[English] 日本語
Yorodumi
- PDB-8dpu: The crystal structure of the IL-11 signalling complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dpu
TitleThe crystal structure of the IL-11 signalling complex
Components
  • Interleukin-11
  • Interleukin-11 receptor subunit alpha
  • Interleukin-6 receptor subunit beta
KeywordsCYTOKINE / Complex / GP130 / glycoprotein 130 / signalling / cancer / CYTOKINE-RECEPTOR complex
Function / homology
Function and homology information


interleukin-11 receptor binding / ciliary neurotrophic factor receptor activity / oncostatin-M-mediated signaling pathway / leukemia inhibitory factor signaling pathway / negative regulation of interleukin-6-mediated signaling pathway / oncostatin-M receptor complex / interleukin-27 receptor activity / ciliary neurotrophic factor receptor binding / ciliary neurotrophic factor-mediated signaling pathway / interleukin-11 receptor activity ...interleukin-11 receptor binding / ciliary neurotrophic factor receptor activity / oncostatin-M-mediated signaling pathway / leukemia inhibitory factor signaling pathway / negative regulation of interleukin-6-mediated signaling pathway / oncostatin-M receptor complex / interleukin-27 receptor activity / ciliary neurotrophic factor receptor binding / ciliary neurotrophic factor-mediated signaling pathway / interleukin-11 receptor activity / interleukin-11 binding / interleukin-27-mediated signaling pathway / ciliary neurotrophic factor receptor complex / interleukin-6 receptor complex / megakaryocyte differentiation / head development / negative regulation of hormone secretion / interleukin-11-mediated signaling pathway / T-helper 17 cell lineage commitment / developmental process / positive regulation of adaptive immune response / positive regulation of acute inflammatory response / positive regulation of astrocyte differentiation / intestinal epithelial cell development / positive regulation of platelet aggregation / IL-6-type cytokine receptor ligand interactions / Interleukin-27 signaling / Interleukin-35 Signalling / cytokine receptor activity / cell surface receptor signaling pathway via STAT / positive regulation of peptidyl-tyrosine phosphorylation / Interleukin-6 signaling / growth factor binding / glycogen metabolic process / interleukin-6-mediated signaling pathway / positive regulation of cardiac muscle hypertrophy / positive regulation of Notch signaling pathway / MAPK3 (ERK1) activation / cytokine binding / fat cell differentiation / MAPK1 (ERK2) activation / protein tyrosine kinase activator activity / positive regulation of vascular endothelial growth factor production / positive regulation of peptidyl-serine phosphorylation / positive regulation of osteoblast differentiation / coreceptor activity / response to cytokine / positive regulation of T cell proliferation / embryo implantation / B cell differentiation / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / transmembrane signaling receptor activity / scaffold protein binding / negative regulation of neuron apoptotic process / cell population proliferation / receptor complex / positive regulation of MAPK cascade / membrane raft / external side of plasma membrane / neuronal cell body / positive regulation of cell population proliferation / dendrite / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Interleukin-11, mammalian / Interleukin-11 / Interleukin 11 / : / : / Type I cytokine receptor, cytokine-binding domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Interleukin-6 receptor alpha chain, binding / Immunoglobulin C2-set-like, ligand-binding ...Interleukin-11, mammalian / Interleukin-11 / Interleukin 11 / : / : / Type I cytokine receptor, cytokine-binding domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Interleukin-6 receptor alpha chain, binding / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Four-helical cytokine-like, core / Fibronectin type III domain / Fibronectin type 3 domain / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-11 / Interleukin-6 receptor subunit beta / Interleukin-11 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.78 Å
AuthorsMetcalfe, R.D. / Aizel, K. / Griffin, M.D.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1147621 Australia
CitationJournal: Nat Commun / Year: 2023
Title: Structures of the interleukin 11 signalling complex reveal gp130 dynamics and the inhibitory mechanism of a cytokine variant.
Authors: Riley D Metcalfe / Eric Hanssen / Ka Yee Fung / Kaheina Aizel / Clara C Kosasih / Courtney O Zlatic / Larissa Doughty / Craig J Morton / Andrew P Leis / Michael W Parker / Paul R Gooley / ...Authors: Riley D Metcalfe / Eric Hanssen / Ka Yee Fung / Kaheina Aizel / Clara C Kosasih / Courtney O Zlatic / Larissa Doughty / Craig J Morton / Andrew P Leis / Michael W Parker / Paul R Gooley / Tracy L Putoczki / Michael D W Griffin /
Abstract: Interleukin (IL-)11, an IL-6 family cytokine, has pivotal roles in autoimmune diseases, fibrotic complications, and solid cancers. Despite intense therapeutic targeting efforts, structural ...Interleukin (IL-)11, an IL-6 family cytokine, has pivotal roles in autoimmune diseases, fibrotic complications, and solid cancers. Despite intense therapeutic targeting efforts, structural understanding of IL-11 signalling and mechanistic insights into current inhibitors are lacking. Here we present cryo-EM and crystal structures of the human IL-11 signalling complex, including the complex containing the complete extracellular domains of the shared IL-6 family β-receptor, gp130. We show that complex formation requires conformational reorganisation of IL-11 and that the membrane-proximal domains of gp130 are dynamic. We demonstrate that the cytokine mutant, IL-11 Mutein, competitively inhibits signalling in human cell lines. Structural shifts in IL-11 Mutein underlie inhibition by altering cytokine binding interactions at all three receptor-engaging sites and abrogating the final gp130 binding step. Our results reveal the structural basis of IL-11 signalling, define the molecular mechanisms of an inhibitor, and advance understanding of gp130-containing receptor complexes, with potential applications in therapeutic development.
History
DepositionJul 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 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-6 receptor subunit beta
B: Interleukin-11
C: Interleukin-11 receptor subunit alpha
D: Interleukin-6 receptor subunit beta
E: Interleukin-11
F: Interleukin-11 receptor subunit alpha
G: Interleukin-6 receptor subunit beta
