[English] 日本語
Yorodumi
- PDB-8xwy: Structure of Interleukin-27 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xwy
TitleStructure of Interleukin-27
Components
  • Interleukin-27 subunit alpha
  • Interleukin-27 subunit beta
KeywordsIMMUNE SYSTEM / CYTOKINE / Interleukin
Function / homology
Function and homology information


interleukin-27 receptor binding / regulation of T-helper 1 cell differentiation / response to Gram-positive bacterium / positive regulation of alpha-beta T cell proliferation / Interleukin-27 signaling / Interleukin-35 Signalling / cytokine receptor activity / T-helper 1 type immune response / regulation of T cell proliferation / humoral immune response ...interleukin-27 receptor binding / regulation of T-helper 1 cell differentiation / response to Gram-positive bacterium / positive regulation of alpha-beta T cell proliferation / Interleukin-27 signaling / Interleukin-35 Signalling / cytokine receptor activity / T-helper 1 type immune response / regulation of T cell proliferation / humoral immune response / T cell proliferation / positive regulation of defense response to virus by host / cytokine activity / positive regulation of type II interferon production / inflammatory response / endoplasmic reticulum lumen / signaling receptor binding / innate immune response / cell surface / extracellular space / extracellular region / plasma membrane / cytosol
Similarity search - Function
Interleukin-27 alpha / : / IL27B N-terminal FN3 domain / : / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Four-helical cytokine-like, core / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. ...Interleukin-27 alpha / : / IL27B N-terminal FN3 domain / : / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Four-helical cytokine-like, core / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-27 subunit beta / Interleukin-27 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsFeng, Y. / Dong, X.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171254 China
CitationJournal: To Be Published
Title: Structure of IL-27 indicates a much broader promiscuous pairing of the IL-6/IL-12 family
Authors: Feng, Y. / Dong, X.C.
History
DepositionJan 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interleukin-27 subunit alpha
B: Interleukin-27 subunit beta
C: Interleukin-27 subunit beta
D: Interleukin-27 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3407
Polymers95,8024
Non-polymers5383
Water19811
1
A: Interleukin-27 subunit alpha
B: Interleukin-27 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1223
Polymers47,9012
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1395.9 Å2
ΔGint-20.1 kcal/mol
MethodPISA
2
C: Interleukin-27 subunit beta
D: Interleukin-27 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2184
Polymers47,9012
Non-polymers3172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1269.3 Å2
ΔGint-16.8 kcal/mol
MethodPISA
Unit cell
Length a, b, c (Å)130.450, 130.450, 260.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11C-302-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNTHRTHR(chain 'B' and (resid 34 through 49 or resid 62...BB34 - 4914 - 29
12PHEPHEMETMET(chain 'B' and (resid 34 through 49 or resid 62...BB62 - 7042 - 50
13PROPROLEULEU(chain 'B' and (resid 34 through 49 or resid 62...BB78 - 8058 - 60
14GLNGLNTHRTHR(chain 'B' and (resid 34 through 49 or resid 62...BB82 - 10762 - 87
15VALVALGLYGLY(chain 'B' and (resid 34 through 49 or resid 62...BB119 - 17399 - 153
16PHEPHEARGARG(chain 'B' and (resid 34 through 49 or resid 62...BB177 - 191157 - 171
17PROPROSERSER(chain 'B' and (resid 34 through 49 or resid 62...BB195 - 226175 - 206
28GLNGLNTHRTHR(chain 'C' and (resid 34 through 70 or resid 78...CC34 - 4914 - 29
29PHEPHEMETMET(chain 'C' and (resid 34 through 70 or resid 78...CC62 - 7042 - 50
210PROPROGLNGLN(chain 'C' and (resid 34 through 70 or resid 78...CC78 - 8158 - 61
211THRTHRTHRTHR(chain 'C' and (resid 34 through 70 or resid 78...CC83 - 10763 - 87
212VALVALGLYGLY(chain 'C' and (resid 34 through 70 or resid 78...CC119 - 17399 - 153
213PHEPHEARGARG(chain 'C' and (resid 34 through 70 or resid 78...CC177 - 191157 - 171
214PROPROSERSER(chain 'C' and (resid 34 through 70 or resid 78...CC195 - 226175 - 206

NCS oper:
IDCodeMatrixVector
1given(-0.962603903888, -0.24611290199, -0.113234993241), (-0.222108154332, 0.477624660565, 0.850025088688), (-0.15511831613, 0.843387884128, -0.514427045271)-16.3031371948, -33.0135470947, 52.1787100806
2given(-0.967313229844, -0.225236844134, -0.116505276334), (-0.21744657092, 0.500361098229, 0.838066680028), (-0.130468786167, 0.836006659916, -0.532982889418)-15.0509893958, -30.9265968112, 51.6463564646

