[English] 日本語
Yorodumi
- PDB-6uib: Crystal structure of IL23 bound to peptide 23-652 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uib
TitleCrystal structure of IL23 bound to peptide 23-652
Components
  • Interleukin-12 subunit beta
  • Interleukin-23 subunit alpha
  • Peptide 23-652
KeywordsSIGNALING PROTEIN / Complex
Function / homology
Function and homology information


late endosome lumen / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell activation / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...late endosome lumen / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell activation / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lymphocyte proliferation / positive regulation of tissue remodeling / tissue remodeling / positive regulation of smooth muscle cell apoptotic process / positive regulation of NK T cell activation / positive regulation of T-helper 1 type immune response / sexual reproduction / positive regulation of mononuclear cell proliferation / interleukin-12 receptor binding / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response / interleukin-12-mediated signaling pathway / positive regulation of NK T cell proliferation / T-helper cell differentiation / positive regulation of memory T cell differentiation / Interleukin-12 signaling / positive regulation of natural killer cell proliferation / positive regulation of osteoclast differentiation / negative regulation of interleukin-17 production / cell surface receptor signaling pathway via STAT / cytokine receptor activity / natural killer cell activation / response to UV-B / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of neutrophil chemotaxis / T-helper 1 type immune response / negative regulation of interleukin-10 production / defense response to protozoan / Interleukin-10 signaling / positive regulation of interleukin-17 production / positive regulation of activated T cell proliferation / positive regulation of interleukin-10 production / cell surface receptor signaling pathway via JAK-STAT / negative regulation of protein secretion / positive regulation of T-helper 17 cell lineage commitment / positive regulation of T cell proliferation / T cell proliferation / positive regulation of defense response to virus by host / positive regulation of interleukin-12 production / positive regulation of cell adhesion / regulation of cytokine production / cytokine activity / negative regulation of smooth muscle cell proliferation / negative regulation of inflammatory response to antigenic stimulus / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of T cell mediated cytotoxicity / cellular response to type II interferon / positive regulation of type II interferon production / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / cell migration / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / defense response to virus / inflammatory response / endoplasmic reticulum lumen / protein heterodimerization activity / innate immune response / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / membrane / cytosol
Similarity search - Function
Interleukin-23 alpha / Interleukin 23 subunit alpha / Interleukin-12 beta / Interleukin-12 beta, central domain / : / Cytokine interleukin-12p40 C-terminus / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core ...Interleukin-23 alpha / Interleukin 23 subunit alpha / Interleukin-12 beta / Interleukin-12 beta, central domain / : / Cytokine interleukin-12p40 C-terminus / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-12 subunit beta / Interleukin-23 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsDurbin, J.D. / Wang, J. / Afshar, S.
CitationJournal: Plos One / Year: 2020
Title: Integration of phage and yeast display platforms: A reliable and cost effective approach for binning of peptides as displayed on-phage.
Authors: Pandya, P. / Sayers, R.O. / Ting, J.P. / Morshedian, S. / Torres, C. / Cudal, J.S. / Zhang, K. / Fitchett, J.R. / Zhang, Q. / Zhang, F.F. / Wang, J. / Durbin, J.D. / Carrillo, J.J. / Espada, ...Authors: Pandya, P. / Sayers, R.O. / Ting, J.P. / Morshedian, S. / Torres, C. / Cudal, J.S. / Zhang, K. / Fitchett, J.R. / Zhang, Q. / Zhang, F.F. / Wang, J. / Durbin, J.D. / Carrillo, J.J. / Espada, A. / Broughton, H. / Qian, Y. / Afshar, S.
History
DepositionSep 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interleukin-23 subunit alpha
B: Interleukin-12 subunit beta
C: Peptide 23-652
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8044
Polymers58,3793
Non-polymers4241
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-13 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.594, 94.665, 101.133
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Interleukin-23 subunit alpha / IL-23-A / Interleukin-23 subunit p19 / IL-23p19


Mass: 19997.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL23A, SGRF, UNQ2498/PRO5798 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NPF7
#2: Antibody Interleukin-12 subunit beta / IL-12B / Cytotoxic lymphocyte maturation factor 40 kDa subunit / CLMF p40 / IL-12 subunit p40 / NK ...IL-12B / Cytotoxic lymphocyte maturation factor 40 kDa subunit / CLMF p40 / IL-12 subunit p40 / NK cell stimulatory factor chain 2 / NKSF2


