[English] 日本語
Yorodumi
- PDB-2gys: 2.7 A structure of the extracellular domains of the human beta co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gys
Title2.7 A structure of the extracellular domains of the human beta common receptor involved in IL-3, IL-5, and GM-CSF signalling
ComponentsCytokine receptor common beta chain
KeywordsSIGNALING PROTEIN / CYTOKINE / DIMER OF INTERLOCKING CHAINS OF FIBRONECTIN-III DOMAINS / FOUR FIBRONECTIN-III DOMAINS PER CHAIN
Function / homology
Function and homology information


granulocyte macrophage colony-stimulating factor receptor complex / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / cellular response to interleukin-3 / granulocyte-macrophage colony-stimulating factor signaling pathway / positive regulation of leukocyte proliferation / interleukin-3-mediated signaling pathway / interleukin-5-mediated signaling pathway / Surfactant metabolism ...granulocyte macrophage colony-stimulating factor receptor complex / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / cellular response to interleukin-3 / granulocyte-macrophage colony-stimulating factor signaling pathway / positive regulation of leukocyte proliferation / interleukin-3-mediated signaling pathway / interleukin-5-mediated signaling pathway / Surfactant metabolism / cytokine receptor activity / immunoglobulin mediated immune response / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / cell surface receptor signaling pathway via JAK-STAT / coreceptor activity / response to lipopolysaccharide / RAF/MAP kinase cascade / signaling receptor activity / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / plasma membrane
Similarity search - Function
Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / : / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Short hematopoietin receptor family 1 signature. / Interferon-alpha/beta receptor, fibronectin type III / Short hematopoietin receptor, family 1, conserved site / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / : / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Short hematopoietin receptor family 1 signature. / Interferon-alpha/beta receptor, fibronectin type III / Short hematopoietin receptor, family 1, conserved site / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Cytokine receptor common subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsCarr, P.D. / Conlan, F. / Ford, S. / Ollis, D.L. / Young, I.G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: An improved resolution structure of the human beta common receptor involved in IL-3, IL-5 and GM-CSF signalling which gives better definition of the high-affinity binding epitope.
Authors: Carr, P.D. / Conlan, F. / Ford, S. / Ollis, D.L. / Young, I.G.
History
DepositionMay 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_chiral / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _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.ptnr1_label_seq_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytokine receptor common beta chain
B: Cytokine receptor common beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2316
Polymers95,6252
Non-polymers2,6064
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint8 kcal/mol
Surface area42520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.909, 184.909, 101.047
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Cytokine receptor common beta chain / GM-CSF/IL-3/IL-5 receptor common beta-chain / CD131 antigen / CDw131


Mass: 47812.473 Da / Num. of mol.: 2 / Fragment: extracellular domain, residues 25-443 / Mutation: N328Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2RB, IL3RB, IL5RB / Plasmid: PBACPAK8 / Production host: Trichoplusia ni (cabbage looper) / References: GenBank: 47678387, UniProt: P32927*PLUS
#2: 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-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 10% polyethylene glycol 5000 mono-methyl ether in phosphate buffer, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.117 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 7, 2004
RadiationMonochromator: Diamond (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.117 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 35381 / Num. obs: 32327 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.96 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.2
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 2.4 / % possible all: 40.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1gh7

1gh7


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.873 / SU B: 26.835 / SU ML: 0.27 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.671 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26913 1392 4.3 %RANDOM
Rwork0.21169 ---
all0.21426 35381 --
obs0.21426 30934 91.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.114 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-0.58 Å20 Å2
2---1.16 Å20 Å2
3---1.74 Å2
Refine analyzeLuzzati coordinate error obs: 0.459 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6280 0 174 0 6454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0216656
X-RAY DIFFRACTIONr_angle_refined_deg2.2171.9639141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2995795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83222.852298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.32115945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0651558
X-RAY DIFFRACTIONr_chiral_restr0.1670.21043
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025076
X-RAY DIFFRACTIONr_nbd_refined0.2540.22722
X-RAY DIFFRACTIONr_nbtor_refined0.330.24457
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.310.27
X-RAY DIFFRACTIONr_mcbond_it0.751.54109
X-RAY DIFFRACTIONr_mcangle_it1.3526529
X-RAY DIFFRACTIONr_scbond_it2.17132903
X-RAY DIFFRACTIONr_scangle_it3.5574.52612
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.541 46 -
Rwork0.394 873 -
obs-1431 34.98 %
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)
19.1155-1.0110.69380.8462-0.22.3907-0.05860.5109-0.4543-0.3549-0.13170.09480.03190.26410.1904-0.2152-0.0394-0.0149-0.2986-0.022-0.1403-21.5591-20.261-33.2171
21.34611.37262.01324.80783.59495.1981-0.0052-0.0199-0.15010.24360.2070.005-0.16940.4323-0.2018-0.1135-0.0296-0.01-0.19440.0813-0.09410.1119-31.708611.4699
32.227-2.7301-4.21714.64274.71718.14380.2888-0.00530.22270.19330.0267-0.34320.12320.5212-0.31550.0372-0.1162-0.1611-0.03890.00810.135733.6766-9.953415.8708
41.563-3.3257-2.07828.5672.64834.87370.26180.42070.52980.17410.09290.7918-0.5861-0.6604-0.35470.3951-0.00440.15310.1413-0.00530.322422.29340.655537.7761
51.27890.3642-0.15649.8212-0.38923.3543-0.0004-0.2357-0.13210.8715-0.0045-0.23120.2696-0.03660.00490.073-0.08050.02410.0729-0.0467-0.143929.487511.828532.8835
66.85360.03795.24220.99790.0957.8950.1386-0.33420.04410.26430.0184-0.26090.4138-0.0808-0.157-0.2838-0.00080.0704-0.292-0.0422-0.00125.1704-22.2292-10.766
71.5821-1.21061.57476.0149-5.64025.43320.1190.0852-0.18950.2473-0.00530.20420.03890.0032-0.1137-0.3369-0.0006-0.0245-0.2443-0.0047-0.0463-4.2762-33.8789-15.6066
83.7481-0.13160.63283.6637-1.70614.0982-0.16780.59740.5906-0.19860.16770.2874-0.8813-0.528200.01970.0739-0.1348-0.05460.00550.0102-45.1186-3.7271-39.1486
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 911 - 91
2X-RAY DIFFRACTION1BB310 - 317310 - 317
3X-RAY DIFFRACTION2AA106 - 215106 - 215
4X-RAY DIFFRACTION3AA220 - 300220 - 300
5X-RAY DIFFRACTION3BB94 - 10394 - 103
6X-RAY DIFFRACTION4AA320 - 418320 - 418
7X-RAY DIFFRACTION5BB1 - 911 - 91
8X-RAY DIFFRACTION5AA310 - 317310 - 317
9X-RAY DIFFRACTION6BB106 - 215106 - 215
10X-RAY DIFFRACTION7BB220 - 307220 - 307
11X-RAY DIFFRACTION7AA94 - 10394 - 103
12X-RAY DIFFRACTION8BB320 - 418320 - 418

+
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