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- PDB-6ye3: IL-2 in complex with a Fab fragment from UFKA-20 -

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Basic information

Entry
Database: PDB / ID: 6ye3
TitleIL-2 in complex with a Fab fragment from UFKA-20
Components
  • Chains: A,D,G
  • Chains: B,E,H
  • Interleukin-2
KeywordsPROTEIN BINDING / IL-2 / Fab / Treg
Function / homology
Function and homology information


kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation ...kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / activated T cell proliferation / natural killer cell activation / positive regulation of regulatory T cell differentiation / : / kinase activator activity / negative regulation of B cell apoptotic process / Interleukin-2 signaling / positive regulation of immunoglobulin production / positive regulation of dendritic spine development / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / T cell differentiation / Interleukin receptor SHC signaling / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein phosphorylation / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of type II interferon production / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / positive regulation of cell growth / carbohydrate binding / response to ethanol / adaptive immune response / transcription by RNA polymerase II / cell adhesion / immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsKarakus, U. / Mittl, P. / Boyman, O.
CitationJournal: Sci Transl Med / Year: 2020
Title: Receptor-gated IL-2 delivery by an anti-human IL-2 antibody activates regulatory T cells in three different species.
Authors: Karakus, U. / Sahin, D. / Mittl, P.R.E. / Mooij, P. / Koopman, G. / Boyman, O.
History
DepositionMar 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chains: A,D,G
B: Chains: B,E,H
C: Interleukin-2
D: Chains: A,D,G
E: Chains: B,E,H
F: Interleukin-2
G: Chains: A,D,G
H: Chains: B,E,H
I: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,68012
Polymers267,4079
Non-polymers1,2733
Water1,63991
1
A: Chains: A,D,G
B: Chains: B,E,H
C: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5604
Polymers89,1363
Non-polymers4241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Chains: A,D,G
E: Chains: B,E,H
F: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5604
Polymers89,1363
Non-polymers4241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Chains: A,D,G
H: Chains: B,E,H
I: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5604
Polymers89,1363
Non-polymers4241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)238.384, 92.547, 121.892
Angle α, β, γ (deg.)90.000, 100.112, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUASPASPchain 'A'AA1 - 2231 - 223
221GLUGLUASPASP(chain 'D' and resid 1 through 223)DD1 - 2231 - 223
331GLUGLUASPASP(chain 'G' and resid 1 through 223)GG1 - 2231 - 223
142ASPASPASNASNchain 'B'BB1 - 2191 - 219
252ASPASPASNASNchain 'E'EE1 - 2191 - 219
362ASPASPASNASNchain 'H'HH1 - 2191 - 219
173SERSERLEULEU(chain 'C' and resid -1 through 127)CC-1 - 1275 - 133
283SERSERLEULEU(chain 'F' and resid -1 through 127)FF-1 - 1275 - 133
393SERSERLEULEU(chain 'I' and resid -1 through 127)II-1 - 1275 - 133

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Chains: A,D,G


Mass: 49417.715 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): B-cell clone / Production host: Homo sapiens (human)
#2: Antibody Chains: B,E,H


Mass: 24150.686 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): B-cell clone / Production host: Homo sapiens (human)
#3: Protein Interleukin-2 / IL-2 / T-cell growth factor / TCGF


Mass: 15567.178 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2 / Production host: Homo sapiens (human) / References: UniProt: P60568
#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-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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10.86% (v/v) PEG 8000, 5.76% (v/v) ethylene glycol, 100 mM HEPES, pH 7.48

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→49.4 Å / Num. obs: 114189 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 99.35 Å2 / CC1/2: 0.992 / CC star: 0.998 / Net I/σ(I): 5.74
Reflection shellResolution: 2.89→2.993 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 0.38 / Num. unique obs: 5708 / CC1/2: 0.186 / CC star: 0.56 / % possible all: 98.21