-
Components

#1: Protein Interleukin-27 subunit alpha / IL-27 subunit alpha / IL-27-A / IL27-A / Interleukin-30 / p28


Mass: 24562.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL27, IL27A, IL30 / Production host: Homo sapiens (human) / References: UniProt: Q8NEV9
#2: Protein Interleukin-27 subunit beta / IL-27 subunit beta / IL-27B / Epstein-Barr virus-induced gene 3 protein / EBV-induced gene 3 protein


Mass: 23338.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EBI3, IL27B / Production host: Homo sapiens (human) / References: UniProt: Q14213
#3: 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
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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.05M Lithium sulfate, 0.05M Sodium sulfate,0.05M Tris-HCl pH 8.5, 35%PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.4→47.4 Å / Num. obs: 33328 / % possible obs: 97.64 % / Redundancy: 23.6 % / Biso Wilson estimate: 132.99 Å2 / CC1/2: 0.999 / Net I/σ(I): 12
Reflection shellResolution: 3.4→3.521 Å / Num. unique obs: 1356 / CC1/2: 0.447 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSVERSION Feb 5, 2021data scaling
PHENIX1.20.1_4487phasing
CootCoot 0.9.8.1model building
XDS1.15.2_3472data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→47.35 Å / SU ML: 0.7416 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 35.3091
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2972 3348 10.05 %Random
Rwork0.2535 29980 --
obs0.258 33328 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 155.62 Å2
Refinement stepCycle: LAST / Resolution: 3.4→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5484 0 33 11 5528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245664
X-RAY DIFFRACTIONf_angle_d0.59457697
X-RAY DIFFRACTIONf_chiral_restr0.04857
X-RAY DIFFRACTIONf_plane_restr0.0049966
X-RAY DIFFRACTIONf_dihedral_angle_d13.62533380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.450.65211110.6007991X-RAY DIFFRACTION76.37
3.45-3.50.50561320.50781158X-RAY DIFFRACTION92.54
3.5-3.550.37151460.36411303X-RAY DIFFRACTION99.66
3.55-3.610.35761400.35991265X-RAY DIFFRACTION99.86
3.61-3.680.53311310.48561224X-RAY DIFFRACTION94.89
3.68-3.740.50931240.38631105X-RAY DIFFRACTION85.76
3.74-3.810.3171360.32441285X-RAY DIFFRACTION99.93
3.81-3.890.4021390.39431257X-RAY DIFFRACTION98.8
3.89-3.980.44121360.4221228X-RAY DIFFRACTION96.53
3.98-4.070.36231480.28721279X-RAY DIFFRACTION100
4.07-4.170.32551370.26061288X-RAY DIFFRACTION100
4.17-4.280.32351440.23621281X-RAY DIFFRACTION100
4.28-4.410.28561500.21691267X-RAY DIFFRACTION100
4.41-4.550.22831440.2191278X-RAY DIFFRACTION100
4.55-4.710.23261440.2021274X-RAY DIFFRACTION100
4.71-4.90.23671380.19751273X-RAY DIFFRACTION100
4.9-5.130.21571440.18931292X-RAY DIFFRACTION100
5.13-5.40.22381510.21271287X-RAY DIFFRACTION100
5.4-5.730.28681400.23191258X-RAY DIFFRACTION100
5.73-6.170.38481410.27971288X-RAY DIFFRACTION100
6.17-6.790.30731400.26931279X-RAY DIFFRACTION100
6.79-7.770.33691460.2311278X-RAY DIFFRACTION99.93
7.77-9.780.22231450.18411276X-RAY DIFFRACTION100
9.78-47.350.26441410.23251266X-RAY DIFFRACTION98.46
Refinement TLS params.Method: refined / Origin x: -0.739935231707 Å / Origin y: -57.5331527831 Å / Origin z: 1.88082247942 Å
111213212223313233
T0.71815518991 Å20.0219795691282 Å20.00779310425367 Å2-1.33210062468 Å2-0.119397525362 Å2--0.775637875254 Å2
L3.79662091957 °21.01854220113 °2-0.00713124499162 °2-2.72491546824 °2-0.00253492434213 °2--2.69937417864 °2
S0.395169619894 Å °-1.0148088916 Å °0.831928233044 Å °0.319047757015 Å °-0.345056075669 Å °0.166003278472 Å °-0.189130583844 Å °-0.162661566181 Å °-0.0659755761788 Å °
Refinement TLS groupSelection details: all

+
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