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- PDB-1n26: Crystal Structure of the extra-cellular domains of Human Interleu... -

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Basic information

Entry
Database: PDB / ID: 1n26
TitleCrystal Structure of the extra-cellular domains of Human Interleukin-6 Receptor alpha chain
ComponentsIL-6 Receptor alpha chain
KeywordsCYTOKINE / Transmembrane / Glycoprotein / Immunoglobulin domain
Function / homology
Function and homology information


ciliary neurotrophic factor binding / interleukin-6 receptor activity / interleukin-6 binding / hepatic immune response / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor receptor complex / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / positive regulation of activation of Janus kinase activity ...ciliary neurotrophic factor binding / interleukin-6 receptor activity / interleukin-6 binding / hepatic immune response / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor receptor complex / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / positive regulation of activation of Janus kinase activity / negative regulation of collagen biosynthetic process / T-helper 17 cell lineage commitment / positive regulation of glomerular mesangial cell proliferation / endocrine pancreas development / negative regulation of interleukin-8 production / vascular endothelial growth factor production / positive regulation of leukocyte chemotaxis / neutrophil mediated immunity / cytokine receptor activity / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / MAPK3 (ERK1) activation / monocyte chemotaxis / MAPK1 (ERK2) activation / positive regulation of osteoblast differentiation / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / response to cytokine / acute-phase response / positive regulation of smooth muscle cell proliferation / positive regulation of interleukin-6 production / cytokine-mediated signaling pathway / Transcriptional regulation of granulopoiesis / positive regulation of peptidyl-tyrosine phosphorylation / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / Potential therapeutics for SARS / positive regulation of MAPK cascade / receptor complex / defense response to Gram-positive bacterium / apical plasma membrane / external side of plasma membrane / positive regulation of cell population proliferation / enzyme binding / protein homodimerization activity / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Type I cytokine receptor, cytokine-binding domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Interleukin-6 receptor alpha chain, binding / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin / Immunoglobulin domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. ...Type I cytokine receptor, cytokine-binding domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Interleukin-6 receptor alpha chain, binding / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin / Immunoglobulin domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CYSTEINE / Interleukin-6 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsVarghese, J.N. / Moritz, R.L. / Lou, M.-Z. / van Donkelaar, A. / Ji, H. / Ivancic, N. / Branson, K.M. / Hall, N.E. / Simpson, R.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structure of the extracellular domains of the human interleukin-6 receptor alpha-chain.
Authors: Varghese, J.N. / Moritz, R.L. / Lou, M.-Z. / van Donkelaar, A. / Ji, H. / Ivancic, N. / Branson, K.M. / Hall, N.E. / Simpson, R.J.
History
DepositionOct 22, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 15, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IL-6 Receptor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5428
Polymers36,4101
Non-polymers2,1327
Water1,49583
1
A: IL-6 Receptor alpha chain
hetero molecules

A: IL-6 Receptor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,08416
Polymers72,8202
Non-polymers4,26414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-y+3/2,x+1/2,z-1/41
Unit cell
Length a, b, c (Å)51.130, 51.130, 303.388
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-806-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein IL-6 Receptor alpha chain / Interleukin-6 receptor alpha chain


Mass: 36409.902 Da / Num. of mol.: 1 / Fragment: IL-6R extral-cellular domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6R / Plasmid: pEE14sIL6RL325 / Cell line (production host): Lec3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO / References: UniProt: P08887

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Sugars , 3 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 951.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2122h-1a_1-5_2*NCC/3=O]/1-1-2-3-4/a4-b1_b4-c1_c6-d1_d4-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(4+1)][a-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: 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
#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 / N-Acetylglucosamine


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

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Non-polymers , 3 types, 86 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulphate, PEG 3350, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
25 mMTris-HCl1droppH8.0
350 mMammonium sulfate1reservoir
418 %PEG33501reservoir
52.5 mMsodium citrate1reservoirpH5.6

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODEMACSCIENCE11.54181.5418
ROTATING ANODERIGAKU RUH3R21.54181.5418
SYNCHROTRONAPS 14-BM-C311
Detector
TypeIDDetectorDetails
RIGAKU RAXIS II1IMAGE PLATEYale Mirrors
RIGAKU RAXIS IV2IMAGE PLATEMonocapillary optics
ADSC QUANTUM 43CCDAPS BM14C optics
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Yale mirrorsSINGLE WAVELENGTHMx-ray1
2Monocapillary opticsSINGLE WAVELENGTHMx-ray1
3Monocapillary opticsSINGLE WAVELENGTHMx-ray1
4APS BM14CSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
211
ReflectionResolution: 2.4→50 Å / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 18.6 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.07 / Net I/σ(I): 39
Reflection shellResolution: 2.35→2.4 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.7 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MIR
Starting model: ab initio built into MIR map

Resolution: 2.4→6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 731 -Random
Rwork0.22 ---
all0.22 15630 --
obs0.22 15298 97.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.369 Å20 Å20 Å2
2---6.369 Å20 Å2
3---12.737 Å2
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 137 83 2580
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.96
X-RAY DIFFRACTIONc_mcbond_it6.3943.5
X-RAY DIFFRACTIONc_mcangle_it7.6194
X-RAY DIFFRACTIONc_scbond_it7.9224
X-RAY DIFFRACTIONc_scangle_it9.1054.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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