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Basic information

Entry
Database: PDB / ID: 6kn9
TitleCrystal structure of human interleukin 18 receptor beta extracellular domain in complex with an antagonistic scFv
Components
  • Interleukin-18 receptor accessory protein
  • scFv
KeywordsCYTOKINE / Interleukin receptor / antibody / complex / antagonist
Function / homology
Function and homology information


interleukin-18 receptor activity / interleukin-18 receptor complex / Interleukin-18 signaling / positive regulation of natural killer cell mediated cytotoxicity / interleukin-18-mediated signaling pathway / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / neutrophil activation / NAD+ nucleotidase, cyclic ADP-ribose generating / coreceptor activity ...interleukin-18 receptor activity / interleukin-18 receptor complex / Interleukin-18 signaling / positive regulation of natural killer cell mediated cytotoxicity / interleukin-18-mediated signaling pathway / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / neutrophil activation / NAD+ nucleotidase, cyclic ADP-ribose generating / coreceptor activity / cellular response to hydrogen peroxide / positive regulation of NF-kappaB transcription factor activity / cell population proliferation / inflammatory response / immune response / plasma membrane
Similarity search - Function
IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / Immunoglobulin domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin subtype ...IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / Immunoglobulin domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-18 receptor accessory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.302 Å
AuthorsWu, D.H. / Liu, C.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (China)81572698 China
National Science Foundation (China)31771006 China
CitationJournal: J.Mol.Biol. / Year: 2020
Title: A Synthetic Human Antibody Antagonizes IL-18R beta Signaling Through an Allosteric Mechanism.
Authors: Liu, S. / Miersch, S. / Li, P. / Bai, B.X, / Liu, C.C. / Qin, W.M. / Su, J. / Huang, H.M. / Pan, J. / Sidhu, S.S. / Wu, D.H.
History
DepositionAug 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-18 receptor accessory protein
B: Interleukin-18 receptor accessory protein
C: Interleukin-18 receptor accessory protein
D: scFv
E: scFv
F: scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,0989
Polymers197,2316
Non-polymers8673
Water00
1
A: Interleukin-18 receptor accessory protein
D: scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9653
Polymers65,7442
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-4 kcal/mol
Surface area23940 Å2
MethodPISA
2
B: Interleukin-18 receptor accessory protein
E: scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1683
Polymers65,7442
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-1 kcal/mol
Surface area21840 Å2
MethodPISA
3
C: Interleukin-18 receptor accessory protein
F: scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9653
Polymers65,7442
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-1 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.160, 163.160, 64.145
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 29 through 30 or (resid 31...
21(chain C and (resid 29 through 31 or (resid 32...
12(chain D and ((resid 1 and (name N or name...
22(chain F and (resid 1 through 84 or (resid 86...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSLEULEU(chain A and (resid 29 through 30 or (resid 31...AA29 - 3010 - 11
121LEULEULEULEU(chain A and (resid 29 through 30 or (resid 31...AA3112
131LYSLYSLYSLYS(chain A and (resid 29 through 30 or (resid 31...AA28 - 3559 - 336
141LYSLYSLYSLYS(chain A and (resid 29 through 30 or (resid 31...AA28 - 3559 - 336
151LYSLYSLYSLYS(chain A and (resid 29 through 30 or (resid 31...AA28 - 3559 - 336
161LYSLYSLYSLYS(chain A and (resid 29 through 30 or (resid 31...AA28 - 3559 - 336
211LYSLYSLEULEU(chain C and (resid 29 through 31 or (resid 32...CC29 - 3110 - 12
221TRPTRPTRPTRP(chain C and (resid 29 through 31 or (resid 32...CC3213
231LYSLYSARGARG(chain C and (resid 29 through 31 or (resid 32...CC29 - 35610 - 337
241LYSLYSARGARG(chain C and (resid 29 through 31 or (resid 32...CC29 - 35610 - 337
251LYSLYSARGARG(chain C and (resid 29 through 31 or (resid 32...CC29 - 35610 - 337
261LYSLYSARGARG(chain C and (resid 29 through 31 or (resid 32...CC29 - 35610 - 337
271LYSLYSARGARG(chain C and (resid 29 through 31 or (resid 32...CC29 - 35610 - 337
281LYSLYSARGARG(chain C and (resid 29 through 31 or (resid 32...CC29 - 35610 - 337
291LYSLYSARGARG(chain C and (resid 29 through 31 or (resid 32...CC29 - 35610 - 337
2101LYSLYSARGARG(chain C and (resid 29 through 31 or (resid 32...CC29 - 35610 - 337
112GLUGLUGLUGLU(chain D and ((resid 1 and (name N or name...DD16
122GLYGLYVALVAL(chain D and ((resid 1 and (name N or name...DD-4 - 2471 - 252
132GLYGLYVALVAL(chain D and ((resid 1 and (name N or name...DD-4 - 2471 - 252
142GLYGLYVALVAL(chain D and ((resid 1 and (name N or name...DD-4 - 2471 - 252
152GLYGLYVALVAL(chain D and ((resid 1 and (name N or name...DD-4 - 2471 - 252
212GLUGLUASNASN(chain F and (resid 1 through 84 or (resid 86...FF1 - 846 - 89
222LEULEUGLUGLU(chain F and (resid 1 through 84 or (resid 86...FF86 - 8991 - 94
232GLUGLUARGARG(chain F and (resid 1 through 84 or (resid 86...FF1 - 2516 - 256
242GLUGLUARGARG(chain F and (resid 1 through 84 or (resid 86...FF1 - 2516 - 256
252GLUGLUARGARG(chain F and (resid 1 through 84 or (resid 86...FF1 - 2516 - 256
262GLUGLUARGARG(chain F and (resid 1 through 84 or (resid 86...FF1 - 2516 - 256

