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- PDB-8sve: Structure of Monomeric Interleukin-10 Grafted into and Antibody CDR -

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Basic information

Entry
Database: PDB / ID: 8sve
TitleStructure of Monomeric Interleukin-10 Grafted into and Antibody CDR
Components
  • Fab Heavy chain
  • Interleukin-10,Fab light chain
KeywordsCYTOKINE / antibody cytokine graft / engineered protein / immune regulatory cytokine
Function / homology
Function and homology information


negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation / negative regulation of interferon-alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / positive regulation of B cell apoptotic process / chronic inflammatory response to antigenic stimulus ...negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation / negative regulation of interferon-alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / positive regulation of B cell apoptotic process / chronic inflammatory response to antigenic stimulus / : / response to inactivity / negative regulation of membrane protein ectodomain proteolysis / positive regulation of plasma cell differentiation / response to carbon monoxide / regulation of isotype switching / negative regulation of heterotypic cell-cell adhesion / negative regulation of cytokine production involved in immune response / negative regulation of interleukin-1 production / negative regulation of MHC class II biosynthetic process / : / branching involved in labyrinthine layer morphogenesis / interleukin-10-mediated signaling pathway / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-8 production / negative regulation of interleukin-12 production / endothelial cell apoptotic process / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of heterotypic cell-cell adhesion / leukocyte chemotaxis / type 2 immune response / CD163 mediating an anti-inflammatory response / negative regulation of cytokine production / positive regulation of immunoglobulin production / cellular response to hepatocyte growth factor stimulus / regulation of synapse organization / positive regulation of sprouting angiogenesis / negative regulation of B cell proliferation / defense response to protozoan / negative regulation of vascular associated smooth muscle cell proliferation / Interleukin-10 signaling / negative regulation of interleukin-6 production / hemopoiesis / negative regulation of type II interferon production / B cell proliferation / negative regulation of mitotic cell cycle / negative regulation of tumor necrosis factor production / response to glucocorticoid / negative regulation of T cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of cell cycle / positive regulation of endothelial cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / B cell differentiation / FCGR3A-mediated IL10 synthesis / negative regulation of autophagy / liver regeneration / positive regulation of cytokine production / cytokine activity / response to activity / positive regulation of DNA-binding transcription factor activity / positive regulation of receptor signaling pathway via JAK-STAT / response to insulin / cellular response to estradiol stimulus / growth factor activity / response to molecule of bacterial origin / positive regulation of miRNA transcription / negative regulation of inflammatory response / Signaling by ALK fusions and activated point mutants / regulation of gene expression / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / protein dimerization activity / defense response to bacterium / response to xenobiotic stimulus / negative regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-10 / Interleukin-10 family / Interleukin 10 / Interleukin-10/19/20/22/24/26 family / Interleukin-10, conserved site / Interleukin-10 family signature. / Four-helical cytokine-like, core
Similarity search - Domain/homology
ACETATE ION / Interleukin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDiDonato, M. / Spraggon, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: A novel interleukin-10 antibody graft to treat inflammatory bowel disease.
Authors: DiDonato, M. / Simpson, C.T. / Vo, T. / Knuth, M. / Geierstanger, B. / Jamontt, J. / Jones, D.H. / Fathman, J.W. / DeLarosa, D. / Junt, T. / Picard, D. / Sommer, U. / Bagger, M. / Peters, E. ...Authors: DiDonato, M. / Simpson, C.T. / Vo, T. / Knuth, M. / Geierstanger, B. / Jamontt, J. / Jones, D.H. / Fathman, J.W. / DeLarosa, D. / Junt, T. / Picard, D. / Sommer, U. / Bagger, M. / Peters, E. / Meeusen, S. / Spraggon, G.
History
DepositionMay 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab Heavy chain
I: Fab Heavy chain
L: Interleukin-10,Fab light chain
M: Interleukin-10,Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,41310
Polymers133,0444
Non-polymers3696
Water4,197233
1
H: Fab Heavy chain
L: Interleukin-10,Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6434
Polymers66,5222
Non-polymers1212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Fab Heavy chain
M: Interleukin-10,Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7706
Polymers66,5222
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.641, 104.662, 82.826
Angle α, β, γ (deg.)90.000, 115.290, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "H" and (resid 1 through 4 or resid 6 through 220))
d_2ens_1(chain "I" and (resid 1 through 4 or resid 6 through 220))
d_1ens_2(chain "L" and (resid 1 through 22 or resid 24...
d_2ens_2(chain "M" and (resid 1 through 22 or resid 24...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1PCAPCALEULEUHA1 - 41 - 4
d_12ens_1GLUGLUPROPROHA6 - 2206 - 220
d_21ens_1PCAPCALEULEUIB1 - 41 - 4
d_22ens_1GLUGLUPROPROIB6 - 2206 - 220
d_11ens_2ASPASPTHRTHRLC1 - 221 - 22
d_12ens_2LYSLYSSERSERLC24 - 2924 - 29
d_13ens_2GLUGLUARGARGLC37 - 5537 - 55
d_14ens_2ALAALAMETMETLC57 - 6757 - 67
d_15ens_2LEULEUCYSCYSLC74 - 14274 - 142
d_16ens_2SERSERPHEPHELC152 - 177152 - 177
d_17ens_2ILEILEARGARGLC179 - 376179 - 376
d_21ens_2ASPASPTHRTHRMD1 - 221 - 22
d_22ens_2LYSLYSARGARGMD24 - 5524 - 55
d_23ens_2ALAALAPHEPHEMD57 - 17757 - 177
d_24ens_2ILEILEARGARGMD179 - 376179 - 376

