoglobulin heavy constant gamma 1 / Uncharacterized protein DKFZp686C11235
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsUltsch, M.H. / Eigenbrot, C.
CitationJournal: Protein Eng. Des. Sel. / Year: 2017
Title: 3-2-1: Structural insights from stepwise shrinkage of a three-helix Fc-binding domain to a single helix.
Authors: Ultsch, M. / Braisted, A. / Maun, H.R. / Eigenbrot, C.
History
DepositionDec 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_struct_special_symmetry / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.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.ptnr1_label_atom_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 3.0Dec 16, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn
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_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _chem_comp.pdbx_synonyms / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Oct 4, 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 3.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: STAPLED PEPTIDE FROM DOMAIN B OF PROTEIN A
A: IgG1 fc derived from CD4-fc fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8963
Polymers25,6202
Non-polymers1,2761
Water4,035224
1
B: STAPLED PEPTIDE FROM DOMAIN B OF PROTEIN A
A: IgG1 fc derived from CD4-fc fusion
hetero molecules

B: STAPLED PEPTIDE FROM DOMAIN B OF PROTEIN A
A: IgG1 fc derived from CD4-fc fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7926
Polymers51,2404
Non-polymers2,5522
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9470 Å2
ΔGint38 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.165, 126.812, 91.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-5119-

HOH

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Components

#1: Protein/peptide STAPLED PEPTIDE FROM DOMAIN B OF PROTEIN A / /


Type: Oligopeptide / Class: Inhibitor / Mass: 2040.327 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: single helix from the B-domain of protein A bound to IgG1 Fc
Source: (synth.) Staphylococcus aureus (bacteria) / References: STAPLED PEPTIDE FROM DOMAIN B OF PROTEIN A
#2: Protein IgG1 fc derived from CD4-fc fusion


Mass: 23579.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686C11235 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q6MZV7, UniProt: P01857*PLUS
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1276.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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][a2112h-1b_1-5]/1-1-2-3-3-1-4/a4-b1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-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]{[(4+1)][b-D-Galp]{}}}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Compound detailsstapled peptide derived from the B-domain of protein A bound to IgG1 Fc

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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: 2.8 Å3/Da / Density % sol: 56.01 % / Description: Blocks.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 20% PEG 4000, 0.1M HEPES pH 7.2, 5mg/mL protein concentration.
PH range: 7.0-7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1801
2801
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSSRL BL7-110.98
ROTATING ANODERIGAKU RU30021
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDMay 15, 1997
MARMOSAIC 300 mm CCD2CCDApr 19, 1997
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
211
ReflectionResolution: 1.7→41 Å / Num. obs: 29486 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 18.2 Å2 / Rsym value: 0.074 / Net I/σ(I): 29.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 4.7 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U52

5u52


Resolution: 1.7→41.02 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.143 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2942 10 %RANDOM
Rwork0.157 ---
obs0.164 26544 92.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2--0.36 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 86 224 2112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191942
X-RAY DIFFRACTIONr_bond_other_d0.0020.021800
X-RAY DIFFRACTIONr_angle_refined_deg1.9642.0132637
X-RAY DIFFRACTIONr_angle_other_deg3.84734188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3524.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80715313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.009158
X-RAY DIFFRACTIONr_chiral_restr0.1280.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212050
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02414
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.9542.136881
X-RAY DIFFRACTIONr_mcbond_other5.952.134880
X-RAY DIFFRACTIONr_mcangle_it7.4253.2141088
X-RAY DIFFRACTIONr_mcangle_other7.4243.2161089
X-RAY DIFFRACTIONr_scbond_it6.9672.8191061
X-RAY DIFFRACTIONr_scbond_other6.9682.8211062
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.314.0571549
X-RAY DIFFRACTIONr_long_range_B_refined8.69728.4792027
X-RAY DIFFRACTIONr_long_range_B_other8.69528.5012028
X-RAY DIFFRACTIONr_rigid_bond_restr4.66133740
X-RAY DIFFRACTIONr_sphericity_free31.5015154
X-RAY DIFFRACTIONr_sphericity_bonded25.13153759
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 208 -
Rwork0.178 1645 -
obs--79.15 %
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)
13.26574.31222.11485.96022.10063.4817-0.0919-0.14830.5122-0.0795-0.20430.74130.10090.02420.29620.24310.06960.10620.06240.00960.2252.348543.893332.4682
20.2299-0.0603-0.45870.14510.25791.06550.017-0.01940.0034-0.00760.0127-0.0076-0.03640.0405-0.02970.1421-0.0024-0.00230.13-0.00070.067724.751667.488639.4259
30.06250.02550.05150.01450.04420.2059-0.0015-0.01030.01080.0039-0.0102-0.00050.0448-0.00270.01170.1397-0.00070.00530.1262-0.00210.06899.279156.390933.4242
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A501 - 507
2X-RAY DIFFRACTION2B5000 - 5014
3X-RAY DIFFRACTION3A237 - 443

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