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5b6f
Resolution: 2.89→49.4 Å / SU ML: 0.7233 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 37.4927
RfactorNum. reflection% reflection
Rfree0.2833 5726 5.01 %
Rwork0.2152 --
obs0.2185 114189 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 116.88 Å2
Refinement stepCycle: LAST / Resolution: 2.89→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13384 0 84 91 13559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009313778
X-RAY DIFFRACTIONf_angle_d1.317218719
X-RAY DIFFRACTIONf_chiral_restr0.0672132
X-RAY DIFFRACTIONf_plane_restr0.00872361
X-RAY DIFFRACTIONf_dihedral_angle_d20.27725007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.920.43971660.42313101X-RAY DIFFRACTION88.08
2.92-2.960.4491920.42693711X-RAY DIFFRACTION99.92
2.96-2.990.45261910.42133690X-RAY DIFFRACTION99.82
2.99-3.030.38651880.41373538X-RAY DIFFRACTION99.73
3.03-3.070.42311930.40973647X-RAY DIFFRACTION99.74
3.07-3.110.44641950.40583673X-RAY DIFFRACTION99.85
3.11-3.160.39971850.41463592X-RAY DIFFRACTION99.45
3.16-3.20.36361940.38343675X-RAY DIFFRACTION99.69
3.2-3.250.42151920.34863620X-RAY DIFFRACTION99.4
3.25-3.310.3841970.36163678X-RAY DIFFRACTION99.77
3.31-3.360.37921920.3343578X-RAY DIFFRACTION99.34
3.36-3.420.33731900.31983626X-RAY DIFFRACTION99.66
3.42-3.490.33191900.30083571X-RAY DIFFRACTION99.39
3.49-3.560.36921930.28283700X-RAY DIFFRACTION99.59
3.56-3.640.35141910.27733577X-RAY DIFFRACTION99.45
3.64-3.720.33691900.27963634X-RAY DIFFRACTION99.51
3.72-3.820.27541960.25723646X-RAY DIFFRACTION99.71
3.82-3.920.32211890.23083631X-RAY DIFFRACTION99.61
3.92-4.030.30061910.21313632X-RAY DIFFRACTION99.61
4.03-4.160.25351910.1973629X-RAY DIFFRACTION99.95
4.16-4.310.28041920.17653601X-RAY DIFFRACTION99.82
4.31-4.490.26261920.16323683X-RAY DIFFRACTION99.72
4.49-4.690.23421950.16013607X-RAY DIFFRACTION99.66
4.69-4.940.23271940.15283671X-RAY DIFFRACTION99.79
4.94-5.250.22191930.15183590X-RAY DIFFRACTION99.24
5.25-5.650.22421870.15383624X-RAY DIFFRACTION99.56
5.65-6.220.24251940.17723623X-RAY DIFFRACTION99.5
6.22-7.110.30651960.18673654X-RAY DIFFRACTION99.87
7.12-8.960.22861890.15553628X-RAY DIFFRACTION99.92
8.96-49.40.23841880.16933633X-RAY DIFFRACTION99.27
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.4795697497330.0241554550243-0.4240770010310.0616261388584-0.1361281622850.822751376013-0.06508075595410.5710072663240.05736388676830.0687792743605-0.148300377010.0671628300995-0.2157766956170.594029475508-0.004870341923810.4057129766590.04672262815830.008461170866660.745100518975-0.155022464770.49417105375-23.0880858286-87.958421419860.3155621993
20.2519529649170.09208264575480.2846090893630.3565577283420.6523116043930.733127788579-0.6771416886110.7357155309380.180720037665-0.4970843312710.7029788276990.126287924217-0.2948212865650.04298970730030.0001081844568090.745526443588-0.177790793118-0.0426412763761.146133723960.01957231164960.87254431515-50.5447460286-88.800689832142.5531119997
31.084737361350.370707147356-0.5189005649950.9823249800840.1397575622370.7401530355310.279689640686-0.316100097164-0.1985264523040.176866185405-0.188302596098-0.02500871097940.02115316114080.044006352221-3.39504673209E-50.6230825030290.02836956388680.03998684336180.813085047863-0.08081466305290.618497388371-37.2674935414-89.586604529876.8142251538
40.6650801025820.153120903378-0.2726006855330.1444725466340.8886638371070.4020753250430.1225549605440.3803546827620.09952657359720.09018880359110.23572196291-0.1247743448620.119227469481-0.44724007568-5.53017678914E-60.53234102595-0.1688357389480.0111060693291.00418215157-0.1797779752660.65517430634-59.1339656323-100.78473985747.4294367073
50.8552281706580.0483394437685-0.0955452490730.6739564677020.3322401411421.08314381914-0.09940628315030.000154936932658-0.04766249103010.0830180921847-0.0728611257661-0.0355137051519-0.240940731346-0.07714958124257.48939780113E-50.539944002304-0.0745886167059-0.06706379172320.948368428116-0.1051113235980.710138922878-10.1097950165-75.419597587183.882006697
60.51043022228-0.1866703366760.7540317486030.775288932860.03908460035780.54785779287-0.4062994626-0.09928274925810.209249114123-0.124699854596-0.06357889735850.126642304803-0.321252386892-0.0201318207074-0.0004412562263570.9447037150270.216864195433-0.1816971764850.522555027798-0.02619556497010.870692686028-35.3621227307-61.56140897672.34225451357