H: Interleukin-11
I: Interleukin-11 receptor subunit alpha
J: Interleukin-6 receptor subunit beta
K: Interleukin-11
L: Interleukin-11 receptor subunit alpha
M: Interleukin-6 receptor subunit beta
N: Interleukin-11
O: Interleukin-11 receptor subunit alpha
P: Interleukin-6 receptor subunit beta
Q: Interleukin-11
R: Interleukin-11 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)561,23148
Polymers551,18318
Non-polymers10,04730
Water00
1
A: Interleukin-6 receptor subunit beta
B: Interleukin-11
C: Interleukin-11 receptor subunit alpha
D: Interleukin-6 receptor subunit beta
E: Interleukin-11
F: Interleukin-11 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,07716
Polymers183,7286
Non-polymers3,34910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Interleukin-6 receptor subunit beta
H: Interleukin-11
I: Interleukin-11 receptor subunit alpha
J: Interleukin-6 receptor subunit beta
K: Interleukin-11
L: Interleukin-11 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,07716
Polymers183,7286
Non-polymers3,34910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
M: Interleukin-6 receptor subunit beta
N: Interleukin-11
O: Interleukin-11 receptor subunit alpha
P: Interleukin-6 receptor subunit beta
Q: Interleukin-11
R: Interleukin-11 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,07716
Polymers183,7286
Non-polymers3,34910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.411, 163.411, 506.623
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Space group name HallP312(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: -y,-x,-z+2/3
#5: -x+y,y,-z+1/3
#6: x,x-y,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "G"
d_2ens_1chain "D"
d_3ens_1chain "A"
d_4ens_1chain "J"
d_5ens_1chain "M"
d_6ens_1chain "P"
d_1ens_2chain "N"
d_2ens_2chain "E"
d_3ens_2chain "H"
d_4ens_2chain "K"
d_5ens_2chain "B"
d_6ens_2chain "Q"
d_1ens_3chain "R"
d_2ens_3chain "F"
d_3ens_3chain "I"
d_4ens_3chain "L"
d_5ens_3chain "O"
d_6ens_3chain "C"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPGLUE1 - 298
d_12ens_1NAGNAGX
d_13ens_1NAGNAGX
d_14ens_1NAGNAGY
d_15ens_1NAGNAGY
d_21ens_1ASPGLUD1 - 298
d_22ens_1NAGNAGV
d_23ens_1NAGNAGV
d_24ens_1NAGNAGW
d_25ens_1NAGNAGW
d_31ens_1ASPGLUA1 - 298
d_32ens_1NAGNAGS
d_33ens_1NAGNAGS
d_34ens_1NAGNAGT
d_35ens_1NAGNAGT
d_41ens_1ASPGLUF1 - 298
d_42ens_1NAGNAGZ
d_43ens_1NAGNAGZ
d_44ens_1NAGNAGAA
d_45ens_1NAGNAGAA
d_51ens_1ASPGLUG1 - 298
d_52ens_1NAGNAGBA
d_53ens_1NAGNAGBA
d_54ens_1NAGNAGCA
d_55ens_1NAGNAGCA
d_61ens_1ASPGLUH1 - 298
d_62ens_1NAGNAGDA
d_63ens_1NAGNAGDA
d_64ens_1NAGNAGEA
d_65ens_1NAGNAGEA
d_11ens_2ARGLEUL1 - 164
d_21ens_2ARGLEUI1 - 164
d_31ens_2ARGLEUJ1 - 164
d_41ens_2ARGLEUK1 - 164
d_51ens_2ARGLEUB1 - 164
d_61ens_2ARGLEUM1 - 164
d_11ens_3PROSERR1 - 283
d_12ens_3NAGNAGVA
d_13ens_3NAGNAGJA
d_14ens_3NAGNAGJA
d_15ens_3BMABMAJA
d_21ens_3PROSERN1 - 283
d_22ens_3NAGNAGRA
d_23ens_3NAGNAGFA
d_24ens_3NAGNAGFA
d_25ens_3BMABMAFA
d_31ens_3PROSERO1 - 283
d_32ens_3NAGNAGSA
d_33ens_3NAGNAGGA
d_34ens_3NAGNAGGA
d_35ens_3BMABMAGA
d_41ens_3PROSERP1 - 283
d_42ens_3NAGNAGTA
d_43ens_3NAGNAGHA
d_44ens_3NAGNAGHA
d_45ens_3BMABMAHA
d_51ens_3PROSERQ1 - 283
d_52ens_3NAGNAGUA
d_53ens_3NAGNAGIA
d_54ens_3NAGNAGIA
d_55ens_3BMABMAIA
d_61ens_3PROSERC1 - 283
d_62ens_3NAGNAGLA
d_63ens_3NAGNAGU
d_64ens_3NAGNAGU
d_65ens_3BMABMAU

