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- PDB-7s2r: nanobody bound to IL-2Rg -

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Basic information

Entry
Database: PDB / ID: 7s2r
Titlenanobody bound to IL-2Rg
Components
  • Cytokine receptor common subunit gamma
  • nanobody gamma-nb6
KeywordsPROTEIN BINDING / nanobody / cytokine receptor
Function / homology
Function and homology information


interleukin-7-mediated signaling pathway / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of T cell differentiation in thymus / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway ...interleukin-7-mediated signaling pathway / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of T cell differentiation in thymus / Interleukin-9 signaling / Interleukin-21 signaling / 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 / interleukin-15-mediated signaling pathway / STAT3 nuclear events downstream of ALK signaling / Interleukin-15 signaling / Interleukin-2 signaling / cytokine receptor activity / positive regulation of B cell differentiation / cytokine binding / Interleukin receptor SHC signaling / coreceptor activity / positive regulation of phagocytosis / Interleukin-7 signaling / cytokine-mediated signaling pathway / gene expression / T cell differentiation in thymus / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / receptor complex / endosome / immune response / external side of plasma membrane / positive regulation of gene expression / cell surface / endoplasmic reticulum / signal transduction / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
: / : / Cytokine receptor-like factor 2-like, D1 domain / Cytokine receptor-like factor 2-like, D2 domain / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Cytokine receptor common subunit gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
Camelus bactrianus (Bactrian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å
AuthorsGlassman, C.R. / Jude, K.M. / Yen, M. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37-AI051321 United States
CitationJournal: Cell / Year: 2022
Title: Facile discovery of surrogate cytokine agonists.
Authors: Yen, M. / Ren, J. / Liu, Q. / Glassman, C.R. / Sheahan, T.P. / Picton, L.K. / Moreira, F.R. / Rustagi, A. / Jude, K.M. / Zhao, X. / Blish, C.A. / Baric, R.S. / Su, L.L. / Garcia, K.C.
History
DepositionSep 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 27, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytokine receptor common subunit gamma
B: nanobody gamma-nb6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,16219
Polymers42,9742
Non-polymers2,18817
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-93 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.082, 120.082, 237.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-312-

SO4

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: 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: 25123.975 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RG / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: P31785
#2: Antibody nanobody gamma-nb6


Mass: 17850.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)

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Sugars , 2 types, 3 molecules

#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


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, 40 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.98 Å3/Da / Density % sol: 75.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5 / Details: 2M ammonium sulfate, 0.2M BIS-Tris pH5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.49→48.64 Å / Num. obs: 30758 / % possible obs: 99.8 % / Redundancy: 11.9 % / CC1/2: 0.981 / Rmerge(I) obs: 0.323 / Rpim(I) all: 0.1 / Rrim(I) all: 0.339 / Net I/σ(I): 4.3 / Num. measured all: 367204 / Scaling rejects: 111
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.49-2.5912.47.2744212033910.3562.137.5840.499.8
8.98-48.6410.90.19282237520.9780.0610.20211.299.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B5I, 5LHR

