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- PDB-5lg1: Room temperature structure of human IgG4-Fc from crystals analyse... -

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Basic information

Entry
Database: PDB / ID: 5lg1
TitleRoom temperature structure of human IgG4-Fc from crystals analysed in situ
ComponentsIg gamma-4 chain C region
KeywordsIMMUNE SYSTEM / Antibody Immunoglobulin
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: 2.7 Å
AuthorsDavies, A.M. / Rispens, T. / Ooijevaar-de Heer, P. / Aalberse, R.C. / Sutton, B.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100090 United Kingdom
CitationJournal: Mol. Immunol. / Year: 2016
Title: Room temperature structure of human IgG4-Fc from crystals analysed in situ.
Authors: Davies, A.M. / Rispens, T. / Ooijevaar-de Heer, P. / Aalberse, R.C. / Sutton, B.J.
History
DepositionJul 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_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_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 2.1Jan 10, 2024Group: 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: Ig gamma-4 chain C region
B: Ig gamma-4 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4234
Polymers48,4972
Non-polymers2,9272
Water36020
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint64 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.294, 81.934, 103.883
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


Mass: 24248.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HUMAN IGG 4 FC REGION / Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG4 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES, 18-20% PEG 20 000

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→48.35 Å / Num. obs: 17764 / % possible obs: 99.9 % / Redundancy: 8.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.171 / Net I/σ(I): 12.2
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 2 / CC1/2: 0.433 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c54

4c54


Resolution: 2.7→48.349 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 26.2
RfactorNum. reflection% reflection
Rfree0.2313 886 5.02 %
Rwork0.1753 --
obs0.1781 17653 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 198 20 3478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033578
X-RAY DIFFRACTIONf_angle_d0.544915
X-RAY DIFFRACTIONf_dihedral_angle_d10.6482161
X-RAY DIFFRACTIONf_chiral_restr0.04590
X-RAY DIFFRACTIONf_plane_restr0.003607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-2.86940.39331590.33552710X-RAY DIFFRACTION99
2.8694-3.09090.30511440.28962753X-RAY DIFFRACTION99
3.0909-3.40190.29051260.22832781X-RAY DIFFRACTION100
3.4019-3.8940.24461590.1882775X-RAY DIFFRACTION100
3.894-4.90520.1821580.13862804X-RAY DIFFRACTION100
4.9052-48.35710.20751400.13762944X-RAY DIFFRACTION99
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)
11.34040.40470.60642.22260.15930.6576-0.08050.32060.0353-0.27470.0553-0.0815-0.03940.241-00.5463-0.04670.11510.66010.05130.511139.672166.0523-3.0347
20.98780.1899-0.2512.08430.6950.368-0.1149-0.00680.2110.24430.0669-0.35080.01540.05210.00780.533-0.02770.00410.48840.08890.498342.542475.780920.2219
30.9992-1.0908-0.32471.5260.97971.2958-0.2186-0.0644-0.23650.41070.0044-0.3330.27560.0986-00.6647-0.0446-0.07610.50960.06260.479842.78771.91228.533
40.1752-0.084-0.02650.79520.38010.1755-0.46480.49430.5783-0.05820.37390.3358-0.07320.4701-0.01890.8741-0.1846-0.29820.94190.01260.84121.307396.322412.7079
50.1033-0.02490.09090.0333-0.04440.0913-0.24040.1310.4725-0.4457-0.14350.5111-0.53050.0671-0.00281.2306-0.1589-0.51231.09260.28841.152415.505998.6153-2.2426
60.0509-0.09910.02390.28130.0960.23070.51650.0426-0.4388-0.2869-0.34370.0885-0.9380.42530.00011.3044-0.1955-0.35761.36480.26631.676919.404100.7392.3204
70.29830.08670.3510.31540.09540.4003-0.279-0.13970.2381-0.4974-0.04990.687-0.14420.1711-0.00261.0568-0.1462-0.34021.0006-0.03651.05414.909493.99277.2079
80.2263-0.5368-0.07861.61920.6830.8547-0.1677-0.12290.04530.27740.16850.01120.3043-0.0371-00.619-0.0407-0.13890.7022-0.02870.714434.113883.934532.354
90.8676-0.9765-0.30421.2625-0.02390.8218-0.0684-0.21150.28730.1304-0.0143-0.16960.035-0.0620.00010.6131-0.055-0.13380.5658-0.05210.664435.496188.567729.4312
100.2806-0.09040.06740.7623-0.51460.3585-0.059-0.24410.43350.48770.18550.0619-0.12610.08870.16150.6625-0.0699-0.14870.6804-0.20890.590330.283393.041836.7575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 236 through 325 )
2X-RAY DIFFRACTION2chain 'A' and (resid 326 through 383 )
3X-RAY DIFFRACTION3chain 'A' and (resid 384 through 444 )
4X-RAY DIFFRACTION4chain 'B' and (resid 237 through 266 )
5X-RAY DIFFRACTION5chain 'B' and (resid 267 through 279 )
6X-RAY DIFFRACTION6chain 'B' and (resid 280 through 299 )
7X-RAY DIFFRACTION7chain 'B' and (resid 300 through 336 )
8X-RAY DIFFRACTION8chain 'B' and (resid 337 through 361 )
9X-RAY DIFFRACTION9chain 'B' and (resid 362 through 418 )
10X-RAY DIFFRACTION10chain 'B' and (resid 419 through 444 )

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