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.856307726963, -0.510750367671, -0.0766233558827), (-0.509150410307, 0.809953713246, 0.291102803291), (-0.0866194921925, 0.288286392886, -0.953618382399)71.6631165449, 30.7871761544, -70.4660354796
2given(-0.864832835345, -0.496098888071, -0.0771366330826), (-0.494660587094, 0.815689565534, 0.299935720204), (-0.0858782305601, 0.297550711533, -0.950835686952)71.2761281843, 30.8966667554, -70.7714999274

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Components

#1: Antibody Fab Heavy chain


Mass: 24349.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Interleukin-10,Fab light chain / IL-10 / Cytokine synthesis inhibitory factor / CSIF


Mass: 42172.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A monomeric version of interleukin-10 is inserted into CDR-L1.
Source: (gene. exp.) Homo sapiens (human) / Gene: IL10 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P22301
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 20% PEG 3350, 0.2M Magnesium Acetate, pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2016
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 47411 / % possible obs: 96.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 38.39 Å2 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.077 / Rrim(I) all: 0.145 / Rsym value: 0.095 / Χ2: 0.932 / Net I/σ(I): 9.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 3890 / CC1/2: 0.646 / CC star: 0.886 / Rpim(I) all: 0.521 / Rrim(I) all: 0.953 / Rsym value: 0.598 / Χ2: 0.876 / % possible all: 79.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DENZO2.3.10data reduction
SCALEPACK2.3.10data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→42.9 Å / SU ML: 0.3046 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2323 2219 5.48 %
Rwork0.1881 38238 -
obs0.1906 40457 82.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.04 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8956 0 24 233 9213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00459222
X-RAY DIFFRACTIONf_angle_d0.85512508
X-RAY DIFFRACTIONf_chiral_restr0.05061410
X-RAY DIFFRACTIONf_plane_restr0.00831593
X-RAY DIFFRACTIONf_dihedral_angle_d14.15763370
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AHX-RAY DIFFRACTIONTorsion NCS0.58041303263
ens_2d_2CLX-RAY DIFFRACTIONTorsion NCS0.786384002309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.450.3946390.2724841X-RAY DIFFRACTION28.93
2.45-2.510.3234580.27111143X-RAY DIFFRACTION39.27
2.51-2.570.2921870.25421478X-RAY DIFFRACTION51.94
2.57-2.640.3298830.25041787X-RAY DIFFRACTION62.04
2.64-2.720.3079950.25782120X-RAY DIFFRACTION72.69
2.72-2.810.30131390.24952337X-RAY DIFFRACTION81.26
2.81-2.910.30081740.24062618X-RAY DIFFRACTION91.99
2.91-3.020.29391640.22762841X-RAY DIFFRACTION99.14
3.02-3.160.27961770.22562859X-RAY DIFFRACTION99.84
3.16-3.330.27951300.20232935X-RAY DIFFRACTION99.84
3.33-3.530.21841780.18972838X-RAY DIFFRACTION99.74
3.53-3.810.23731770.17352877X-RAY DIFFRACTION99.9
3.81-4.190.21471530.16272904X-RAY DIFFRACTION99.93
