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- PDB-4nqt: anti-parallel Fc-hole(T366S/L368A/Y407V) homodimer -

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Basic information

Entry
Database: PDB / ID: 4nqt
Titleanti-parallel Fc-hole(T366S/L368A/Y407V) homodimer
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / immunoglobulin
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / 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/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: 2.1 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ig gamma-1 chain C region


Theoretical massNumber of molelcules
Total (without water)24,0001
Polymers24,0001
Non-polymers00
Water1,910106
1
A: Ig gamma-1 chain C region

A: Ig gamma-1 chain C region


Theoretical massNumber of molelcules
Total (without water)48,0002
Polymers48,0002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2570 Å2
ΔGint-10 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.468, 44.478, 68.895
Angle α, β, γ (deg.)90.00, 106.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-559-

HOH

21A-594-

HOH

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Components

#1: Protein Ig gamma-1 chain C region / hole Fc T366S/L368A/Y407V


Mass: 24000.146 Da / Num. of mol.: 1 / Fragment: UNP residues 118-330 / Mutation: T366S/L368A/Y407V
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 25% PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 23, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→38 Å / Num. all: 13006 / Num. obs: 12855 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellHighest resolution: 2.1 Å

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L6X

1l6x


Resolution: 2.1→37.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.412 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25284 905 7 %RANDOM
Rwork0.19407 ---
obs0.19824 11950 99.26 %-
all-13006 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.057 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å2-0 Å2-0.51 Å2
2--1.15 Å20 Å2
3---0.43 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 0 106 1762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191703
X-RAY DIFFRACTIONr_bond_other_d0.0070.021594
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.9562320
X-RAY DIFFRACTIONr_angle_other_deg0.7573.0023698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1335207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85125.06775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4315290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.219156
X-RAY DIFFRACTIONr_chiral_restr0.0620.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211901
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02369
LS refinement shellResolution: 2.1→2.213 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.304 126 -
Rwork0.237 1727 -
obs--99.14 %
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)
11.9560.21990.37710.69170.04310.9143-0.06660.2374-0.0529-0.08750.0789-0.02310.00640.0363-0.01230.0983-0.03180.03640.0686-0.00710.01581.8852-0.649-20.1234
21.1540.21020.53332.0597-0.31821.37130.1234-0.0503-0.16410.1169-0.03130.06770.0592-0.0648-0.0920.0808-0.01080.00750.00470.00530.09857.8398-11.38398.4953
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A237 - 340
2X-RAY DIFFRACTION2A341 - 444

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