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.265502677675, -0.607468399371, -0.748659115962), (-0.494124936406, 0.752524864168, -0.435369815249), (0.827858004352, 0.254339286337, -0.499962650661)64.3196395708, 28.0701618481, -2.77641223555
2given(0.207530926847, 0.583564528786, 0.785100856671), (0.589169859717, -0.715245742134, 0.37590212125), (0.780903189136, 0.384546445961, -0.492254243349)-32.0944372553, 80.001359607, -9.42690200553
3given(0.305230767718, 0.52263165459, -0.796046689622), (0.515168696934, -0.793675965127, -0.323542386836), (-0.800896617634, -0.311343244668, -0.511497792626)-5.80309904303, 95.8581225286, 52.6418124918
4given(-0.264708655941, -0.473110354611, 0.840295138525), (-0.61484299365, 0.754094181011, 0.23088971247), (-0.742897988037, -0.455531073062, -0.490503843865)32.6795368088, 18.6717441804, 58.9286040231
5given(-0.997965627298, -0.00174258728427, -0.0637304489334), (-0.00712443167537, -0.990317081147, 0.138640979735), (-0.0633549461763, 0.138812975539, 0.988289992167)30.9926959637, 107.671478275, -6.73788040851
6given(-0.259679754212, -0.494293328862, 0.829602633973), (-0.617592094866, 0.745430581297, 0.250825143925), (-0.742392369042, -0.447221816897, -0.498844882584)33.4399713689, 18.52637232, 59.698583476
7given(-0.262262431744, -0.600122701799, -0.755692503391), (-0.487883457164, 0.758105359218, -0.432719304574), (0.832579214923, 0.255203854027, -0.491612493503)63.8896057244, 27.6011481879, -3.51719518762
8given(-0.997094342645, -0.00194371235277, -0.0761517816489), (-0.00806343742546, -0.991365093811, 0.130882511247), (-0.0757486161121, 0.131116256642, 0.988468853531)31.4997573263, 107.747502421, -6.31553693328
9given(0.296119546705, 0.510621020962, -0.807204674795), (0.510799794421, -0.798764593135, -0.317897302242), (-0.807091558671, -0.318184376902, -0.497354921778)-5.28763941826, 96.4068041566, 52.5687514727
10given(0.168127048406, 0.566182676873, 0.80695134426), (0.598334568756, -0.709174491051, 0.372917263042), (0.783408603109, 0.42012940584, -0.45799808179)-33.7182816613, 78.7812047954, -12.257861583
11given(0.359651129657, 0.474640526023, -0.803347643298), (0.524014615532, -0.815109215772, -0.246993216651), (-0.772049057797, -0.332134517055, -0.541873523006)-3.52213797283, 98.9104767687, 52.487046771
12given(-0.993964522421, -0.00336027702879, -0.109650520779), (-0.0117526444181, -0.990516456043, 0.136890560879), (-0.109070635453, 0.137353044549, 0.984498724039)29.6434415412, 107.608542679, -6.00569020228
13given(-0.223107972388, -0.627123184881, -0.746283688446), (-0.452268739193, 0.744787941913, -0.490656610196), (0.863525228471, 0.228051381414, -0.449796339725)64.5159651821, 26.6438332739, -0.476070901639
14given(0.169495466074, 0.606399440772, 0.776885451796), (0.563323891613, -0.706433768662, 0.428506153552), (0.808664009412, 0.365008285831, -0.461336613717)-32.8155660641, 81.0176723607, -7.67236481184
15given(-0.335286205015, -0.448112895716, 0.828720696869), (-0.610264981608, 0.773449966672, 0.171323674015), (-0.717746343042, -0.448296756343, -0.532794712157)31.1616174886, 15.4212891613, 57.0914501454

