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- PDB-5hvw: Monomeric IgG4 Fc -

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Basic information

Entry
Database: PDB / ID: 5hvw
TitleMonomeric IgG4 Fc
ComponentsIg gamma-4 chain C region
KeywordsIMMUNE SYSTEM / Biotechnology / antibody engineering / monomeric Fc / monovalent targeting / fusion protein
Function / homology
Function and homology information


IgG immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade ...IgG immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / antigen binding / 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 / Resolution: 1.95 Å
AuthorsOganesyan, V.Y. / Shan, L. / Dall'Acqua, W.F.
CitationJournal: Plos One / Year: 2016
Title: Generation and Characterization of an IgG4 Monomeric Fc Platform.
Authors: Shan, L. / Colazet, M. / Rosenthal, K.L. / Yu, X.Q. / Bee, J.S. / Ferguson, A. / Damschroder, M.M. / Wu, H. / Dall'Acqua, W.F. / Tsui, P. / Oganesyan, V.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
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 / 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_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_special_symmetry / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / 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 / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7485
Polymers23,9001
Non-polymers1,8484
Water1,45981
1
A: Ig gamma-4 chain C region
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)154,49030
Polymers143,3996
Non-polymers11,09024
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area31380 Å2
ΔGint-187 kcal/mol
Surface area70390 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-3 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.379, 121.379, 99.729
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-510-

ZN

21A-676-

HOH

31A-681-

HOH

DetailsThe natural dimerization interface in constant region of an antibody has been altered, and in the solution the molecule is indeed monomeric. However, at high Zn concentrations it is dimeric.

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Components

#1: Protein Ig gamma-4 chain C region


Mass: 23899.879 Da / Num. of mol.: 1 / Mutation: L351F, T366R, P395K, F405R, Y407E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG4 / Production host: Mammalian expression vector pCK9 (others) / References: UniProt: P01861
#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-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.8 Å3/Da / Density % sol: 53 % / Description: Rhombohedral
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 9 mM ZnCl2, 90 mM Hepes, pH 7.0, 18% PEG 6000 (w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→46.5 Å / Num. obs: 19638 / % possible obs: 99.9 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 33.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 1.95→24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.624 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25824 1041 5 %RANDOM
Rwork0.20923 ---
obs0.21165 19638 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.32 Å2-0 Å2
2---0.65 Å2-0 Å2
3---2.1 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 118 81 1879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191848
X-RAY DIFFRACTIONr_bond_other_d0.0030.021692
X-RAY DIFFRACTIONr_angle_refined_deg1.8452.032523
X-RAY DIFFRACTIONr_angle_other_deg0.9933953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0955209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9642580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.57515301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.615158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211959
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02385
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3413.618839
X-RAY DIFFRACTIONr_mcbond_other2.3393.615838
X-RAY DIFFRACTIONr_mcangle_it3.7515.4091047
X-RAY DIFFRACTIONr_mcangle_other3.755.4121048
X-RAY DIFFRACTIONr_scbond_it2.9474.7091009
X-RAY DIFFRACTIONr_scbond_other2.9234.7091009
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6046.9371477
X-RAY DIFFRACTIONr_long_range_B_refined8.38831.991901
X-RAY DIFFRACTIONr_long_range_B_other8.32531.8011886
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 75 -
Rwork0.282 1424 -
obs--100 %
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)
14.60591.1073-2.48860.2852-0.71182.05070.1308-0.18030.22240.1179-0.07130.0555-0.54950.2956-0.05950.45-0.0380.06590.19720.00160.2642-3.789221.50319.3575
20.8286-1.04060.42752.09010.20951.1111-0.0901-0.1031-0.41280.17790.24770.44060.0822-0.0489-0.15760.22620.0020.13550.23590.08890.391-5.807314.277726.2477
33.15411.0763-2.14851.0201-0.41781.73280.08990.0276-0.0407-0.0186-0.05380.1977-0.1114-0.04-0.03610.08710.04920.01930.1180.01220.3143-2.9714.694315.37
43.48794.4381-4.80195.8952-5.45688.399-0.07130.62690.3601-0.2150.60090.4908-0.2738-1.3532-0.52950.11550.12580.10940.3990.12330.3932-8.362818.6628.2008
51.11651.40361.95945.82912.50113.709-0.0238-0.39450.3450.0694-0.45290.4718-0.0159-0.94770.47670.35670.18160.00450.4958-0.05690.47888.501152.53863.4805
63.97123.39722.72963.06862.27021.9055-0.3826-0.08730.4388-0.17770.13430.4651-0.3394-0.1320.24840.36330.05380.09120.39040.08190.18395.902441.78656.0728
72.03851.48830.52721.19350.5070.284-0.08930.34280.3498-0.13840.10250.1757-0.0685-0.0738-0.01320.26460.08880.00640.25110.15080.174913.204135.17752.6145
819.105122.92653.498332.2535.12094.8358-0.12070.15350.30960.20280.01320.2891-0.02230.48020.10750.14730.00720.06270.1922-0.02590.142428.91834.7573-0.693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A235 - 269
2X-RAY DIFFRACTION2A270 - 300
3X-RAY DIFFRACTION3A301 - 327
4X-RAY DIFFRACTION4A328 - 345
5X-RAY DIFFRACTION5A346 - 362
6X-RAY DIFFRACTION6A363 - 418
7X-RAY DIFFRACTION7A419 - 435
8X-RAY DIFFRACTION8A436 - 444

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