[English] 日本語
Yorodumi
- PDB-6hg4: Crystal Structure of the human IL-17RC ECD in complex with human ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hg4
TitleCrystal Structure of the human IL-17RC ECD in complex with human IL-17F
Components
  • Interleukin-17 receptor C
  • Interleukin-17F
KeywordsIMMUNE SYSTEM / Cystine-knot / FnIII domains / receptor-cytokine complex
Function / homology
Function and homology information


regulation of granulocyte macrophage colony-stimulating factor production / regulation of interleukin-2 production / interleukin-17 receptor activity / positive regulation of lymphotoxin A production / granulocyte chemotaxis / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / interleukin-17A-mediated signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production ...regulation of granulocyte macrophage colony-stimulating factor production / regulation of interleukin-2 production / interleukin-17 receptor activity / positive regulation of lymphotoxin A production / granulocyte chemotaxis / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / interleukin-17A-mediated signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / regulation of transforming growth factor beta receptor signaling pathway / cytokine receptor binding / positive regulation of cytokine production involved in inflammatory response / cartilage development / regulation of interleukin-6 production / cytokine binding / defense response to fungus / coreceptor activity / negative regulation of angiogenesis / positive regulation of cytokine production / cytokine activity / positive regulation of interleukin-6 production / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / inflammatory response / protein heterodimerization activity / innate immune response / signaling receptor binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Interleukin-17 receptor C/E, N-terminal / Interleukin-17 receptor extracellular region / Interleukin-17 receptor-like / SEFIR domain / SEFIR domain / SEFIR domain profile. / Interleukin-17, chordata / Interleukin-17 family / Interleukin-17 / Cystine Knot Cytokines, subunit B ...Interleukin-17 receptor C/E, N-terminal / Interleukin-17 receptor extracellular region / Interleukin-17 receptor-like / SEFIR domain / SEFIR domain / SEFIR domain profile. / Interleukin-17, chordata / Interleukin-17 family / Interleukin-17 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Interleukin-17 receptor C / Interleukin-17F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsRondeau, J.M. / Goepfert, A.
CitationJournal: Immunity / Year: 2020
Title: Structural Analysis Reveals that the Cytokine IL-17F Forms a Homodimeric Complex with Receptor IL-17RC to Drive IL-17RA-Independent Signaling.
Authors: Goepfert, A. / Lehmann, S. / Blank, J. / Kolbinger, F. / Rondeau, J.M.
History
DepositionAug 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interleukin-17F
B: Interleukin-17 receptor C


Theoretical massNumber of molelcules
Total (without water)66,1502
Polymers66,1502
Non-polymers00
Water00
1
A: Interleukin-17F
B: Interleukin-17 receptor C

A: Interleukin-17F
B: Interleukin-17 receptor C


Theoretical massNumber of molelcules
Total (without water)132,3004
Polymers132,3004
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+11
Buried area12470 Å2
ΔGint-53 kcal/mol
Surface area52160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.322, 154.322, 78.792
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

-
Components

#1: Protein Interleukin-17F / IL-17F / Cytokine ML-1


Mass: 15695.895 Da / Num. of mol.: 1 / Fragment: IL-17F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17F / Plasmid: pCI-derived / Cell line (production host): HEK293S GnTi- / Production host: Homo sapiens (human) / References: UniProt: Q96PD4
#2: Protein Interleukin-17 receptor C / IL-17RC / Interleukin-17 receptor homolog / IL17Rhom / Interleukin-17 receptor-like protein / IL- ...IL-17RC / Interleukin-17 receptor homolog / IL17Rhom / Interleukin-17 receptor-like protein / IL-17RL / ZcytoR14


Mass: 50454.312 Da / Num. of mol.: 1 / Mutation: N186Q, N226Q, N253Q, N263Q, N349Q, N372Q, N406Q
Source method: isolated from a genetically manipulated source
Details: Q307R variant with the following N-glycosylation site mutations: ,N186Q, N226Q, N253Q, N263Q, N349Q, N372Q, N406Q
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17RC, UNQ6118/PRO20040/PRO38901 / Plasmid: pCI-derived / Cell line (production host): HEK293S GnTi- / Production host: Homo sapiens (human) / References: UniProt: Q8NAC3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.96 % / Mosaicity: 0.21 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 200mM ammonium citrate tribasic, 20.0% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99994 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 3.32→133.66 Å / Num. obs: 16301 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 23.5 % / Biso Wilson estimate: 125.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.038 / Rrim(I) all: 0.185 / Net I/σ(I): 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.32-3.518.23.75723480.4540.8993.865100
10.49-133.6621.50.0515710.9990.0120.05399.9

-
Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
BUSTERrefinement
PDB_EXTRACT3.24data extraction
XDSAutoprocdata reduction
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jpy

1jpy


Resolution: 3.32→78.79 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.853 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.391
RfactorNum. reflection% reflectionSelection details
Rfree0.239 815 5 %RANDOM
Rwork0.198 ---
obs0.2 16293 99.9 %-
Displacement parametersBiso max: 273.63 Å2 / Biso mean: 164.64 Å2 / Biso min: 78.74 Å2
Baniso -1Baniso -2Baniso -3
1-20.8557 Å20 Å20 Å2
2--20.8557 Å20 Å2
3----41.7114 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: final / Resolution: 3.32→78.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 0 0 4176
Num. residues----531
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1444SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes720HARMONIC5
X-RAY DIFFRACTIONt_it4294HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion545SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4498SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4294HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5881HARMONIC21.26
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion22.49
LS refinement shellResolution: 3.32→3.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3039 146 5.01 %
Rwork0.2429 2767 -
all0.2459 2913 -
obs--99.69 %
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)
17.62740.64510.94133.25040.94994.2405-0.07040.3684-0.1411-0.28960.2387-1.18510.13250.8974-0.1683-0.25640.00260.1060.1190.0299-0.4616-32.0443129.350536.7455
27.21732.38221.32785.3442-0.05254.3237-0.10850.1510.708-0.77960.0011-0.4841-0.51940.49110.10730.00820.04620.1941-0.00480.0555-0.5519-45.5992134.83614.8126
32.69381.22820.01566.5483-0.987811.4292-0.24640.44640.7157-0.3741-0.0541-0.1758-0.73660.16580.3004-0.7769-0.17260.2270.2580.55240.6963-6.3266154.230724.7676
423.7908-11.1412-1.62038.5783-3.00240-0.0007-0.10951.10980.27060.79221.14660.2877-0.9466-0.7915-0.6243-0.04010.14390.13040.00930.351523.7437142.553423.9632
58.8282-1.55310.411511.30495.33857.9938-0.0012-0.62440.98420.3248-0.03440.1151-0.26140.11880.0356-0.29610.080.0562-0.0937-0.0631-0.264546.8678136.162522.3616
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 161
2X-RAY DIFFRACTION2B21 - 207
3X-RAY DIFFRACTION3B208 - 292
4X-RAY DIFFRACTION4B293 - 387
5X-RAY DIFFRACTION5B388 - 465

+
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://pdbjlvh1.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