[English] 日本語
Yorodumi
- PDB-6nmy: A Cytokine-receptor complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nmy
TitleA Cytokine-receptor complex
Components
  • (Cytokine receptor common subunit ...) x 2
  • Interleukin-3 receptor subunit alpha
  • Interleukin-3Interleukin 3
KeywordsCYTOKINE / cytokine-receptor complex / receptor assembly / cell surface
Function / homology
Function and homology information


interleukin-3 receptor activity / interleukin-3 receptor binding / RUNX1 regulates transcription of genes involved in interleukin signaling / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / Surfactant metabolism / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway ...interleukin-3 receptor activity / interleukin-3 receptor binding / RUNX1 regulates transcription of genes involved in interleukin signaling / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / Surfactant metabolism / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / interleukin-3-mediated signaling pathway / cellular response to interleukin-3 / cytokine receptor activity / embryonic hemopoiesis / cytokine binding / cell surface receptor signaling pathway via JAK-STAT / immunoglobulin mediated immune response / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / coreceptor activity / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / signaling receptor activity / nervous system development / RAF/MAP kinase cascade / response to lipopolysaccharide / receptor complex / immune response / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin-like - #3850 / Interleukin-3 / Interleukin-3 / IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / : / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. ...Immunoglobulin-like - #3850 / Interleukin-3 / Interleukin-3 / IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / : / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Short hematopoietin receptor family 1 signature. / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Short hematopoietin receptor, family 1, conserved site / Interferon-alpha/beta receptor, fibronectin type III / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-3 / Interleukin-3 receptor subunit alpha / Cytokine receptor common subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.301 Å
AuthorsDhagat, U. / Kan, W.L. / Hercus, T.R. / Broughton, S.E. / Nero, T.L. / Lopez, A.F. / Parker, M.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: Signalling conformation of cell surface receptor
Authors: Dhagat, U. / Parker, M.W.
History
DepositionJan 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Interleukin-3 receptor subunit alpha
M: Interleukin-3 receptor subunit alpha
A: Cytokine receptor common subunit beta
C: Cytokine receptor common subunit beta
I: Interleukin-3
J: Interleukin-3
B: Cytokine receptor common subunit beta
D: Cytokine receptor common subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,06416
Polymers187,7698
Non-polymers4,2958
Water21612
1
F: Interleukin-3 receptor subunit alpha
A: Cytokine receptor common subunit beta
J: Interleukin-3
B: Cytokine receptor common subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5238
Polymers93,8854
Non-polymers2,6384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: Interleukin-3 receptor subunit alpha
C: Cytokine receptor common subunit beta
I: Interleukin-3
D: Cytokine receptor common subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5418
Polymers93,8854
Non-polymers1,6574
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.647, 157.251, 168.306
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules FMIJ

#1: Protein Interleukin-3 receptor subunit alpha / / IL-3RA


Mass: 33225.520 Da / Num. of mol.: 2 / Mutation: N194Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL3RA, IL3R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P26951
#3: Protein Interleukin-3 / Interleukin 3 / IL-3 / Hematopoietic growth factor / Mast cell growth factor / MCGF / Multipotential colony- ...IL-3 / Hematopoietic growth factor / Mast cell growth factor / MCGF / Multipotential colony-stimulating factor / P-cell-stimulating factor


Mass: 13382.270 Da / Num. of mol.: 2 / Mutation: W13Y
Source method: isolated from a genetically manipulated source
Details: The first 4 N-terminal residues (GAMG) are derived from fusion protein
Source: (gene. exp.) Homo sapiens (human) / Gene: IL3 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P08700

-
Cytokine receptor common subunit ... , 2 types, 4 molecules ACBD

#2: Protein Cytokine receptor common subunit beta / CDw131 / GM-CSF/IL-3/IL-5 receptor common beta subunit


Mass: 24585.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2RB, IL3RB, IL5RB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32927
#4: Protein Cytokine receptor common subunit beta / CDw131 / GM-CSF/IL-3/IL-5 receptor common beta subunit


Mass: 22691.234 Da / Num. of mol.: 2 / Mutation: N346Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2RB, IL3RB, IL5RB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32927

-
Sugars , 4 types, 8 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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.: 2 / Source method: isolated from a natural 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
#8: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural 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

-
Non-polymers , 1 types, 12 molecules

#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.69 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Crystals were grown in 10 mM Tris pH6.8, 8% PEG 8000, 0.15 M magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.3→47.76 Å / Num. obs: 45227 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 97.58 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.081 / Rrim(I) all: 0.194 / Net I/σ(I): 8.8 / Num. measured all: 248002 / Scaling rejects: 95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.3-3.425.61.7282448843680.310.8071.9141.199.5
12.78-47.764.60.02738838360.9990.0130.0341.195

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.39 Å47.72 Å
Translation3.39 Å47.72 Å

-
Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.15data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NKQ, 5UV8

4nkq

5uv8


Resolution: 3.301→47.448 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 2233 4.95 %RANDOM
Rwork0.2364 42916 --
obs0.2384 45149 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.51 Å2 / Biso mean: 95.1938 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.301→47.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12678 0 285 12 12975
Biso mean--133.92 76.94 -
Num. residues----1571
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.301-3.37240.40711380.3917264799
3.3724-3.45090.36191490.37142609100
3.4509-3.53710.38151350.3372652100
3.5371-3.63280.34921680.31852614100
3.6328-3.73960.33491440.30672668100
3.7396-3.86030.33491300.29352668100
3.8603-3.99820.32991370.27862656100
3.9982-4.15820.32551310.25472660100
4.1582-4.34730.27851260.23642698100
4.3473-4.57630.23791160.21322693100
4.5763-4.86280.22721300.20532683100
4.8628-5.23780.25551510.19652684100
5.2378-5.76410.25991590.20322679100
5.7641-6.59620.26381560.2242713100
6.5962-8.30330.26191400.21282745100
8.3033-47.4480.21651230.1906284798
Refinement TLS params.Method: refined / Origin x: 21.9225 Å / Origin y: 6.5856 Å / Origin z: 24.6947 Å
111213212223313233
T0.6564 Å20.055 Å20.0642 Å2-0.8364 Å20.0862 Å2--0.6774 Å2
L0.2107 °2-0.0572 °2-0.005 °2-1.0793 °2-0.0536 °2--0.1449 °2
S-0.0495 Å °-0.1211 Å °-0.0638 Å °0.0063 Å °0.0631 Å °0.091 Å °0.0732 Å °0.0384 Å °-0.0108 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allF26 - 411
2X-RAY DIFFRACTION1allM28 - 405
3X-RAY DIFFRACTION1allA25 - 502
4X-RAY DIFFRACTION1allC25 - 401
5X-RAY DIFFRACTION1allI13 - 120
6X-RAY DIFFRACTION1allJ13 - 120
7X-RAY DIFFRACTION1allB241 - 436
8X-RAY DIFFRACTION1allD241 - 437
9X-RAY DIFFRACTION1allE1 - 13

+
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