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- PDB-8ywp: Crystal structure of the Fab fragment of anti-IL-6 antibody I9H -

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Basic information

Entry
Database: PDB / ID: 8ywp
TitleCrystal structure of the Fab fragment of anti-IL-6 antibody I9H
Components
  • Heavy chain of the Fab fragment of anti-IL-6 antibody I9H
  • Light chain of the Fab fragment of anti-IL-6 antibody I9H
KeywordsIMMUNE SYSTEM / interleukin / dimer / swap
Function / homologyTRIETHYLENE GLYCOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYudenko, A. / Bukhdruker, S. / Eliseev, I. / Rodin, S. / Burtseva, A. / Petrov, A. / Zlobina, O. / Ischenko, A. / Borshchevskiy, V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Education and Science of the Russian Federation075-15-2021-1354 Russian Federation
CitationJournal: Structure / Year: 2025
Title: Structural basis of signaling complex inhibition by IL-6 domain-swapped dimers
Authors: Yudenko, A. / Bukhdruker, S. / Shishkin, P. / Rodin, S. / Burtseva, A. / Petrov, A. / Pigareva, N. / Sokolov, A. / Zinovev, E. / Eliseev, I. / Remeeva, A. / Marin, E. / Mishin, A. / Godeliy, ...Authors: Yudenko, A. / Bukhdruker, S. / Shishkin, P. / Rodin, S. / Burtseva, A. / Petrov, A. / Pigareva, N. / Sokolov, A. / Zinovev, E. / Eliseev, I. / Remeeva, A. / Marin, E. / Mishin, A. / Godeliy, V. / Gushchin, I. / Ischenko, A. / Borshchevskiy, V.
History
DepositionMar 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain of the Fab fragment of anti-IL-6 antibody I9H
L: Light chain of the Fab fragment of anti-IL-6 antibody I9H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6435
Polymers48,3092
Non-polymers3343
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-22 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.360, 126.360, 143.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11H-353-

HOH

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Components

#1: Antibody Heavy chain of the Fab fragment of anti-IL-6 antibody I9H


Mass: 24912.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-IL69hum
#2: Antibody Light chain of the Fab fragment of anti-IL-6 antibody I9H


Mass: 23396.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-IL69hum
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.42 Å3/Da / Density % sol: 64.03 % / Description: bipyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris-HCl, 20% PEG 20000 / PH range: 8.6 - 8.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.542 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.5→47.8 Å / Num. obs: 23296 / % possible obs: 97.1 % / Redundancy: 23.8 % / Biso Wilson estimate: 42.4 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.06 / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1423 / CC1/2: 0.131 / Rpim(I) all: 1.766 / % possible all: 84.7

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Processing

Software
NameVersionClassification
XDS20190315data reduction
XSCALE20190315data scaling
PHASER2.8.3phasing
PHENIX1.18_3855refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YK4

4yk4


Resolution: 2.5→47.79 Å / SU ML: 0.4158 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.2285
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2847 1965 8.57 %
Rwork0.258 20962 -
obs0.2603 22927 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.65 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 19 136 3493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223445
X-RAY DIFFRACTIONf_angle_d0.5874694
X-RAY DIFFRACTIONf_chiral_restr0.0419534
X-RAY DIFFRACTIONf_plane_restr0.0042595
X-RAY DIFFRACTIONf_dihedral_angle_d14.00611224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.3761070.36381118X-RAY DIFFRACTION72.87
2.56-2.630.41061210.35111318X-RAY DIFFRACTION85.6
2.63-2.710.36581400.34561502X-RAY DIFFRACTION98.5
2.71-2.80.35911450.31971533X-RAY DIFFRACTION99.76
2.8-2.90.32611450.29211541X-RAY DIFFRACTION99.94
2.9-3.010.33441440.27721542X-RAY DIFFRACTION100
3.01-3.150.33391440.28851532X-RAY DIFFRACTION99.94
3.15-3.320.30691460.2791556X-RAY DIFFRACTION100
3.32-3.520.32341460.2811543X-RAY DIFFRACTION98.95
3.52-3.80.3321280.33721363X-RAY DIFFRACTION87.45
3.8-4.180.26911400.25781488X-RAY DIFFRACTION94.87
4.18-4.780.18771480.18031597X-RAY DIFFRACTION99.89
4.78-6.020.24111520.18661606X-RAY DIFFRACTION99.83
6.02-47.790.22951590.21271723X-RAY DIFFRACTION99.21
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)
10.891157083435-0.8355609559680.3541829166231.98087864347-0.1055752002891.45707239148-0.0203896552836-0.203456996752-0.06415672069390.0127650266630.01310981994280.1954022377-0.0996599871162-0.2560947436050.002610975232720.1763487519190.01335230831260.005845161398010.458709495631-0.0006338083149350.33931737218711.741501289946.919351883582.1093993607
20.838641484790.54058951955-0.5705767765331.712949831560.4039673264820.8156370276140.02488509896960.09271252411040.0140329077608-0.167288185424-0.08576365421950.002373252552240.0853126140314-0.129962575181-1.72847818742E-50.2982030019560.000277153516637-0.01425977798470.337849315545-0.003194424698240.30255492971734.31487263229.631741603564.9008932182
31.39917072929-0.04140513722830.3852847195480.778862135569-0.3633436634970.997740247990.0491614838326-0.0651251466236-0.0008447319553710.116708012256-0.004397760334190.016514020434-0.0832838876936-0.210001750083-1.21627313617E-50.3652150922190.04075011695950.02565408930360.473918387980.0004534632352220.32359375943324.629792386439.875789832698.147796227
40.9989182804880.146090792488-0.9779059172530.09473695218410.1199651056481.462860238160.06637468822320.1111064318340.0991826372723-0.0913624046288-0.00500131026656-0.07732226609040.230948420820.1089013583082.76283446965E-50.332756962340.06532787035380.01923158737910.3799309957920.05124161521760.36147891000948.835394489633.137195652170.2865348039
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain H and resid 1:124)HA1 - 1241 - 124
22(chain H and resid 125:231)HA125 - 231125 - 226
33(chain L and resid 1:107)LE1 - 1071 - 108
44(chain L and resid 108:214)LE108 - 214109 - 215

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