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- PDB-4c54: Crystal structure of recombinant human IgG4 Fc -

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Basic information

Entry
Database: PDB / ID: 4c54
TitleCrystal structure of recombinant human IgG4 Fc
ComponentsIG GAMMA-4 CHAIN C REGION
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / IGG1
Function / homology
Function and homology information


Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / FCGR3A-mediated IL10 synthesis / antigen binding ...Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / FCGR3A-mediated IL10 synthesis / antigen binding / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / 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
Immunoglobulin heavy constant gamma 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDavies, A.M. / Rispens, T. / Ooijevaar-deHeer, P. / Gould, H.J. / Jefferis, R. / Aalberse, R.C. / Sutton, B.J.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural Determinants of Unique Properties of Human Igg4-Fc
Authors: Davies, A.M. / Rispens, T. / Ooijevaar-Deheer, P. / Gould, H.J. / Jefferis, R. / Aalberse, R.C. / Sutton, B.J.
History
DepositionSep 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Mar 11, 2020Group: Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn
Item: _chem_comp.type / _pdbx_database_status.status_code_sf / _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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IG GAMMA-4 CHAIN C REGION
B: IG GAMMA-4 CHAIN C REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,37215
Polymers48,4972
Non-polymers3,87613
Water5,224290
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint93 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.837, 78.973, 97.881
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-4 CHAIN C REGION / IGG4


Mass: 24248.312 Da / Num. of mol.: 2 / Fragment: FC FRAGMENT, RESIDUES 114-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P01861
#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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.98 Å3/Da / Density % sol: 58.75 % / Description: RPIM 0.029 OVERALL AND 0.421 OUTER SHELL
Crystal growpH: 6.5 / Details: MES PH6.5. 18-20% PEG 20 000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→74.8 Å / Num. obs: 46409 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 30.09 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSIN XIA2 PACKAGEdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ADQ

1adq


Resolution: 1.9→48.941 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2086 2306 5 %
Rwork0.1701 --
obs0.172 46337 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→48.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 252 290 3847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133734
X-RAY DIFFRACTIONf_angle_d1.495107
X-RAY DIFFRACTIONf_dihedral_angle_d28.4851479
X-RAY DIFFRACTIONf_chiral_restr0.108610
X-RAY DIFFRACTIONf_plane_restr0.008624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94130.30371340.26552712X-RAY DIFFRACTION100
1.9413-1.98650.32661280.22432735X-RAY DIFFRACTION100
1.9865-2.03620.26621410.19872721X-RAY DIFFRACTION100
2.0362-2.09120.22411500.19212734X-RAY DIFFRACTION100
2.0912-2.15280.2291320.18292713X-RAY DIFFRACTION100
2.1528-2.22230.21481460.18472723X-RAY DIFFRACTION100
2.2223-2.30170.21921420.18622696X-RAY DIFFRACTION100
2.3017-2.39380.25131460.19012748X-RAY DIFFRACTION100
2.3938-2.50280.25391430.19132734X-RAY DIFFRACTION100
2.5028-2.63470.25421470.19112744X-RAY DIFFRACTION100
2.6347-2.79980.22731410.19732766X-RAY DIFFRACTION100
2.7998-3.01590.25471450.19662746X-RAY DIFFRACTION100
3.0159-3.31940.20961570.18412764X-RAY DIFFRACTION100
3.3194-3.79950.20961510.16172775X-RAY DIFFRACTION100
3.7995-4.78640.15751510.12592809X-RAY DIFFRACTION100
4.7864-48.95670.161520.14412911X-RAY DIFFRACTION98
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)
14.65571.03420.45061.74120.80781.9433-0.10810.475-0.0339-0.26550.0547-0.0311-0.04290.03090.0440.2232-0.02590.04950.1970.04510.25813.7915-13.7352-3.321
22.6677-0.06-0.62392.34580.20763.8189-0.1063-0.1861-0.16870.3464-0.0077-0.16850.22110.16260.10660.2560.0045-0.03520.18330.01470.18986.0736-8.20928.373
32.55050.05541.86242.5706-0.83453.686-0.37350.32640.2316-0.31350.057-0.1708-0.61680.07810.30030.3828-0.0779-0.06690.3422-0.06170.3443-19.512913.01836.1953
43.70210.09671.16882.24270.75553.3231-0.0526-0.27220.27850.22470.0141-0.1802-0.1236-0.01910.04140.2536-0.0154-0.06020.2054-0.02810.231-0.93177.22131.0064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 236 THROUGH 346
2X-RAY DIFFRACTION2CHAIN A AND RESID 347 THROUGH 445
3X-RAY DIFFRACTION3CHAIN B AND RESID 236 THROUGH 346
4X-RAY DIFFRACTION4CHAIN B AND RESID 347 THROUGH 444

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