Mass: 36041.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL12B, NKSF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29460
#3: Protein/peptide Peptide 23-652


Mass: 2340.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 100 mM Hepes pH 7, 17% w/v PEG 3350 and 150 mM Potassium Nitrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.74→101.133 Å / Num. all: 18723 / Num. obs: 18723 / % possible obs: 97.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 89.94 Å2 / Rpim(I) all: 0.021 / Rrim(I) all: 0.057 / Rsym value: 0.05 / Net I/av σ(I): 11.9 / Net I/σ(I): 23.9 / Num. measured all: 135345
Reflection shellResolution: 2.74→2.905 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3053 / Rpim(I) all: 0.181 / Rrim(I) all: 0.495 / Rsym value: 0.428 / % possible all: 100

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DUH

3duh


Resolution: 2.74→19.9 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.887 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.428 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.424 / SU Rfree Blow DPI: 0.273 / SU Rfree Cruickshank DPI: 0.277
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1003 5.39 %RANDOM
Rwork0.206 ---
obs0.208 18625 97.5 %-
Displacement parametersBiso max: 193.07 Å2 / Biso mean: 84.89 Å2 / Biso min: 42.43 Å2
Baniso -1Baniso -2Baniso -3
1-8.2178 Å20 Å20 Å2
2--16.0397 Å20 Å2
3----24.2576 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.74→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 28 26 3234
Biso mean--89.78 63.86 -
Num. residues----421
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1048SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes66HARMONIC2
X-RAY DIFFRACTIONt_gen_planes477HARMONIC5
X-RAY DIFFRACTIONt_it3287HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion450SEMIHARMONIC5
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_contact3585SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3287HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg4485HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion20.01
LS refinement shellResolution: 2.74→2.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.278 171 5.6 %
Rwork0.22 2882 -
all0.223 3053 -
obs--100 %
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)
12.55170.8035-1.31055.4442-1.27445.5175-0.0320.55920.1522-0.84030.00680.49880.243-0.16850.0252-0.13490.0462-0.107-0.1691-0.1316-0.2412-33.74924.0151-40.0396
27.89655.4110.1582.7453-1.18112.56550.03030.11180.76570.27920.0855-0.0303-0.4085-0.1938-0.1158-0.2157-0.1847-0.0324-0.260.0230.23324.203637.0264-17.5642
31.02380.89621.172200.543500.02130.006-0.0524-0.0577-0.009-0.01760.09780.0423-0.0124-0.0572-0.25280.03280.2485-0.08650.20382.52520.7323-27.6589
45.3043.94171.73854.60491.96922.59760.5357-0.089-0.15270.8507-0.5528-0.5453-0.17050.25020.01720.0667-0.1866-0.0577-0.14630.0416-0.1577-15.788916.3453-18.4332
51.10011.5285-0.7815.69-1.66392.4020.5656-0.3609-0.23720.8824-0.48190.1617-0.04760.1797-0.0837-0.0345-0.1323-0.0237-0.0734-0.0727-0.1396-32.1591-8.6429-15.6259
60.72880.4683-0.02510-0.444800.01140.0433-0.001-0.01540.0082-0.0244-0.01910.0114-0.0196-0.0545-0.304-0.00550.14520.13810.1224-6.929829.3331-27.2245
71.0284-1.5287-4.68832.3882-1.8424.37320.03830.2231-0.0922-0.4362-0.266-0.39140.57570.21620.22770.05490.0638-0.0312-0.0469-0.1046-0.0336-27.1873-8.9554-30.6282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A8 - 168
2X-RAY DIFFRACTION2{ B|0 - 86}B0 - 86
3X-RAY DIFFRACTION3{ B|87 - 91}B87 - 91
4X-RAY DIFFRACTION4{ B|92 - 211}B92 - 211
5X-RAY DIFFRACTION5{ B|212 - 312}B212 - 312
6X-RAY DIFFRACTION6{ B|313 - 314}B313 - 314
7X-RAY DIFFRACTION7{ C|* }C4 - 18

+
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