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- PDB-4nqu: anti-parallel Fc-knob (T366W) homodimer -

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Basic information

Entry
Database: PDB / ID: 4nqu
Titleanti-parallel Fc-knob (T366W) homodimer
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / immunoglobulin
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: 2.5 Å
AuthorsEigenbrot, C. / Ultsch, M.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Antiparallel Conformation of Knob and Hole Aglycosylated Half-Antibody Homodimers Is Mediated by a CH2-CH3 Hydrophobic Interaction.
Authors: Elliott, J.M. / Ultsch, M. / Lee, J. / Tong, R. / Takeda, K. / Spiess, C. / Eigenbrot, C. / Scheer, J.M.
History
DepositionNov 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3012
Polymers24,2051
Non-polymers961
Water63135
1
A: Ig gamma-1 chain C region
hetero molecules

A: Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6034
Polymers48,4112
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3260 Å2
ΔGint-34 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.500, 44.500, 205.551
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ig gamma-1 chain C region / knob Fc T366W


Mass: 24205.400 Da / Num. of mol.: 1 / Fragment: UNP residues 118-330 / Mutation: T366W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01857
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsD356E and L358M (UNP D239E and L241M) ARE NATURAL VARIANTS.

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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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG2000 MME, 0.2 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2009
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 8852 / Num. obs: 8571 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellHighest resolution: 2.5 Å

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L6X

1l6x


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.883 / SU B: 26.061 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.656 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28689 425 5 %RANDOM
Rwork0.22232 ---
obs0.22556 8571 96.83 %-
all-9058 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.828 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20.68 Å20 Å2
2--1.35 Å20 Å2
3----2.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 5 35 1712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221726
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.9562353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5515207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19424.93577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.24715292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.525156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021309
X-RAY DIFFRACTIONr_nbd_refined0.2030.2635
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21136
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0450.22
X-RAY DIFFRACTIONr_mcbond_it2.8192.51081
X-RAY DIFFRACTIONr_mcangle_it4.3351722
X-RAY DIFFRACTIONr_scbond_it2.7522.5748
X-RAY DIFFRACTIONr_scangle_it4.2385631
LS refinement shellResolution: 2.5→2.635 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.444 55 -
Rwork0.307 1077 -
obs--89.63 %
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)
10.89420.67420.22212.3786-1.11712.36830.0973-0.14730.01980.2267-0.1232-0.06870.1322-0.02980.02590.1188-0.02590.0158-0.02330.0144-0.080922.84863.6242-14.5684
23.3987-0.7891.38261.48240.18831.27540.06630.2871-0.2390.0228-0.02260.1672-0.1130.0917-0.04380.0839-0.01560.0325-0.0906-0.0093-0.024711.58789.2942-41.4048
39.03613.29170.06826.27014.44032.80441.00151.3520.1395-0.1823-1.24732.69110.424-1.97740.24580.3355-0.35920.01390.35680.00780.171511.6938-11.5301-9.8796
413.00785.4678.66235.56766.63628.5127-0.48241.3887-1.5859-1.45460.82530.4870.83480.6726-0.34280.3294-0.1205-0.08550.0184-0.27780.27820.9423-1.4224-53.0928
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A237 - 290
2X-RAY DIFFRACTION1A302 - 341
3X-RAY DIFFRACTION2A342 - 351
4X-RAY DIFFRACTION2A363 - 444
5X-RAY DIFFRACTION3A291 - 301
6X-RAY DIFFRACTION4A352 - 362

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