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- PDB-3fjt: Crystal structure of a human Fc fragment engineered for extended ... -

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Basic information

Entry
Database: PDB / ID: 3fjt
TitleCrystal structure of a human Fc fragment engineered for extended serum half-life
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / Fc / IgG1 / FcRn binding / CH3-CH3 association / Glycoprotein / Immunoglobulin C region / Immunoglobulin domain / Secreted
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsOganesyan, V. / Wu, H. / Dall'Acqua, W.F.
CitationJournal: Mol.Immunol. / Year: 2009
Title: Structural characterization of a human Fc fragment engineered for extended serum half-life.
Authors: Oganesyan, V. / Damschroder, M.M. / Woods, R.M. / Cook, K.E. / Wu, H. / Dall'acqua, W.F.
History
DepositionDec 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 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 / database_PDB_caveat / 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_chiral / struct_asym / struct_conn / 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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)50,4584
Polymers47,5312
Non-polymers2,9272
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-9.9 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.660, 79.605, 145.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ig gamma-1 chain C region


Mass: 23765.738 Da / Num. of mol.: 2 / Fragment: UNP residues 119-327 / Mutation: M252Y, S254T, T256E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Human / Gene: IgG1, IGHG1 / Plasmid: pABOE / Cell (production host): Human embryonic kidney cell line / Cell line (production host): HEK 293 / Organ (production host): KIDNEY / Production host: homo sapiens (human) / 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)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 6000, 5% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 6, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.492→72.739 Å / Num. all: 20852 / Num. obs: 19236 / % possible obs: 92.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 66 Å2 / Limit h max: 19 / Limit h min: 0 / Limit k max: 31 / Limit k min: 0 / Limit l max: 58 / Limit l min: 0 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 7.4
Reflection shellResolution: 2.492→2.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.44 / % possible all: 93.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→12 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.895 / Occupancy max: 1 / Occupancy min: 1 / SU B: 24.923 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.291 988 5.2 %RANDOM
Rwork0.227 ---
obs0.23 19134 93.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.82 Å2 / Biso mean: 63.806 Å2 / Biso min: 31.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å20 Å2
2---2.13 Å20 Å2
3---4.24 Å2
Refinement stepCycle: LAST / Resolution: 2.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 198 68 3616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223662
X-RAY DIFFRACTIONr_bond_other_d0.0010.022468
X-RAY DIFFRACTIONr_angle_refined_deg1.4122.0235018
X-RAY DIFFRACTIONr_angle_other_deg0.8513.0036022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2685416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31825156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67115578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.131512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02644
X-RAY DIFFRACTIONr_nbd_refined0.1990.2624
X-RAY DIFFRACTIONr_nbd_other0.1910.22331
X-RAY DIFFRACTIONr_nbtor_refined0.180.21680
X-RAY DIFFRACTIONr_nbtor_other0.0880.21898
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2134
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.26
X-RAY DIFFRACTIONr_mcbond_it1.4241.52675
X-RAY DIFFRACTIONr_mcbond_other0.1871.5818
X-RAY DIFFRACTIONr_mcangle_it1.56723456
X-RAY DIFFRACTIONr_scbond_it1.8631822
X-RAY DIFFRACTIONr_scangle_it2.2324.51562
X-RAY DIFFRACTIONr_rigid_bond_restr3.12137519
X-RAY DIFFRACTIONr_sphericity_free5.34368
X-RAY DIFFRACTIONr_sphericity_bonded1.2736016
LS refinement shellResolution: 2.5→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 59 -
Rwork0.321 1349 -
all-1408 -
obs--97.71 %

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