70.677181884511-0.3779251786980.3637870228040.444988057826-0.3817528449810.7620457633890.1900481238940.888843813592-0.120510562609-0.2023961109530.2148183585950.1055302205840.3187959538331.78075346058-0.0003297260293670.9964618432490.1175083051580.09881179143621.21481561876-0.2376205938950.831198310555-36.906156111-27.96467359087.06845584883
80.497674946262-0.0608762009515-0.03290488663890.232688658643-0.05469250436520.427219610394-0.600084938571-0.3766317146140.126155284510.08143677633540.290273375255-0.0587716540354-0.605810631498-0.0417471140741-7.65354286442E-51.163020342870.263543833283-0.331319308180.758811126156-0.1247847469070.894875795506-30.9030722688-61.211471580523.7351371101
90.1215290788780.205271235640.1938870329631.176564683821.135139821351.066601619620.307499107072-0.080599349244-0.5195195328180.4431977439530.3052951045990.4206089157560.04140828440150.4785238732460.000314782467561.024662194890.08077230488440.08915032422310.651206308374-0.1016418220810.834070017755-45.7707653798-26.287466541819.2979617822
100.518890500899-0.3232002530670.3153277592090.9282978936330.1514507125270.9077464628950.137820224223-0.107114169866-0.149830325982-0.129828163991-0.00500321401743-0.08665199652450.2859222146660.6303125628480.001620920342440.5737327344430.194542797307-0.08150843175240.575011920021-0.05924076995920.632603183402-21.3302075822-87.15948879847.81091908881
110.439920731712-0.06468663032020.05647572213681.52456303428-0.4597327877891.13605140107-0.176806457021-0.364677264845-0.0217031015117-0.5116967699010.1640715849980.335375822032-0.165967199095-4.0786793927E-5-9.10436260416E-50.62595628066-0.06413088440270.09572344933180.43440368453-0.06764115899080.511728308118-78.9343065134-35.184010778513.495818075
120.126509119439-0.26390046924-0.1648354766820.9257246062040.4640074628150.3001448955170.615054616559-0.97729861865-0.541067447488-0.434083301289-0.005275263420460.1549170073630.729856192567-1.197354660650.03616076804670.776836006047-0.440745401364-0.2881777821760.8999930024750.4941379217260.92937840196-74.9391697918-68.173008277517.3484371933
130.347188969202-0.129268533840.3537857652880.312982110210.1875330511641.034198829870.15037524415-0.775592187157-0.1304546485680.1118890219660.180942125636-0.178070345492-0.04389694277570.692870367405-9.95170781469E-50.591830692229-0.08508549380440.0693604726280.901020953445-0.04186640233860.589411903496-71.0299977881-34.956910156233.8224626157
142.16933885328-0.3793300315770.7313658602260.6426284959090.2719467711160.8702950947770.982807962449-1.59736487315-0.853536637659-0.04070390216150.507762077779-0.1376535669491.39926322164-0.8787426062850.3508615902981.095452044190.0327387236389-0.3715502722480.2874512666180.2317626933591.04178874141-60.8221509572-70.220851861523.0797766255
150.1674093703730.0970857058363-0.1404526184450.8165004762150.3135401423141.03683128953-0.318754282109-0.5536942376140.298931379452-0.002104061636760.06935292248140.398092834701-0.453420229778-0.2799505678494.12959883259E-50.9619984826710.1270534542040.1407247864990.751433276719-0.1186306987740.76514142547-88.4947609696-9.8834027242825.6544069245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 124 )
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 223 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 114 )
4X-RAY DIFFRACTION4chain 'B' and (resid 115 through 219 )
5X-RAY DIFFRACTION5chain 'C' and (resid -2 through 128 )
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 124 )
7X-RAY DIFFRACTION7chain 'D' and (resid 125 through 225 )
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 114 )
9X-RAY DIFFRACTION9chain 'E' and (resid 115 through 219 )
10X-RAY DIFFRACTION10chain 'F' and (resid -1 through 128 )
11X-RAY DIFFRACTION11chain 'G' and (resid 1 through 124 )
12X-RAY DIFFRACTION12chain 'G' and (resid 125 through 225 )
13X-RAY DIFFRACTION13chain 'H' and (resid 1 through 114 )
14X-RAY DIFFRACTION14chain 'H' and (resid 115 through 219 )
15X-RAY DIFFRACTION15chain 'I' and (resid -3 through 128 )

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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

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