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- PDB-5v43: Engineered human IgG Fc domain aglyco801 -

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Basic information

Entry
Database: PDB / ID: 5v43
TitleEngineered human IgG Fc domain aglyco801
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / antibody engineering / Fc fragment
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / 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 / 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 / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsYan, W. / Marshall, N. / Zhang, Y.J.
CitationJournal: Nat. Immunol. / Year: 2017
Title: IgG Fc domains that bind C1q but not effector Fc gamma receptors delineate the importance of complement-mediated effector functions.
Authors: Lee, C.H. / Romain, G. / Yan, W. / Watanabe, M. / Charab, W. / Todorova, B. / Lee, J. / Triplett, K. / Donkor, M. / Lungu, O.I. / Lux, A. / Marshall, N. / Lindorfer, M.A. / Goff, O.R. / ...Authors: Lee, C.H. / Romain, G. / Yan, W. / Watanabe, M. / Charab, W. / Todorova, B. / Lee, J. / Triplett, K. / Donkor, M. / Lungu, O.I. / Lux, A. / Marshall, N. / Lindorfer, M.A. / Goff, O.R. / Balbino, B. / Kang, T.H. / Tanno, H. / Delidakis, G. / Alford, C. / Taylor, R.P. / Nimmerjahn, F. / Varadarajan, N. / Bruhns, P. / Zhang, Y.J. / Georgiou, G.
History
DepositionMar 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support

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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: Ig gamma-1 chain C region


Theoretical massNumber of molelcules
Total (without water)50,9862
Polymers50,9862
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-16 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.260, 66.260, 370.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

DetailsDimer as determined by gel filtration

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Components

#1: Protein Ig gamma-1 chain C region


Mass: 25492.828 Da / Num. of mol.: 2 / Fragment: residues 104-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 50 mM sodium citrate pH 5.0 0.44 M NaCl 24% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.32→40 Å / Num. obs: 22297 / % possible obs: 100 % / Redundancy: 9.2 % / Net I/σ(I): 25.625
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1090 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→38.915 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.97
RfactorNum. reflection% reflection
Rfree0.2253 1943 4.93 %
Rwork0.1954 --
obs0.1969 22162 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.32→38.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 0 84 3370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023381
X-RAY DIFFRACTIONf_angle_d0.554608
X-RAY DIFFRACTIONf_dihedral_angle_d16.3732058
X-RAY DIFFRACTIONf_chiral_restr0.044504
X-RAY DIFFRACTIONf_plane_restr0.004594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3199-2.37790.31321490.27462663X-RAY DIFFRACTION99
2.3779-2.44220.30081240.24782735X-RAY DIFFRACTION100
2.4422-2.51410.28431350.23542631X-RAY DIFFRACTION100
2.5141-2.59520.261410.23562685X-RAY DIFFRACTION100
2.5952-2.68790.29771280.22692680X-RAY DIFFRACTION100
2.6879-2.79550.29431290.22742689X-RAY DIFFRACTION100
2.7955-2.92270.28571120.24062708X-RAY DIFFRACTION100
2.9227-3.07670.27761330.2442672X-RAY DIFFRACTION100
3.0767-3.26940.24851450.22012681X-RAY DIFFRACTION100
3.2694-3.52170.21711610.20162650X-RAY DIFFRACTION100
3.5217-3.87580.21291290.18562689X-RAY DIFFRACTION100
3.8758-4.4360.20281470.15572668X-RAY DIFFRACTION100
4.436-5.58620.15311620.14292631X-RAY DIFFRACTION100
5.5862-38.92080.23121480.19252675X-RAY DIFFRACTION100
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)
12.81820.93070.39095.0090.9723.02890.3298-0.37270.1084-0.0561-0.11130.3801-0.7908-0.1304-0.15330.4096-0.16090.11380.6119-0.07020.449944.19950.7153-22.8083
27.38113.32640.71322.72192.17697.4291-0.4778-0.2690.37870.3225-0.28960.8693-0.91360.01580.63040.9621-0.33690.23720.7142-0.2550.660652.774822.147-18.0406
32.14291.0421-0.30463.59850.11322.36270.3701-0.45180.14540.4202-0.1952-0.0961-0.38960.2518-0.26470.4244-0.21070.09450.5957-0.15530.468153.05915.3581-20.4774
48.0599-0.30650.08243.15110.10893.05060.0895-0.2618-0.7170.0695-0.19950.38320.1575-0.38090.12860.3003-0.10380.07660.2736-0.11470.234620.1953-14.1305-18.1594
53.9302-0.84610.74931.7025-0.08382.7317-0.03840.4602-0.08120.0066-0.1995-0.05450.1535-0.04290.26560.24-0.04990.0720.3512-0.09050.367624.02-13.3011-23.7081
61.20412.2321.53775.63650.36066.486-0.06060.6036-0.5728-0.256-0.60330.4041-0.04270.23210.35720.5735-0.07-0.02340.99840.01340.683221.132514.9578-11.9997
76.7324-1.5542.37416.125-2.62295.66470.36991.12730.3222-0.76350.08340.02520.64391.5391-0.31270.9634-0.21070.07991.7292-0.03390.914732.66919.4183-13.5023
86.2971-0.70022.70135.1943-0.14225.1172-0.30150.34010.6024-0.2386-0.06680.1916-0.54770.09260.25160.7408-0.0430.03470.81710.02090.797824.661520.1395-10.0779
94.50871.86791.44952.20121.10571.8828-0.62271.87330.4337-0.81530.5212-0.1469-0.53831.23730.08690.814-0.1842-0.06251.32450.09740.621221.200517.5946-20.6777
102.46240.0223-0.41063.8748-0.75723.8861-0.1434-0.1546-0.03340.3657-0.05660.21310.0132-0.23470.16550.3095-0.03270.04780.3822-0.13560.372614.5551-8.4581-8.6984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 236:263)
2X-RAY DIFFRACTION2(chain A and resid 264:271)
3X-RAY DIFFRACTION3(chain A and resid 272:338)
4X-RAY DIFFRACTION4(chain A and resid 339:362)
5X-RAY DIFFRACTION5(chain A and resid 363:444)
6X-RAY DIFFRACTION6(chain B and resid 236:267)
7X-RAY DIFFRACTION7(chain B and resid 268:279)
8X-RAY DIFFRACTION8(chain B and resid 280:312)
9X-RAY DIFFRACTION9(chain B and resid 313:344)
10X-RAY DIFFRACTION10(chain B and resid 345:444)

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