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- PDB-8ent: Interleukin-21 signaling complex with IL-21R and IL-2Rg -

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Basic information

Entry
Database: PDB / ID: 8ent
TitleInterleukin-21 signaling complex with IL-21R and IL-2Rg
Components
  • Cytokine receptor common subunit gamma
  • Interleukin-21
  • Interleukin-21 receptor
KeywordsCYTOKINE/CYTOKINE RECEPTOR / IL-21 / receptor / complex / signaling / CYTOKINE / CYTOKINE-CYTOKINE RECEPTOR complex
Function / homology
Function and homology information


interleukin-21 receptor activity / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / positive regulation of natural killer cell differentiation / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of natural killer cell cytokine production / interleukin-2 receptor binding / tyrosine phosphorylation of STAT protein / germinal center B cell differentiation ...interleukin-21 receptor activity / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / positive regulation of natural killer cell differentiation / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of natural killer cell cytokine production / interleukin-2 receptor binding / tyrosine phosphorylation of STAT protein / germinal center B cell differentiation / positive regulation of tissue remodeling / positive regulation of T cell differentiation in thymus / lymphocyte differentiation / natural killer cell differentiation / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-7-mediated signaling pathway / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-2-mediated signaling pathway / positive regulation of natural killer cell mediated cytotoxicity / cytokine receptor binding / T follicular helper cell differentiation / interleukin-15-mediated signaling pathway / cellular homeostasis / STAT3 nuclear events downstream of ALK signaling / Interleukin-15 signaling / cytokine receptor activity / Interleukin-2 signaling / natural killer cell activation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of B cell differentiation / positive regulation of immunoglobulin production / natural killer cell mediated cytotoxicity / cytokine binding / positive regulation of interleukin-17 production / positive regulation of interleukin-10 production / Interleukin receptor SHC signaling / coreceptor activity / cell maturation / positive regulation of B cell proliferation / positive regulation of T cell proliferation / Interleukin-7 signaling / positive regulation of phagocytosis / positive regulation of cytokine production / cytokine activity / cellular response to virus / positive regulation of type II interferon production / cytokine-mediated signaling pathway / positive regulation of inflammatory response / transmembrane signaling receptor activity / T cell differentiation in thymus / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / defense response to virus / gene expression / receptor complex / endosome / immune response / external side of plasma membrane / positive regulation of cell population proliferation / cell surface / signal transduction / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Interleukin-15/Interleukin-21 family / Interleukin 15 / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Four-helical cytokine-like, core / Fibronectin type-III domain profile. ...Interleukin-15/Interleukin-21 family / Interleukin 15 / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Four-helical cytokine-like, core / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Cytokine receptor common subunit gamma / Interleukin-21 / Interleukin-21 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsAbhiraman, G.C. / Jude, K.M. / Garcia, K.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1-AI51321 United States
Bill & Melinda Gates Foundation United States
CitationJournal: Cell Rep / Year: 2023
Title: A structural blueprint for interleukin-21 signal modulation.
Authors: Gita C Abhiraman / Theodora U J Bruun / Nathanael A Caveney / Leon L Su / Robert A Saxton / Qian Yin / Shaogeng Tang / Mark M Davis / Kevin M Jude / K Christopher Garcia /
Abstract: Interleukin-21 (IL-21) plays a critical role in generating immunological memory by promoting the germinal center reaction, yet clinical use of IL-21 remains challenging because of its pleiotropy and ...Interleukin-21 (IL-21) plays a critical role in generating immunological memory by promoting the germinal center reaction, yet clinical use of IL-21 remains challenging because of its pleiotropy and association with autoimmune disease. To better understand the structural basis of IL-21 signaling, we determine the structure of the IL-21-IL-21R-γc ternary signaling complex by X-ray crystallography and a structure of a dimer of trimeric complexes using cryo-electron microscopy. Guided by the structure, we design analogs of IL-21 by introducing substitutions to the IL-21-γc interface. These IL-21 analogs act as partial agonists that modulate downstream activation of pS6, pSTAT3, and pSTAT1. These analogs exhibit differential activity on T and B cell subsets and modulate antibody production in human tonsil organoids. These results clarify the structural basis of IL-21 signaling and offer a potential strategy for tunable manipulation of humoral immunity.
History
DepositionSep 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-21
B: Interleukin-21 receptor
C: Cytokine receptor common subunit gamma
D: Interleukin-21
E: Interleukin-21 receptor
F: Cytokine receptor common subunit gamma
G: Interleukin-21
H: Interleukin-21 receptor
I: Cytokine receptor common subunit gamma
J: Interleukin-21
K: Interleukin-21 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,81136
Polymers251,53311
Non-polymers4,27725
Water99155
1
A: Interleukin-21
B: Interleukin-21 receptor
C: Cytokine receptor common subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5379
Polymers69,1213
Non-polymers1,4156
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Interleukin-21
E: Interleukin-21 receptor
F: Cytokine receptor common subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8129
Polymers69,1213
Non-polymers6916
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Interleukin-21
H: Interleukin-21 receptor
I: Cytokine receptor common subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4969
Polymers69,1213
Non-polymers1,3746
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Interleukin-21
K: Interleukin-21 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9669
Polymers44,1692
Non-polymers7977
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.167, 66.464, 162.684
Angle α, β, γ (deg.)83.340, 83.710, 73.100
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 80 or resid 91 through 125))
d_2ens_1(chain "D" and (resid 3 through 80 or resid 91 through 125))
d_3ens_1(chain "G" and (resid 3 through 80 or resid 91 through 125))
d_4ens_1chain "J"
d_1ens_2(chain "B" and (resid 1 through 40 or (resid 41...
d_2ens_2(chain "E" and (resid 1 through 40 or (resid 41...
d_3ens_2(chain "H" and (resid 1 through 40 or (resid 41...
d_4ens_2(chain "K" and (resid 1 through 82 or resid 85 through 129 or resid 131 through 208))
d_1ens_3(chain "C" and (resid 32 through 36 or (resid 37...
d_2ens_3(chain "F" and (resid 32 through 97 or (resid 98...
d_3ens_3(chain "I" and (resid 32 through 36 or (resid 37...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNSERA1 - 78
d_12ens_1LEUSERA89 - 123
d_21ens_1GLNSERK1 - 78
d_22ens_1LEUSERK81 - 115
d_31ens_1GLNSERQ3 - 80
d_32ens_1LEUSERQ91 - 125
d_41ens_1GLNSERZ1 - 113
d_11ens_2CYSGLNB1 - 82
d_12ens_2GLNTYRB85 - 129
d_13ens_2LEUSERB131 - 208
d_21ens_2CYSTYRL1 - 127
d_22ens_2LEUSERL129 - 206
d_31ens_2CYSGLNR1 - 82
d_32ens_2GLNTYRR85 - 129
d_33ens_2LEUSERR131 - 208
d_41ens_2CYSGLNAA1 - 82
d_42ens_2GLNTYRAA85 - 129
d_43ens_2LEUSERAA131 - 208
d_11ens_3PROTRPE1 - 21
d_12ens_3ASNLYSE31 - 67
d_13ens_3ILEGLYE69 - 193
d_21ens_3PROLYSO1 - 58
d_22ens_3ILEARGO60 - 74
d_23ens_3PROGLYO76 - 185
d_31ens_3PROTRPT1 - 21
d_32ens_3ASNLYST31 - 67
d_33ens_3ILEARGT69 - 83
d_34ens_3PROGLYT85 - 194

