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- PDB-3d6g: Fc fragment of IgG1 (Herceptin) with protein-A mimetic peptide de... -

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Basic information

Entry
Database: PDB / ID: 3d6g
TitleFc fragment of IgG1 (Herceptin) with protein-A mimetic peptide dendrimer ligand.
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / Fc fragment / IgG1 / glycosilated protein / protein A mimetic peptide dendrimer ligand / Glycoprotein / Immunoglobulin C region / Immunoglobulin domain / Secreted
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
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/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
Chem-X12 / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBujacz, A.D. / Redzynia, I. / Bujacz, G.D. / Dinon, F. / Pengo, P. / Fassina, G.
CitationJournal: J.Phys.Chem.B / Year: 2009
Title: Structural characterization of a Protein A mimetic peptide dendrimer bound to human IgG.
Authors: Moiani, D. / Salvalaglio, M. / Cavallotti, C. / Bujacz, A. / Redzynia, I. / Bujacz, G. / Dinon, F. / Pengo, P. / Fassina, G.
History
DepositionMay 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 25, 2019Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / citation_author / diffrn_source / struct_conn
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.label_asym_id ..._atom_site.auth_asym_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6465
Polymers47,5782
Non-polymers5,0683
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint53 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.778, 79.155, 139.223
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ig gamma-1 chain C region


Mass: 23788.842 Da / Num. of mol.: 2 / Fragment: Fc fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Human / Gene: IGHG1 / Cell (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01857
#2: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-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
#3: Chemical ChemComp-X12 / 2-[[(2S)-2,6-bis[[(2S)-2,6-bis[[(2R)-2-[[(2R,3R)-2-[[(2R)-2-amino-5-carbamimidamido-pentanoyl]amino]-3-hydroxy-butanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]hexanoyl]amino]hexanoyl]amino]ethanoic acid


Mass: 2141.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C96H153N31O25
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-20% PEG 20K, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8162 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 19, 2006 / Details: SI[111] horizontally focussing monochromator
RadiationMonochromator: SI[111] horizontally focussing monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8162 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 25671 / Num. obs: 25480 / % possible obs: 99.3 % / Redundancy: 10.8 % / Biso Wilson estimate: 56.5 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 35.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.37 / Num. unique all: 2442 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HZH

1hzh


Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 14.478 / SU ML: 0.187 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25716 806 3.2 %RANDOM
Rwork0.18811 ---
obs0.19025 24234 99.31 %-
all-25805 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 72.418 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å20 Å20 Å2
2--0.2 Å20 Å2
3---1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 350 268 3961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223857
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.862.0815283
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6875429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54424.873158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40515593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3071514
X-RAY DIFFRACTIONr_chiral_restr0.1010.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022832
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21592
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22546
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.811.52209
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14123519
X-RAY DIFFRACTIONr_scbond_it1.89431866
X-RAY DIFFRACTIONr_scangle_it2.7434.51757
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 69 -
Rwork0.231 1731 -
obs-1854 97.19 %
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)
14.110.03762.23121.74291.01726.48340.09430.4022-0.2554-0.21530.0492-0.11560.1338-0.0306-0.1435-0.2096-0.0360.0349-0.2669-0.0739-0.144141.693625.6781.3483
26.038-0.6134-0.70812.450.35582.6534-0.1997-1.1982-0.60720.50730.30510.17490.3770.0385-0.1053-0.13870.1496-0.00580.030.1288-0.152228.623432.5565111.4685
34.78560.5201-3.39555.5875-0.09217.0836-0.19660.69350.3526-2.24360.1248-0.0647-0.53620.13050.07190.8615-0.112-0.0389-0.11680.0749-0.139315.765551.468777.8752
45.50090.43471.48323.46641.7713.6541-0.2256-0.84770.43770.32290.12470.0633-0.02790.1930.1009-0.25310.07530.0125-0.1089-0.0871-0.194519.629146.9264109.7316
59.3959-6.00851.808911.9738-5.624222.20160.1372-0.61730.12850.14-0.0510.2535-0.5135-0.7449-0.0862-0.1752-0.00440.08090.1654-0.0832-0.152329.129629.626181.3565
613.8983-13.149-4.228917.68393.17038.0075-0.14190.46850.1363-1.27040.6373-0.6536-1.23710.3365-0.49540.7213-0.02940.33580.21310.06240.044327.077945.318381.5195
78.0344-8.15551.9417.93424.70875.0870.8156-0.64450.4565-0.8268-0.89771.3754-0.61620.7520.08210.13340.04680.02070.11040.03430.2597-2.491666.408694.51
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA236 - 3401 - 105
2X-RAY DIFFRACTION2AA341 - 445106 - 210
3X-RAY DIFFRACTION3BB236 - 3401 - 105
4X-RAY DIFFRACTION4BB341 - 444106 - 209
5X-RAY DIFFRACTION5AC1 - 87 - 8
6X-RAY DIFFRACTION6BD1 - 87 - 8
7X-RAY DIFFRACTION7BE4461

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