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- PDB-5w5l: Crystal structure of human IgG1-Sigma Fc fragment -

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Basic information

Entry
Database: PDB / ID: 5w5l
TitleCrystal structure of human IgG1-Sigma Fc fragment
ComponentsImmunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / FC / IMMUNOGLOBULIN FOLD
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / 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
Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsArmstrong, A.A. / Gilliland, G.L.
CitationJournal: Antibodies / Year: 2017
Title: Functional, Biophysical, and Structural Characterization of Human IgG1 and IgG4 Fc Variants with Ablated Immune Functionality.
Authors: Tam, S.H. / McCarthy, S.G. / Armstrong, A.A. / Somani, S. / Wu, S.J. / Liu, X. / Gervais, A. / Ernst, R. / Saro, D. / Decker, R. / Luo, J. / Gilliland, G.L. / Chiu, M.L. / Scallon, B.J.
History
DepositionJun 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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_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 / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Oct 4, 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: Immunoglobulin gamma-1 heavy chain
B: Immunoglobulin gamma-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1634
Polymers49,9122
Non-polymers3,2512
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint68 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.360, 79.170, 101.440
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: Antibody Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 24956.156 Da / Num. of mol.: 2 / Fragment: Sigma Fc fragment, UNP residues 227-449 / Mutation: L234A, L235A, A237G, P238S, H268A, A330S, P331S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#2: 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)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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: 1625.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 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]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 9% PEG 20,000, 0.1 M Sodium Acetate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→33.282 Å / Num. obs: 47175 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Net I/σ(I): 21.27
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.93 / Num. unique obs: 3427 / CC1/2: 0.939 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIXdev_1428refinement
XDSdata reduction
XDSdata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AVE

3ave


Resolution: 1.9→33.282 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.42
RfactorNum. reflection% reflection
Rfree0.2288 2273 4.83 %
Rwork0.1919 --
obs0.1937 47088 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→33.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 0 220 262 3719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093625
X-RAY DIFFRACTIONf_angle_d1.2134979
X-RAY DIFFRACTIONf_dihedral_angle_d12.5821355
X-RAY DIFFRACTIONf_chiral_restr0.081610
X-RAY DIFFRACTIONf_plane_restr0.005609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.94140.37771550.26912743X-RAY DIFFRACTION100
1.9414-1.98660.30051210.24412778X-RAY DIFFRACTION99
1.9866-2.03620.30711490.22682771X-RAY DIFFRACTION100
2.0362-2.09130.2611460.22072734X-RAY DIFFRACTION100
2.0913-2.15280.22341540.20732761X-RAY DIFFRACTION100
2.1528-2.22230.24181420.19792759X-RAY DIFFRACTION100
2.2223-2.30170.24121330.20192787X-RAY DIFFRACTION100
2.3017-2.39380.28281450.20582789X-RAY DIFFRACTION100
2.3938-2.50270.23741330.20652798X-RAY DIFFRACTION100
2.5027-2.63460.24861480.21672773X-RAY DIFFRACTION100
2.6346-2.79960.27081570.20682785X-RAY DIFFRACTION100
2.7996-3.01560.23151280.21032815X-RAY DIFFRACTION100
3.0156-3.31890.22261280.19732830X-RAY DIFFRACTION100
3.3189-3.79850.21571460.18152838X-RAY DIFFRACTION100
3.7985-4.78350.19671630.15882839X-RAY DIFFRACTION99
4.7835-33.28660.20451250.18213015X-RAY DIFFRACTION100

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