[English] 日本語
Yorodumi
- PDB-3se3: human IFNa2-IFNAR ternary complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3se3
Titlehuman IFNa2-IFNAR ternary complex
Components
  • Interferon alpha 2b
  • Interferon alpha/beta receptor 1
  • Interferon alpha/beta receptor 2
KeywordsIMMUNE SYSTEM RECEPTOR / Type I interferon signaling complex / extracellular space
Function / homology
Function and homology information


type I interferon receptor activity / type I interferon binding / type I interferon receptor binding / B cell activation involved in immune response / JAK pathway signal transduction adaptor activity / response to interferon-beta / natural killer cell activation involved in immune response / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation ...type I interferon receptor activity / type I interferon binding / type I interferon receptor binding / B cell activation involved in immune response / JAK pathway signal transduction adaptor activity / response to interferon-beta / natural killer cell activation involved in immune response / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / positive regulation of cellular respiration / cellular response to interferon-alpha / response to interferon-alpha / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / host-mediated suppression of symbiont invasion / cytokine receptor binding / cell surface receptor signaling pathway via STAT / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / cytokine binding / response to exogenous dsRNA / humoral immune response / Regulation of IFNA/IFNB signaling / cell surface receptor signaling pathway via JAK-STAT / cellular response to interferon-beta / cytokine activity / Evasion by RSV of host interferon responses / cellular response to virus / response to virus / Interferon alpha/beta signaling / late endosome / cell-cell signaling / : / Factors involved in megakaryocyte development and platelet production / response to lipopolysaccharide / defense response to virus / adaptive immune response / Potential therapeutics for SARS / cell surface receptor signaling pathway / lysosome / receptor complex / inflammatory response / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Interferon alpha/beta receptor 1 / Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Growth Hormone; Chain: A; - #10 ...Interferon alpha/beta receptor 1 / Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interferon alpha-2 / Interferon alpha/beta receptor 1 / Interferon alpha/beta receptor 2 / Interferon alpha 2b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.0001 Å
AuthorsThomas, C. / Garcia, K.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural linkage between ligand discrimination and receptor activation by type I interferons.
Authors: Thomas, C. / Moraga, I. / Levin, D. / Krutzik, P.O. / Podoplelova, Y. / Trejo, A. / Lee, C. / Yarden, G. / Vleck, S.E. / Glenn, J.S. / Nolan, G.P. / Piehler, J. / Schreiber, G. / Garcia, K.C.
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Aug 21, 2013Group: Structure summary
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 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 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interferon alpha/beta receptor 1
B: Interferon alpha 2b
C: Interferon alpha/beta receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1384
Polymers89,9163
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-24 kcal/mol
Surface area30010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.370, 93.370, 401.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Interferon alpha/beta receptor 1 / IFN-R-1 / IFN-alpha/beta receptor 1 / Cytokine receptor class-II member 1 / Cytokine receptor ...IFN-R-1 / IFN-alpha/beta receptor 1 / Cytokine receptor class-II member 1 / Cytokine receptor family 2 member 1 / CRF2-1 / Type I interferon receptor 1


Mass: 47629.965 Da / Num. of mol.: 1 / Fragment: IFNa2(YNS) (UNP Residues 28-436)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNAR1, IFNAR / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P17181
#2: Protein Interferon alpha 2b


Mass: 19392.270 Da / Num. of mol.: 1 / Mutation: H58Y, E59N, Q62S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q86UP4, UniProt: P01563*PLUS
#3: Protein Interferon alpha/beta receptor 2 / IFN-R-2 / IFN-alpha binding protein / IFN-alpha/beta receptor 2 / Interferon alpha binding protein ...IFN-R-2 / IFN-alpha binding protein / IFN-alpha/beta receptor 2 / Interferon alpha binding protein / Type I interferon receptor 2