4.19-4.790.17932180.13832841X-RAY DIFFRACTION99.9
4.8-6.040.18071850.16362872X-RAY DIFFRACTION99.74
6.04-42.90.21431620.17432947X-RAY DIFFRACTION99.2
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)
10.2564335069120.1116331997580.2086643644550.344528987925-0.3891256246570.9078465155150.220899416785-0.2007771544350.254608921664-0.05610060384260.0408813041819-0.174287710814-0.732428277563-0.3364020902710.00514945041160.3446354633870.105326051693-0.02665612360660.317076476398-0.02718611588910.3266396654447.9989566232437.456981296-44.4391119205
20.07209783557290.257547531581-0.2249577422790.3773940905830.5088129612043.01062537685-0.0422446288824-0.1392279789420.02111053315450.0257943617021-0.0204110382106-0.00380879056153-0.0600113389649-0.241424249272-0.002886449531760.1692907290780.04820061714520.02564752081260.3046017114820.007275559672030.2707620106899.2830192859330.5706232344-45.0766593297
30.3307205431420.2542995111370.5646985060441.321802686260.2677644196230.8762201851950.4830599584950.654728221714-0.158639750617-0.12006391508-0.243061721636-0.152170400589-0.468332695620.6663832335260.03900203314650.2187215689110.02550301319150.01786145071860.6689322035440.02284898716520.29650154452718.358031290831.0009141011-24.1510554939
40.870353475510.05834210378730.9090853462290.3102730309360.1474502504640.89095435953-0.4422729583590.4315373392330.95495744415-0.216478995944-0.0698639043065-0.387726396437-0.5748308511140.190899370404-0.07632304689740.389229718255-0.122282038482-0.06168261924960.7791451513070.1194086255610.44029049720524.287329712739.0344209048-23.1027892853
51.255916219810.396083466171.036523654671.98117108146-0.6700453686533.45309827967-0.225323695454-0.001761520405450.273003283105-0.123649936408-0.04601526519850.134465362006-0.5585228121070.0328069607627-0.04394132052770.248877781571-0.0275707317202-0.04607709246560.1435749504-0.03288616186630.29546157337153.658613148637.9820079775-13.8644692333
61.002631217050.3417080715381.837550134072.106290144080.8627539215253.35035113465-0.2368574200490.1135277762390.230425746105-0.0758269655141-0.0679381462811-0.002360265219-0.586057054623-0.0804322475108-0.006864027394890.408322002867-0.0678684889587-0.06103728324480.3420545558860.0593586700720.35133991580738.527150018140.9515556481-42.1043269819
71.783149007140.853518441212-1.190277531271.625427027890.4338609276621.673804536920.250461245427-0.158999965667-0.3631178992490.1038082761910.3569780881460.7458377441780.686745578083-0.9035355813810.03973267299380.538994803892-0.05199351712240.1069317724020.468726766280.04364861256510.4678499529832.489679602759.72373576601-47.9571737637
82.60648800169-0.137362178616-0.3614866601262.91684923830.1822611327531.99069540593-0.0113106340921-0.156732958653-0.4681559555170.179792515405-0.03422323250.2133496691730.491461675328-0.5374178534750.007286982651680.456899671848-0.149248656523-0.04229547729870.419587137346-0.02075085766570.639188998274-4.448085122326.23892491778-83.0144251717
