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- PDB-4c55: Crystal structure of serum-derived human IgG4 Fc -

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Basic information

Entry
Database: PDB / ID: 4c55
TitleCrystal structure of serum-derived human IgG4 Fc
ComponentsIG GAMMA-4 CHAIN C REGION
KeywordsIMMUNE SYSTEM / IGG / ANTIBODY / 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: 2.35 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_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_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_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_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

Downloads & links

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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)52,9679
Polymers49,2852
Non-polymers3,6827
Water1,29772
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A: IG GAMMA-4 CHAIN C REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5885
Polymers24,6431
Non-polymers1,9454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: IG GAMMA-4 CHAIN C REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3794
Polymers24,6431
Non-polymers1,7373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.298, 80.738, 99.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein IG GAMMA-4 CHAIN C REGION / IGG4


Mass: 24642.734 Da / Num. of mol.: 2 / Fragment: FC FRAGMENT, RESIDUES 110-327 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P01861

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Sugars , 2 types, 2 molecules

#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.: 1
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-6-deoxy-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1479.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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][a2112h-1b_1-5]/1-1-2-3-1-3-1-4/a4-b1_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]{}}}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 77 molecules

#4: 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
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.02 Å3/Da / Density % sol: 59.25 %
Description: RPIM VALUES OF 0.032 OVERALL AND 0.696 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
DetectorDate: Jul 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.35→80.74 Å / Num. obs: 25471 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 60.91 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.4
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
XDSIN XIA2 PACKAGEdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C54

4c54


Resolution: 2.35→49.595 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 28.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 1279 5 %
Rwork0.1879 --
obs0.1903 25411 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→49.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 232 72 3488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093531
X-RAY DIFFRACTIONf_angle_d1.1234843
X-RAY DIFFRACTIONf_dihedral_angle_d29.3511354
X-RAY DIFFRACTIONf_chiral_restr0.071589
X-RAY DIFFRACTIONf_plane_restr0.005590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.44410.37841500.31612613X-RAY DIFFRACTION100
2.4441-2.55530.33711370.2842662X-RAY DIFFRACTION100
2.5553-2.690.32731280.26372653X-RAY DIFFRACTION100
2.69-2.85860.31311500.24642624X-RAY DIFFRACTION100
2.8586-3.07920.29031420.24122676X-RAY DIFFRACTION100
3.0792-3.38910.30771420.21442683X-RAY DIFFRACTION100
3.3891-3.87930.24021410.19012689X-RAY DIFFRACTION100
3.8793-4.88680.20661380.1472722X-RAY DIFFRACTION100
4.8868-49.6060.18181510.15742810X-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)
16.26740.2972-1.30453.3312-0.57851.84470.06830.8704-0.1613-0.4145-0.14210.34390.0287-0.28130.08470.4028-0.001-0.14710.479-0.18630.468970.196194.9015-2.8645
25.561-1.51281.17654.2956-1.2575.2028-0.3957-0.4933-0.11930.85980.0570.6331-0.356-0.25690.30130.52040.01480.19060.4418-0.07420.424368.229288.675428.2899
35.97340.7622-0.51356.45730.14886.9494-0.51830.9358-0.4366-0.43910.02010.49690.3757-0.40320.43050.4672-0.0090.08890.6118-0.06360.45789.023369.328911.5839
44.68461.3438-0.80134.1476-1.9274.7422-0.2660.2597-0.6177-0.2184-0.5013-0.0871.39120.58090.87240.7253-0.08190.25190.77620.15570.662991.220863.905412.7598
57.11441.4092.72235.98611.74967.967-0.22320.3158-0.7004-0.6397-0.20130.21410.9021-0.01680.41150.7951-0.03760.19680.6780.04560.546594.179364.70942.6308
64.0410.6956-0.63713.38112.34673.3541-0.50710.73540.1936-1.0174-0.14190.44190.54231.03780.22871.0009-0.04590.16530.83340.09180.435798.203171.4977-0.1868
76.53050.1275-0.72491.8312-0.08781.9109-0.4182-0.6172-0.63240.94990.19890.56260.0353-0.00190.16990.70360.08780.38060.4280.09830.814377.789378.495330.9394
84.4307-1.22160.15652.5128-0.56893.6287-0.1097-0.3535-0.91980.69130.02540.71680.03350.05770.10820.50480.02670.23550.53130.05820.630777.576874.179527.2717
90.6451-0.74510.02991.22950.61720.9874-0.6516-0.4746-1.14560.5471-0.17961.6987-0.1243-0.2058-0.3760.35440.02170.59630.69510.14611.225369.186373.016830.9495
107.8060.5969-1.6980.71831.00833.11670.1399-0.8978-1.0611.6390.34830.682-0.19990.31250.00130.70850.12190.35220.74190.32680.739481.40769.539634.7366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 237 THROUGH 346
2X-RAY DIFFRACTION2CHAIN A AND RESID 347 THROUGH 444
3X-RAY DIFFRACTION3CHAIN B AND RESID 238 THROUGH 251
4X-RAY DIFFRACTION4CHAIN B AND RESID 252 THROUGH 264
5X-RAY DIFFRACTION5CHAIN B AND RESID 265 THROUGH 315
6X-RAY DIFFRACTION6CHAIN B AND RESID 316 THROUGH 336
7X-RAY DIFFRACTION7CHAIN B AND RESID 337 THROUGH 361
8X-RAY DIFFRACTION8CHAIN B AND RESID 362 THROUGH 403
9X-RAY DIFFRACTION9CHAIN B AND RESID 404 THROUGH 418
10X-RAY DIFFRACTION10CHAIN B AND RESID 419 THROUGH 443

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