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- PDB-5dvl: Fc Design 20.8.37 A chain homodimer Y349S/T366M/K370Y/K409V -

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Basic information

Entry
Database: PDB / ID: 5dvl
TitleFc Design 20.8.37 A chain homodimer Y349S/T366M/K370Y/K409V
Components
  • Fc-III peptide
  • Ig gamma-1 chain C region
KeywordsIMMUNE SYSTEM / head-to-tail homodimer / Immunoglobulin / Fc
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / 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 ...: / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
Model detailsDesign XXX
AuthorsAtwell, S. / Leaver-Fay, A. / Froning, K.J. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Dhanani, S.H. / Chamberlain, A.K. ...Atwell, S. / Leaver-Fay, A. / Froning, K.J. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Dhanani, S.H. / Chamberlain, A.K. / Fitchett, J.R. / Gutierrez, B. / Hendle, J. / Demarest, S.J. / Kuhlman, B.
CitationJournal: Structure / Year: 2016
Title: Computationally Designed Bispecific Antibodies using Negative State Repertoires.
Authors: Leaver-Fay, A. / Froning, K.J. / Atwell, S. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Hassanali, S. / Chamberlain, A.K. / Fitchett, J.R. / Demarest, S.J. / Kuhlman, B.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Data collection
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ig gamma-1 chain C region
B: Fc-III peptide


Theoretical massNumber of molelcules
Total (without water)27,1052
Polymers27,1052
Non-polymers00
Water2,522140
1
A: Ig gamma-1 chain C region
B: Fc-III peptide

A: Ig gamma-1 chain C region
B: Fc-III peptide


Theoretical massNumber of molelcules
Total (without water)54,2094
Polymers54,2094
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5150 Å2
ΔGint-34 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.502, 110.502, 57.872
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ig gamma-1 chain C region


Mass: 25570.959 Da / Num. of mol.: 1 / Fragment: UNP residues 104-330 / Mutation: Y349S, T366M, K370Y, K409V
Source method: isolated from a genetically manipulated source
Details: transient expression / Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Protein/peptide Fc-III peptide


Mass: 1533.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 4.05 Å3/Da / Density % sol: 69.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: 100mM Tris HCl pH 8.5 + 15% PEG 20K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 10, 2014 / Details: Diamond (111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.9→31.899 Å / Num. obs: 32319 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rpim(I) all: 0.047 / Rrim(I) all: 0.145 / Rsym value: 0.131 / Net I/av σ(I): 3.884 / Net I/σ(I): 10.1 / Num. measured all: 297787
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-290.74214201446900.2720.7423.299.8
2-2.129.10.4541.63998044010.1660.4544.8100
2.12-2.279.20.3271.93803541460.1190.3276.3100
2.27-2.459.30.2423.13636739020.0870.2427.9100
2.45-2.699.40.1813.83363235770.0650.1819.8100
2.69-39.40.13453070232600.0480.13412.8100
3-3.479.40.1214.82720128930.0430.12116.7100
3.47-4.259.30.09862284824480.0350.09819.5100
4.25-6.019.20.078.11771819240.0260.0721100
6.01-31.8998.60.0648.9929010780.0250.06419.897.9

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.7.0017refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
MOSFLMdata reduction
RefinementResolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.567 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 1636 5.1 %RANDOM
Rwork0.2006 ---
obs0.2017 30667 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.35 Å2 / Biso mean: 26.576 Å2 / Biso min: 14.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20.56 Å20 Å2
2--1.11 Å20 Å2
3----1.67 Å2
Refinement stepCycle: final / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 0 140 1890
Biso mean---31.67 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021814
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.9472479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7425219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38424.93881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45415294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.938156
X-RAY DIFFRACTIONr_chiral_restr0.0790.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211385
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 128 -
Rwork0.267 2239 -
all-2367 -
obs--99.66 %

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