[English] 日本語
Yorodumi
- PDB-8ywp: Crystal structure of the Fab fragment of anti-IL-6 antibody I9H -

+
Open data


ID or keywords:

Loading...

-
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. / ...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. / Gordeliy, 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
Revision 1.1Dec 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 15, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more