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- PDB-4nqs: Knob-into-hole IgG Fc -

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Basic information

Entry
Database: PDB / ID: 4nqs
TitleKnob-into-hole IgG Fc
Components
  • (Ig gamma-1 chain C region) x 2
  • miniZ
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 / 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)
Staphylococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
D: miniZ
E: miniZ
G: Ig gamma-1 chain C region
H: Ig gamma-1 chain C region
I: miniZ
J: miniZ


Theoretical massNumber of molelcules
Total (without water)113,1748
Polymers113,1748
Non-polymers00
Water21612
1
A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region
D: miniZ
E: miniZ


Theoretical massNumber of molelcules
Total (without water)56,5874
Polymers56,5874
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-21 kcal/mol
Surface area24740 Å2
MethodPISA
2
G: Ig gamma-1 chain C region
H: Ig gamma-1 chain C region
I: miniZ
J: miniZ


Theoretical massNumber of molelcules
Total (without water)56,5874
Polymers56,5874
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-20 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.238, 66.083, 102.896
Angle α, β, γ (deg.)90.00, 95.18, 90.00
Int Tables number4
Space group name H-MP1211

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


Mass: 24205.400 Da / Num. of mol.: 2 / 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
#3: Protein/peptide
miniZ


Mass: 4190.682 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Staphylococcus (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG2000 MME, 10% 2-propanol, 0.1 M MES, 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: 5.0.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2009
RadiationMonochromator: liquid nitrogen cooled dual crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. all: 30484 / Num. obs: 30472 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.12 Å2
Reflection shellHighest resolution: 2.64 Å

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
BUSTER2.11.4refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L6X

1l6x


Resolution: 2.64→46.5 Å / Cor.coef. Fo:Fc: 0.8939 / Cor.coef. Fo:Fc free: 0.8583 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.859 / SU Rfree Blow DPI: 0.345 / Stereochemistry target values: maxIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 961 3.15 %RANDOM
Rwork0.2286 ---
obs0.2298 30472 97.01 %-
all-30488 --
Displacement parametersBiso mean: 51.74 Å2
Baniso -1Baniso -2Baniso -3
1--3.6512 Å20 Å29.5724 Å2
2--4.9548 Å20 Å2
3----1.3036 Å2
Refine analyzeLuzzati coordinate error obs: 0.458 Å
Refinement stepCycle: LAST / Resolution: 2.64→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7820 0 0 12 7832
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088034HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9910914HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2780SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes228HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1120HARMONIC5
X-RAY DIFFRACTIONt_it8034HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion19.23
X-RAY DIFFRACTIONt_chiral_improper_torsion1009SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8581SEMIHARMONIC4
LS refinement shellResolution: 2.64→2.73 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3367 73 3.32 %
Rwork0.2649 2127 -
all0.2672 2200 -
obs--97.01 %
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)
1-0.06651.0060.46030.8921-0.4028.46780.008-0.5411-0.06770.3524-0.0847-0.09520.13560.03350.0767-0.2260.1448-0.04260.3040.0044-0.1621-49.28479.9714-33.8623
22.01970.55830.35941.80210.7714.8445-0.0372-0.29880.15510.1333-0.12540.3673-0.103-0.53350.1626-0.12660.01960.0007-0.0803-0.0255-0.0198-16.266227.7342-25.9996
32.74780.4382.15420.33230.05450.368-0.00720.2568-0.0601-0.2987-0.07290.4406-0.1375-0.37650.0802-0.17210.0768-0.06710.3040.0495-0.1124-21.59638.1727.349
43.69620.62650.87912.3710.79623.33180.047-0.33140.02420.3769-0.05280.22240.1431-0.49020.0059-0.06860.02790.05-0.08210.009-0.1228-16.5859-7.0029-26.7288
54.20840.03140.43991.67-0.06063.3141-0.1320.156-0.145-0.38420.15480.08490.30440.137-0.0228-0.0576-0.0094-0.031-0.10710.0109-0.1099-31.256310.3708-60.3546
64.7181-0.81651.64262.8425-1.91314.4524-0.06270.4730.2574-0.21150.0934-0.0559-0.0298-0.0628-0.0307-0.07310.00150.0093-0.1324-0.0513-0.0729-17.539919.6848-57.0409
73.6924-0.2095-0.45232.9092-1.16196.5870.00330.01870.31280.16330.1216-0.2507-0.17190.1152-0.1248-0.09860.0265-0.0483-0.1868-0.0062-0.10029.747110.3408-0.2074
82.1564-0.75970.75181.6512-0.05964.9587-0.0267-0.03430.11280.09460.1043-0.23140.28260.5427-0.0776-0.0773-0.019-0.0368-0.0706-0.0226-0.033711.7851.0419-14.1753
92.4464-1.8522.13130.964-1.14961.2070.03920.0808-0.2310.03150.0239-0.03530.0173-0.0586-0.0631-0.0561-0.0202-0.0255-0.10150.04680.1234-58.976511.3372-58.6537
106.5005-0.3703-1.30051.17330.26124.6516-0.0469-0.02690.0846-0.0420.0401-0.1297-0.04850.16150.0067-0.1242-0.01580.00370.0026-0.01160.01075.062622.7046-41.4123
110.05251.01961.66381.1838-0.82663.56890.0386-0.04370.0058-0.0690.02420.0141-0.27830.0133-0.06280.11960.04570.0136-0.1399-0.0066-0.0199-1.76559.424725.0583
123.98631.2055-2.10351.14121.05554.2276-0.0150.1529-0.0841-0.10020.0204-0.12970.15810.0469-0.0054-0.02660.01670.038-0.0429-0.0562-0.03565.6921-1.8923-40.9187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|235 - A|341}A235 - 341
2X-RAY DIFFRACTION2{B|237 - B|341}B237 - 341
3X-RAY DIFFRACTION3{G|237 - G|341}G237 - 341
4X-RAY DIFFRACTION4{H|237 - H|341}H237 - 341
5X-RAY DIFFRACTION5{A|342 - A|444}A342 - 444
6X-RAY DIFFRACTION6{B|342 - B|443}B342 - 443
7X-RAY DIFFRACTION7{G|342 - G|444}G342 - 444
8X-RAY DIFFRACTION8{H|342 - H|443}H342 - 443
9X-RAY DIFFRACTION9{D|6 - D|39}D6 - 39
10X-RAY DIFFRACTION10{E|6 - E|39}E6 - 39
11X-RAY DIFFRACTION11{I|6 - I|39}I6 - 39
12X-RAY DIFFRACTION12{J|6 - J|39}J6 - 39

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