Mass: 22894.078 Da / Num. of mol.: 1 / Fragment: UNP Residues 34-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNAR2, IFNABR, IFNARB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P48551
#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.: 1
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 15% (w/v) PEG 3350, 100 mM Na malonate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→46.8 Å / Num. obs: 9537 / % possible obs: 99.8 % / Redundancy: 11 % / Biso Wilson estimate: 137 Å2 / Rsym value: 0.172 / Net I/σ(I): 11.7
Reflection shellResolution: 4→4.1 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 2.6 / Rsym value: 1.03 / % possible all: 100

-
Processing

Software
NameClassification
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SE4, 3S9D

3se4

3s9d


Resolution: 4.0001→46.78 Å / σ(F): 2.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.311 477 5.01 %
Rwork0.251 --
obs-9530 99.84 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 162.55 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 160.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.21 Å2-0 Å20 Å2
2---6.21 Å2-0 Å2
3---12.41 Å2
Refinement stepCycle: LAST / Resolution: 4.0001→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 14 0 4462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014574
X-RAY DIFFRACTIONf_angle_d1.8176242
X-RAY DIFFRACTIONf_dihedral_angle_d13.8211523
X-RAY DIFFRACTIONf_chiral_restr0.106728
X-RAY DIFFRACTIONf_plane_restr0.008794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0001-4.57850.32531530.23442907X-RAY DIFFRACTION100
4.5785-5.76670.31451560.21782969X-RAY DIFFRACTION100
5.7667-46.7860.30491680.2743177X-RAY DIFFRACTION100
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)
10.480.3832-0.11081.42680.11540.072-0.04870.18150.1508-0.0107-0.17180.5325-0.07060.004-0.02450.55940.1467-0.73651.171-0.25890.38110.3368-18.7501-23.1307
22.6812-0.8219-0.37340.2716-0.0520.96510.5225-0.00940.25970.0150.06950.1029-0.831-0.07540.28461.0709-0.185-0.4720.5259-0.22771.00125.7498-14.023810.6866
30.3163-0.04160.03940.4219-0.04570.0929-0.0668-0.20790.1171-0.25180.00890.23750.1396-0.0798-0.10880.35910.2099-0.52780.4341-0.45240.356135.4643-25.640218.2765
40.53620.281-0.5270.54190.04260.6758-0.58550.1680.0002-0.2465-0.1721-0.0582-0.2895-0.4208-0.02850.8369-0.0238-0.25240.65540.020.64539.2725-33.2853-12.7755
51.3585-0.1131-0.31680.6658-0.48830.47130.08990.0842-0.98340.2039-0.28690.07040.3986-0.3399-0.00251.2907-0.1277-0.0710.8594-0.15370.832134.8903-32.2404-9.4076
60.06620.06870.00010.09060.00230.0030.2166-0.4312-0.8569-0.2653-0.0172-0.43020.71560.7026-0.00251.05550.0473-0.11761.0641-0.14391.031359.7397-49.2569-13.9927
70.2462-0.5841-0.28651.27070.68260.3781-0.02720.02280.24220.0976-0.5594-0.3494-0.0843-0.325-0.00621.35110.00380.13950.9047-0.3010.99351.8943-52.2719-19.405
81.38530.24980.30010.90490.06040.21110.8576-0.3498-0.85050.6086-0.2914-1.137-0.1508-0.28770.00650.7513-0.06620.03290.8706-0.16181.021374.6321-32.666-14.536
91.1566-0.0843-1.00070.0649-0.08261.3977-0.54070.5734-0.2287-0.10880.5427-0.2612-0.3651-0.62930.01721.1326-0.25040.07260.49670.0191.173276.0711-28.8018-6.6267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:104)
2X-RAY DIFFRACTION2chain 'A' and (resseq 105:232)
3X-RAY DIFFRACTION3chain 'A' and (resseq 233:302)
4X-RAY DIFFRACTION4chain 'B' and (resseq 8:66)
5X-RAY DIFFRACTION5chain 'B' and (resseq 67:156)
6X-RAY DIFFRACTION6chain 'C' and (resseq 11:29)
7X-RAY DIFFRACTION7chain 'C' and (resseq 30:104)
8X-RAY DIFFRACTION8chain 'C' and (resseq 105:139)
9X-RAY DIFFRACTION9chain 'C' and (resseq 140:204)

+
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