-
Components

-
Protein , 3 types, 18 molecules ADGJMPBEHKNQCFILOR

#1: Protein
Interleukin-6 receptor subunit beta / IL-6 receptor subunit beta / IL-6R subunit beta / IL-6R-beta / IL-6RB / CDw130 / Interleukin-6 ...IL-6 receptor subunit beta / IL-6R subunit beta / IL-6R-beta / IL-6RB / CDw130 / Interleukin-6 signal transducer / Membrane glycoprotein 130 / gp130 / Oncostatin-M receptor subunit alpha


Mass: 34563.961 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6ST / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P40189
#2: Protein
Interleukin-11 / IL-11 / Adipogenesis inhibitory factor / AGIF


Mass: 19226.416 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20809
#3: Protein
Interleukin-11 receptor subunit alpha / IL-11 receptor subunit alpha / IL-11R subunit alpha / IL-11R-alpha / IL-11RA


Mass: 38073.508 Da / Num. of mol.: 6 / Mutation: C226S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL11RA / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14626

-
Sugars , 3 types, 30 molecules

#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.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 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.: 18
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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.25
Details: 180 mM magnesium chloride, 15.3% PEG 3350, 100 mM potassium sodium tartrate, 90 mM sodium HEPES pH 7.25 and 1.8% tert-butanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.779→49.275 Å / Num. obs: 48027 / % possible obs: 92.8 % / Redundancy: 20.9 % / Biso Wilson estimate: 126.31 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.064 / Rrim(I) all: 0.294 / Rsym value: 0.286 / Net I/σ(I): 10.6
Reflection shellResolution: 3.779→4.197 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2262 / CC1/2: 0.548 / Rpim(I) all: 0.558 / Rrim(I) all: 2.584 / Rsym value: 2.522

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DPS

8dps


Resolution: 3.78→40.86 Å / SU ML: 0.6282 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.2385
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2951 2054 4.54 %
Rwork0.2756 43181 -
obs0.2765 45235 58.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 175.3 Å2
Refinement stepCycle: LAST / Resolution: 3.78→40.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34914 0 654 0 35568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005636546
X-RAY DIFFRACTIONf_angle_d1.203549956
X-RAY DIFFRACTIONf_chiral_restr0.05885682
X-RAY DIFFRACTIONf_plane_restr0.00726360
X-RAY DIFFRACTIONf_dihedral_angle_d9.68325160
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2GX-RAY DIFFRACTIONNCS constraints5.31069407811E-12
ens_1d_3GX-RAY DIFFRACTIONNCS constraints1.48377315684E-12
ens_1d_4GX-RAY DIFFRACTIONNCS constraints1.63812474458E-12
ens_1d_5GX-RAY DIFFRACTIONNCS constraints6.08173820582E-12
ens_1d_6GX-RAY DIFFRACTIONNCS constraints2.26776251009E-12
ens_2d_2NX-RAY DIFFRACTIONNCS constraints7.89311033029E-12
ens_2d_3NX-RAY DIFFRACTIONNCS constraints2.29790034744E-12
ens_2d_4NX-RAY DIFFRACTIONNCS constraints1.47088919813E-12
ens_2d_5NX-RAY DIFFRACTIONNCS constraints4.29345428365E-12
ens_2d_6NX-RAY DIFFRACTIONNCS constraints5.82794000469E-12
ens_3d_2RX-RAY DIFFRACTIONNCS constraints6.09787184976E-12
ens_3d_3RX-RAY DIFFRACTIONNCS constraints1.18757147017E-12
ens_3d_4RX-RAY DIFFRACTIONNCS constraints1.43696834152E-12
ens_3d_5RX-RAY DIFFRACTIONNCS constraints1.5985643932E-12
ens_3d_6RX-RAY DIFFRACTIONNCS constraints5.58443611491E-12
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.78-3.870.732710.4297137X-RAY DIFFRACTION2.69
3.87-3.960.4274200.3648403X-RAY DIFFRACTION8.27
3.96-4.070.4193530.3934632X-RAY DIFFRACTION13.31
4.07-4.190.368550.3883923X-RAY DIFFRACTION18.98
4.19-4.330.3815910.36881150X-RAY DIFFRACTION24.08
4.33-4.480.4545100.35271647X-RAY DIFFRACTION32.45
4.48-4.660.33691760.32962199X-RAY DIFFRACTION45.66
4.66-4.870.32221330.28962881X-RAY DIFFRACTION58.58
4.87-5.130.33921190.28273580X-RAY DIFFRACTION71.19
5.13-5.450.3021650.28844590X-RAY DIFFRACTION91.67
5.45-5.870.3232970.29174889X-RAY DIFFRACTION99.96
5.87-6.460.34742570.30634945X-RAY DIFFRACTION100
6.46-7.390.32131980.27955029X-RAY DIFFRACTION100
7.39-9.290.23212150.23975032X-RAY DIFFRACTION99.98
9.29-40.860.25242640.2455144X-RAY DIFFRACTION99.8

+
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