91.722352918570.001120062444690.1545782946072.672337994290.02035684120771.323664045410.167844764065-0.0938860729238-0.565145537452-0.081394054097-0.1885636678450.1377010888260.494782283614-0.2611459577010.001909069497540.3208748495-0.0999750202177-0.01089983629440.3128422942940.004377092746670.507160983593-0.7727466944327.66565412663-81.0481024658
100.2782753497790.143696884181-0.1510543484480.1450658388530.9574355921094.40673940076-0.169330650185-0.101159091633-0.09752375977290.07450300422650.0609807063984-0.02052155545460.6180350636420.232063739205-0.01353112513650.3872141655970.03779759330450.07046539152510.2570229822670.04916225502410.32474694245312.865882168215.2828011695-34.6634919917
111.893125958741.13242526528-0.04451407147911.58689013335-0.8870972481192.61302315888-0.00123276751441-0.1703909846010.0900071566850.276497845037-0.1636951363810.0155069553640.3983388554330.345695029666-0.0004596119535440.2759912463220.0405764134846-0.01750022457620.3650173264030.04411044221370.21185896802611.956414876723.4230654639-10.3071047746
122.25287031385-0.500073017384-0.8545061190632.38390750608-0.7567971148451.2247057340.3378175230770.08628202535240.1371864976480.249939811386-0.0196925938149-0.4639898868560.2520047007721.064653767660.01257340801330.27600999355-0.0292110856680.008477687387390.504036594188-0.05767852238330.45193756646968.297041952623.6854347777-20.5095650885
134.265471125580.108205889966-0.4725453949553.19401793537-0.3054646489562.15136547203-0.0537282831893-0.0487405613255-0.213030217083-0.133900522450.195521269816-0.1120660762260.2476939459550.693967242912-0.002351610700090.3621942661240.07140776213950.01312935356960.3854215572790.001567587905070.42090531699877.695906727413.071166331710.0018664652
141.83466311195-0.6011604177932.310380890420.669380412597-0.7894689908854.263438070280.09355685438820.4974479249360.00892792325021-0.174476703639-0.1351545421470.03441414426480.1007741426440.717905156253-0.001325482706270.260719557716-0.03887029623040.06698653232410.340249999998-0.02807476904380.30145318694559.639125508226.0821715509-26.5877185179
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 2 through 17 )HA2 - 172 - 17
22chain 'H' and (resid 18 through 152 )HA18 - 15218 - 152
33chain 'H' and (resid 153 through 195 )HA153 - 195153 - 195
44chain 'H' and (resid 196 through 220 )HA196 - 220196 - 220
55chain 'I' and (resid 2 through 126 )IB2 - 1262 - 126
66chain 'I' and (resid 127 through 220 )IB127 - 220127 - 220
77chain 'L' and (resid 1 through 42 )LC1 - 421 - 36
88chain 'L' and (resid 43 through 112 )LC43 - 11237 - 106
99chain 'L' and (resid 113 through 192 )LC113 - 192107 - 178
1010chain 'L' and (resid 193 through 315 )LC193 - 315179 - 301
1111chain 'L' and (resid 316 through 376 )LC316 - 376302 - 362
1212chain 'M' and (resid 1 through 46 )MD1 - 461 - 39
1313chain 'M' and (resid 47 through 112 )MD47 - 11240 - 99
1414chain 'M' and (resid 113 through 376 )MD113 - 376100 - 354

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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

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