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- PDB-7dc8: Crystal structure of Switch Ab Fab and hIL6R in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 7dc8
TitleCrystal structure of Switch Ab Fab and hIL6R in complex with ATP
Components
  • (Switch Ab Fab ...) x 2
  • Interleukin-6 receptor subunit alpha
KeywordsIMMUNE SYSTEM / ANTIBODY / COMPLEX / FAB / CYTOKINE
Function / homology
Function and homology information


ciliary neurotrophic factor binding / interleukin-6 receptor activity / interleukin-6 binding / hepatic immune response / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor receptor complex / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / positive regulation of activation of Janus kinase activity ...ciliary neurotrophic factor binding / interleukin-6 receptor activity / interleukin-6 binding / hepatic immune response / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor receptor complex / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / positive regulation of activation of Janus kinase activity / negative regulation of collagen biosynthetic process / T-helper 17 cell lineage commitment / positive regulation of glomerular mesangial cell proliferation / endocrine pancreas development / negative regulation of interleukin-8 production / vascular endothelial growth factor production / positive regulation of leukocyte chemotaxis / neutrophil mediated immunity / cytokine receptor activity / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / MAPK3 (ERK1) activation / monocyte chemotaxis / MAPK1 (ERK2) activation / positive regulation of osteoblast differentiation / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / response to cytokine / acute-phase response / positive regulation of smooth muscle cell proliferation / positive regulation of interleukin-6 production / cytokine-mediated signaling pathway / Transcriptional regulation of granulopoiesis / positive regulation of peptidyl-tyrosine phosphorylation / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / Potential therapeutics for SARS / positive regulation of MAPK cascade / receptor complex / defense response to Gram-positive bacterium / apical plasma membrane / external side of plasma membrane / positive regulation of cell population proliferation / enzyme binding / protein homodimerization activity / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Type I cytokine receptor, cytokine-binding domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Interleukin-6 receptor alpha chain, binding / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin / Immunoglobulin domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. ...Type I cytokine receptor, cytokine-binding domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Interleukin-6 receptor alpha chain, binding / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin / Immunoglobulin domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Interleukin-6 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.757 Å
AuthorsKadono, S. / Fukami, T.A. / Kawauchi, H. / Torizawa, T. / Mimoto, F.
CitationJournal: Cell Rep / Year: 2020
Title: Exploitation of Elevated Extracellular ATP to Specifically Direct Antibody to Tumor Microenvironment.
Authors: Mimoto, F. / Tatsumi, K. / Shimizu, S. / Kadono, S. / Haraya, K. / Nagayasu, M. / Suzuki, Y. / Fujii, E. / Kamimura, M. / Hayasaka, A. / Kawauchi, H. / Ohara, K. / Matsushita, M. / Baba, T. ...Authors: Mimoto, F. / Tatsumi, K. / Shimizu, S. / Kadono, S. / Haraya, K. / Nagayasu, M. / Suzuki, Y. / Fujii, E. / Kamimura, M. / Hayasaka, A. / Kawauchi, H. / Ohara, K. / Matsushita, M. / Baba, T. / Susumu, H. / Sakashita, T. / Muraoka, T. / Aso, K. / Katada, H. / Tanaka, E. / Nakagawa, K. / Hasegawa, M. / Ayabe, M. / Yamamoto, T. / Tanba, S. / Ishiguro, T. / Kamikawa, T. / Nambu, T. / Kibayashi, T. / Azuma, Y. / Tomii, Y. / Kato, A. / Ozeki, K. / Murao, N. / Endo, M. / Kikuta, J. / Kamata-Sakurai, M. / Ishii, M. / Hattori, K. / Igawa, T.
History
DepositionOct 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Switch Ab Fab light chain
B: Switch Ab Fab heavy chain
C: Interleukin-6 receptor subunit alpha
D: Switch Ab Fab light chain
E: Switch Ab Fab heavy chain
F: Interleukin-6 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,11718
Polymers145,1426
Non-polymers1,97512
Water1,13563
1
A: Switch Ab Fab light chain
B: Switch Ab Fab heavy chain
C: Interleukin-6 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5589
Polymers72,5713
Non-polymers9876
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Switch Ab Fab light chain
E: Switch Ab Fab heavy chain
F: Interleukin-6 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5589
Polymers72,5713
Non-polymers9876
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.043, 185.612, 152.085
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

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Protein , 1 types, 2 molecules CF

#3: Protein Interleukin-6 receptor subunit alpha / / IL-6RA / IL-6R 1 / Membrane glycoprotein 80 / gp80


Mass: 25001.795 Da / Num. of mol.: 2 / Mutation: C193S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6R / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P08887

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Antibody , 2 types, 4 molecules ADBE

#1: Antibody Switch Ab Fab light chain


Mass: 22824.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody Switch Ab Fab heavy chain


Mass: 24744.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 75 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 50.9 % / Mosaicity: 0.1 °
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 0.06 M Tris, 12.0 %(w/v) Polyethylene glycol 1500, 0.06 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.75→92.81 Å / Num. obs: 38295 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.03 / Rrim(I) all: 0.111 / Net I/σ(I): 20 / Num. measured all: 510514 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.75-2.913.30.81855220.9240.2320.85199.7
8.69-92.81120.03132810.0090.03299.9

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Processing

Software
NameVersionClassification
PHENIX1.14rc2_3184refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N26

1n26


Resolution: 2.757→90.091 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.46
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2779 1957 5.15 %
Rwork0.2071 --
obs0.2107 37987 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.4 Å2 / Biso mean: 58.3162 Å2 / Biso min: 22.29 Å2
Refinement stepCycle: final / Resolution: 2.757→90.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9063 0 112 63 9238
Biso mean--59.56 42.58 -
Num. residues----1212
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.757-2.82540.36711240.2572565100
2.8254-2.90180.28271240.24342558100
2.9018-2.98720.3331480.24232519100
2.9872-3.08370.30441560.24642521100
3.0837-3.19390.31791600.23772540100
3.1939-3.32180.32831400.23492568100
3.3218-3.47290.30691640.22422494100
3.4729-3.65610.26421130.20712596100
3.6561-3.88510.31321520.21022537100
3.8851-4.18510.25481660.18832551100
4.1851-4.60620.22891280.16492606100
4.6062-5.27270.2412990.16372627100
5.2727-6.64280.26111340.21532637100
6.6428-90.0910.26681490.2243271199

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