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- PDB-6wmh: Next generation monomeric IgG4 Fc -

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Basic information

Entry
Database: PDB / ID: 6wmh
TitleNext generation monomeric IgG4 Fc
ComponentsImmunoglobulin heavy constant gamma 4
KeywordsIMMUNE SYSTEM / antibody constant region / fragment crystallizable / mutated
Function / homology
Function and homology information


IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis ...IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOganesyan, V.Y. / Shan, L. / van Dyk, N. / Dall'Acqua, W.F.
CitationJournal: Commun Biol / Year: 2021
Title: In vivo pharmacokinetic enhancement of monomeric Fc and monovalent bispecific designs through structural guidance.
Authors: Shan, L. / Dyk, N.V. / Haskins, N. / Cook, K.M. / Rosenthal, K.L. / Mazor, R. / Dragulin-Otto, S. / Jiang, Y. / Wu, H. / Dall'Acqua, W.F. / Borrok, M.J. / Damschroder, M.M. / Oganesyan, V.
History
DepositionApr 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Immunoglobulin heavy constant gamma 4
A: Immunoglobulin heavy constant gamma 4


Theoretical massNumber of molelcules
Total (without water)47,5792
Polymers47,5792
Non-polymers00
Water2,774154
1
H: Immunoglobulin heavy constant gamma 4


Theoretical massNumber of molelcules
Total (without water)23,7901
Polymers23,7901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Immunoglobulin heavy constant gamma 4


Theoretical massNumber of molelcules
Total (without water)23,7901
Polymers23,7901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.974, 110.925, 87.175
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11H
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 238 - 442 / Label seq-ID: 1 - 205

Dom-IDAuth asym-IDLabel asym-ID
1HA
2AB

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Components

#1: Protein Immunoglobulin heavy constant gamma 4 / Ig gamma-4 chain C region


Mass: 23789.652 Da / Num. of mol.: 2 / Fragment: domains Ch2 and Ch3
Mutation: M252Y, S254T, T256E, N297D, L351F, S354E, T366R, P395K, F405R, Y407E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG4 / Production host: Homo sapiens (human) / References: UniProt: P01861
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: DL-Glutamic acid monohydrate, DL-Alanine, Glycine, DL-Lysine monohydrochloride, DL-Serine, Sodium HEPES, MOPS (acid), Ethylene glycol, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.19499 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19499 Å / Relative weight: 1
ReflectionResolution: 2.3→37 Å / Num. obs: 22417 / % possible obs: 99.2 % / Redundancy: 6.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.069 / Net I/σ(I): 7.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.282 / Num. unique obs: 2147 / CC1/2: 0.599 / Rpim(I) all: 0.528 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hvw

5hvw


Resolution: 2.3→35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.019 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.231
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 1047 4.7 %RANDOM
Rwork0.2007 ---
obs0.2028 21334 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 201.11 Å2 / Biso mean: 44.781 Å2 / Biso min: 21.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å20 Å2
2---0.88 Å2-0 Å2
3---1.25 Å2
Refinement stepCycle: final / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 0 154 3496
Biso mean---38.17 -
Num. residues----413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133432
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173076
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.6554664
X-RAY DIFFRACTIONr_angle_other_deg1.31.5767214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5555411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95923.736182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18515597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6561516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02675
Refine LS restraints NCS

Ens-ID: 1 / Number: 5799 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1H
2A
LS refinement shellResolution: 2.3→2.357 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.29 75 -
Rwork0.29 1540 -
obs--97.06 %

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