NCS ensembles :
ID
1
2

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Components

#1: Protein Interleukin-18 receptor accessory protein / IL-18RAcP / Accessory protein-like / AcPL / CD218 antigen-like family member B / CDw218b / IL-1R ...IL-18RAcP / Accessory protein-like / AcPL / CD218 antigen-like family member B / CDw218b / IL-1R accessory protein-like / IL-1RAcPL / Interleukin-1 receptor 7 / IL-1R7 / Interleukin-18 receptor accessory protein-like / Interleukin-18 receptor beta / IL-18Rbeta


Mass: 38495.781 Da / Num. of mol.: 3 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18RAP, IL1R7
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: O95256
#2: Antibody scFv


Mass: 27247.980 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium iodide, 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 28309 / % possible obs: 98.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 45.95 Å2 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.071 / Rrim(I) all: 0.134 / Χ2: 0.908 / Net I/σ(I): 7.7 / Num. measured all: 96462
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.4230.65227430.5580.450.7960.88495.3
3.42-3.553.30.55628350.6940.350.660.92799.4
3.55-3.723.50.46228860.7990.2830.5440.97199.3
3.72-3.913.50.3428400.8680.2060.3990.98299.2
3.91-4.163.30.21528170.9330.1370.2560.9298.2
4.16-4.483.60.13928390.9740.0830.1630.92499.8
4.48-4.933.60.09928930.9830.0590.1150.87799.6
4.93-5.643.40.08828000.9820.0550.1040.89497.7
5.64-7.13.60.08128490.9860.0480.0950.87899.5
7.1-503.30.06128070.9880.0420.0750.81697.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WO4, 3PNW

3wo4

3pnw


Resolution: 3.302→39.19 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 30.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2769 1204 4.83 %
Rwork0.2469 23719 -
obs0.2484 24923 86.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.61 Å2 / Biso mean: 50.0901 Å2 / Biso min: 8.97 Å2
Refinement stepCycle: final / Resolution: 3.302→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9712 0 56 0 9768
Biso mean--64.5 --
Num. residues----1320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119970
X-RAY DIFFRACTIONf_angle_d1.37613554
X-RAY DIFFRACTIONf_chiral_restr0.0631593
X-RAY DIFFRACTIONf_plane_restr0.0091678
X-RAY DIFFRACTIONf_dihedral_angle_d12.2715818
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2108X-RAY DIFFRACTION14.918TORSIONAL
12C2108X-RAY DIFFRACTION14.918TORSIONAL
21D1723X-RAY DIFFRACTION14.918TORSIONAL
22F1723X-RAY DIFFRACTION14.918TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3022-3.42010.3988500.3314104538
3.4201-3.5570.2971890.2819198772
3.557-3.71870.29861130.257240087
3.7187-3.91460.25121400.2443247892
3.9146-4.15960.27851300.235251092
4.1596-4.48040.24041030.2089268198
4.4804-4.93050.22891810.1968268198
4.9305-5.64210.26591290.2256263997
5.6421-7.10160.29071550.287268199
7.1016-39.190.33351140.279261795

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