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.744978658953, -0.0717278831469, 0.663220859506), (0.59320765357, 0.526002872623, -0.609447009787), (-0.305141733382, 0.84745270592, 0.434410443909)-1.49507335794, 30.4406357023, -114.876251213
2given(-0.293229132128, -0.956041679757, -0.000991281205704), (-0.956037641057, 0.293230777992, -0.00278203540926), (0.00295041596497, 0.000131928316919, -0.999995638811)2.97316398712, 1.87165890684, -80.0610122397
3given(-0.790141682394, -0.473157315636, 0.389612982847), (-0.534148292431, 0.219813912294, -0.816313325663), (0.300602267849, -0.853114293997, -0.426420306673)-26.0247553637, 12.8753247344, 34.9841916331
4given(0.727473012763, -0.066728320185, 0.682883845896), (0.594074238171, 0.559230252981, -0.578219096618), (-0.343305716881, 0.826322488764, 0.446466492943)-1.8638369681, 30.0338225714, -114.847286051
5given(-0.294350547625, -0.955696462371, 0.00142370098029), (-0.95569397323, 0.294353187903, 0.00228698554356), (-0.00260473491564, -0.000687446999389, -0.99999637138)2.97941020973, 1.96355993, -80.100158132
6given(-0.781492376951, -0.516685455933, 0.349722467674), (-0.518370765735, 0.225756736107, -0.824818552976), (0.347219547261, -0.825875314881, -0.444261803749)-25.2936826344, 13.0400805612, 34.8530215759
7given(0.708789702308, -0.109429244551, 0.696880476365), (0.623391370253, 0.559522869499, -0.546184362648), (-0.330152021644, 0.821559126871, 0.464801294813)-0.394697458332, 31.3022610094, -113.941005
8given(-0.296089301806, -0.955160217842, 0.00028914983134), (-0.955158880994, 0.296088345557, -0.00178988373353), (0.00162401184165, -0.000806149454317, -0.999998356353)2.95672373815, 1.80153076271, -80.0251676687

