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- PDB-4dz8: human IgG1 Fc fragment Heterodimer -

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Basic information

Entry
Database: PDB / ID: 4dz8
Titlehuman IgG1 Fc fragment Heterodimer
Components(Ig gamma-1 chain C region) x 2
KeywordsIMMUNE SYSTEM / Fc Fragment / Antibody
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 / FCGR activation / Role of phospholipids in phagocytosis ...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 / 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/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
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsStrop, P.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Generating Bispecific Human IgG1 and IgG2 Antibodies from Any Antibody Pair.
Authors: Strop, P. / Ho, W.H. / Boustany, L.M. / Abdiche, Y.N. / Lindquist, K.C. / Farias, S.E. / Rickert, M. / Appah, C.T. / Pascua, E. / Radcliffe, T. / Sutton, J. / Chaparro-Riggers, J. / Chen, W. ...Authors: Strop, P. / Ho, W.H. / Boustany, L.M. / Abdiche, Y.N. / Lindquist, K.C. / Farias, S.E. / Rickert, M. / Appah, C.T. / Pascua, E. / Radcliffe, T. / Sutton, J. / Chaparro-Riggers, J. / Chen, W. / Casas, M.G. / Chin, S.M. / Wong, O.K. / Liu, S.H. / Vergara, G. / Shelton, D. / Rajpal, A. / Pons, J.
History
DepositionFeb 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_label_seq_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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)53,2584
Polymers50,3312
Non-polymers2,9272
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint54 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.929, 81.292, 136.151
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: 25157.514 Da / Num. of mol.: 1 / Fragment: unp residues 108-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK / Production host: HOMO SAPIENS (human) / References: UniProt: P01857
#2: Protein Ig gamma-1 chain C region


Mass: 25173.402 Da / Num. of mol.: 1 / Fragment: unp residues 108-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK / Production host: HOMO SAPIENS (human) / References: UniProt: P01857
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE TWO CRYSTALLIZED SEQUENCES THOUGH PRESENTING MICROHETEROGENEITY ARE DIFFERENT

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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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 mM Hepes, pH 7.0, 1% Tryptone, and 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2011
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 43830 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rsym value: 0.078 / Net I/σ(I): 28.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.44 / Num. unique all: 4309 / Rsym value: 0.471 / % possible all: 100

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.451 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23658 2201 5 %RANDOM
Rwork0.20484 ---
obs0.20638 41549 99.53 %-
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: 32.058 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.9 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.91→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3355 0 198 436 3989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223629
X-RAY DIFFRACTIONr_bond_other_d0.0030.022446
X-RAY DIFFRACTIONr_angle_refined_deg1.2652.0244972
X-RAY DIFFRACTIONr_angle_other_deg1.0913.0035968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7165412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52224.935154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69415578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2531513
X-RAY DIFFRACTIONr_chiral_restr0.1220.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023772
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02637
X-RAY DIFFRACTIONr_nbd_refined0.180.2540
X-RAY DIFFRACTIONr_nbd_other0.1890.22387
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21702
X-RAY DIFFRACTIONr_nbtor_other0.090.21888
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2306
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0790.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7481.52676
X-RAY DIFFRACTIONr_mcbond_other0.1141.5809
X-RAY DIFFRACTIONr_mcangle_it0.82323431
X-RAY DIFFRACTIONr_scbond_it1.45931782
X-RAY DIFFRACTIONr_scangle_it2.1864.51541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.908→1.957 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 150 -
Rwork0.238 2832 -
obs--94.13 %

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