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Components

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Protein , 3 types, 11 molecules ADGJBEHKCFI

#1: Protein
Interleukin-21 / IL-21 / Za11


Mass: 16703.977 Da / Num. of mol.: 4 / Mutation: N68Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL21 / Production host: Homo sapiens (human) / References: UniProt: Q9HBE4
#2: Protein
Interleukin-21 receptor / IL-21 receptor / IL-21R / Novel interleukin receptor


Mass: 27465.482 Da / Num. of mol.: 4 / Mutation: N78Q, N85Q, N106D, N116Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL21R, NILR, UNQ3121/PRO10273 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9HBE5
#3: Protein Cytokine receptor common subunit gamma / Interleukin-2 receptor subunit gamma / IL-2 receptor subunit gamma / IL-2R subunit gamma / IL-2RG / ...Interleukin-2 receptor subunit gamma / IL-2 receptor subunit gamma / IL-2R subunit gamma / IL-2RG / gammaC / p64


Mass: 24951.838 Da / Num. of mol.: 3 / Mutation: N53Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RG / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P31785

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Sugars , 3 types, 11 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.: 3
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.: 1 / Source method: obtained synthetically
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.: 7 / Source method: obtained synthetically / 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 , 2 types, 69 molecules

#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris pH 8, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.83→48.17 Å / Num. obs: 57754 / % possible obs: 91.66 % / Redundancy: 3.7 % / Biso Wilson estimate: 70.14 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rpim(I) all: 0.1292 / Rsym value: 0.2143 / Net I/σ(I): 4.22
Reflection shellResolution: 2.831→2.932 Å / Num. unique obs: 5757 / CC1/2: 0.401

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487model building
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TGX, 2B5I

3tgx

2b5i


Resolution: 2.83→48.17 Å / SU ML: 0.5576 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.3321
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2997 1962 3.42 %random
Rwork0.2536 55437 --
obs0.2551 57399 91.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.21 Å2
Refinement stepCycle: LAST / Resolution: 2.83→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15503 0 277 55 15835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002316225
X-RAY DIFFRACTIONf_angle_d0.588522007
X-RAY DIFFRACTIONf_chiral_restr0.04152371
X-RAY DIFFRACTIONf_plane_restr0.00482809
X-RAY DIFFRACTIONf_dihedral_angle_d13.25276019
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.20817591276
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.765354142107
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.24524359338
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.773081879451
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.642445498043
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.701217896471
ens_3d_2EX-RAY DIFFRACTIONTorsion NCS1.10656700392
ens_3d_3EX-RAY DIFFRACTIONTorsion NCS0.855964192661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.90.55071290.45943629X-RAY DIFFRACTION82.88
2.9-2.980.41981410.39873924X-RAY DIFFRACTION91.7
2.98-3.060.41741430.35383952X-RAY DIFFRACTION91.1
3.06-3.160.36851350.31593824X-RAY DIFFRACTION86.9
3.16-3.280.38031410.29614053X-RAY DIFFRACTION94.97
3.28-3.410.38091470.29914077X-RAY DIFFRACTION94.16
3.41-3.560.31781410.28244047X-RAY DIFFRACTION93.38
3.56-3.750.28621430.25474024X-RAY DIFFRACTION92.76
3.75-3.980.2641350.24053934X-RAY DIFFRACTION91.15
3.98-4.290.2971430.23163887X-RAY DIFFRACTION89.56
4.29-4.720.23761410.20344134X-RAY DIFFRACTION94.92
4.72-5.410.25481410.2134035X-RAY DIFFRACTION93.51
5.41-6.810.2881390.25543896X-RAY DIFFRACTION89.97
6.81-48.170.27391430.22044021X-RAY DIFFRACTION92.64

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