2b5i

5lhr


Resolution: 2.49→48.64 Å / SU ML: 0.5309 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.4442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2713 2301 7.54 %
Rwork0.2461 28219 -
obs0.248 30520 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.32 Å2
Refinement stepCycle: LAST / Resolution: 2.49→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 132 26 2841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282880
X-RAY DIFFRACTIONf_angle_d0.55133918
X-RAY DIFFRACTIONf_chiral_restr0.0401407
X-RAY DIFFRACTIONf_plane_restr0.0054497
X-RAY DIFFRACTIONf_dihedral_angle_d13.01181022
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.540.48761310.51421652X-RAY DIFFRACTION95.09
2.54-2.60.47251450.47921751X-RAY DIFFRACTION98.75
2.6-2.670.49521410.50861710X-RAY DIFFRACTION98.46
2.67-2.740.46591410.47071742X-RAY DIFFRACTION99.58
2.74-2.820.4021410.41931727X-RAY DIFFRACTION99.57
2.82-2.910.40631420.38321761X-RAY DIFFRACTION99.48
2.91-3.020.35031400.35121735X-RAY DIFFRACTION98.94
3.02-3.140.32191430.29361743X-RAY DIFFRACTION98.85
3.14-3.280.32211440.28651749X-RAY DIFFRACTION99.21
3.28-3.450.30831440.27041775X-RAY DIFFRACTION99.58
3.45-3.670.32031440.23641754X-RAY DIFFRACTION99.11
3.67-3.950.281450.23381772X-RAY DIFFRACTION99.58
3.95-4.350.23871450.20051784X-RAY DIFFRACTION99.95
4.35-4.980.18281480.16251811X-RAY DIFFRACTION100
4.98-6.270.20181490.2041826X-RAY DIFFRACTION100
6.27-48.640.25921580.23041927X-RAY DIFFRACTION99.71
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)
12.08321045711.1215579875-3.064210892920.908227624298-1.781858264334.156522944540.0397565849826-0.582048114382-0.163750006112-0.0256841117142-0.2110220390770.027983047498-0.1532740819450.81212211250.1147106403011.17753901795-0.0297792416540.03921205114080.9225177714060.047089321090.49021608076718.5490649014-38.48897033123.38849553329
23.165321728921.75057963154-2.447294814985.1154655451-0.0279274756352.725175926490.0550694344354-0.662273984082-0.2408355271550.5993463147650.108137873662-0.4197721912190.3174558626430.1368995223340.05849335660221.05462161017-0.168340364997-0.06698229912891.107767973320.02591358619420.54283163660613.2386765335-42.93195428159.72498028829
33.66955012802-0.204082788635-1.10743660541-0.0121384917181-0.07433847799497.986212900780.4066161885570.4642847827220.39926425361-0.0444283183511-0.428427784665-0.240263924880.772789327234-0.771118536858-0.06728880243190.748402066428-0.266520337464-0.008659241621850.9465620449030.004642331557360.6727781231779.77607039114-40.74210461520.036667072971
43.280887950160.713286455406-1.864769450023.12699426573-2.872034516793.068457065860.1666133139250.0725049063978-0.1963140589660.2869514937060.05569393751050.260563747642-0.217322670517-0.737177713618-0.2161819018220.782528033383-0.137796607204-0.04235064411710.89142566819-0.01909008727240.5367916172716.174923221-34.37876131260.586660256132
55.465113267076.2980518831-6.989748055258.75209859966-8.057760732059.43889706755-1.094277966921.058087274310.0956734434328-0.9121187641480.3757230530.3353378857050.505805974214-0.9273371604280.6342297166081.12346509571-0.01942942712710.01288127423041.020131065360.01872666180710.6010013624643.8444310673-32.6203492893-30.1334706025
67.03190475112-2.68131728406-0.9234940140914.144075125671.112870017186.226981384050.2060859633340.0292612878937-0.5304200155820.07990868665090.0475562876089-0.4755889007570.8032655266210.892019863731-0.287434656850.8301659791960.1737298940530.006511411524340.860930323232-0.08824347554820.66297682569639.0775540905-32.6386806923-16.0487085719
73.14942458567-3.11902370177-0.4787432700568.07638160850.2828807832349.79419252893-0.1602000057240.888706539920.024160703312-0.440325776102-0.0324583715533-0.492527400328-1.1227343340.435690336079-0.2059239294010.934338365813-0.0797106334641-0.04191032591591.004622411480.01334283675120.77648395998544.4532194534-30.3542697695-23.5863235558
84.03325493244-4.00425630619-5.499280209434.044293393975.512146938197.24646361244-0.20235986542-0.2661164476370.08135432113730.3923090740020.471616348724-0.2838418623230.8125209899331.00194973123-0.2332339162290.7948092242630.06532622842230.008315086879890.823831324141-0.01697981157740.58176000556335.2276937297-33.9008879654-13.5488940132
91.839698987581.42026286072-0.2050291562576.3237757925-1.245251116170.2484335382960.951249039762-1.153858212490.459791279241.56230661903-1.316778695454.01151207915-7.13036358583-5.889242316720.5340375588411.091446895280.3141781064260.3863430214241.08161604257-0.4962123046270.63990524721353.0249340847-42.7463330262-26.4249416303
104.643899354861.299071360840.4455748908797.136323121820.8145710635295.08643292962-0.2850985222670.0801143785129-0.377232333765-0.803756313920.3028686642120.841606356452-0.177979887589-1.15883158632-0.1409316105270.6284856165820.1255405343460.009016862813731.14008075723-0.08752062215280.541552782034-0.459244929895-15.2471563937-22.440781251
114.60048354906-0.2718763431470.4740552249838.56731815088-5.07458054436.70721283803-0.2855940864650.151658171566-0.0561990126629-0.09907655137720.142559420466-0.514459071533-0.0413833021173-0.2142596025810.06457686439940.7511049454410.09429887134420.05616223721280.807727044383-0.04443302395080.43632572440911.1148522577-15.1893782059-23.7729616974
129.236087828230.7094306670042.017343789052.52125715274-1.267438681652.675475633780.179536927682-1.36442224175-0.860916613151.65931645793-0.200254952413-0.263823398935-0.3640662224020.374717764335-0.1435614117711.157112882930.102539243518-0.0327306406741.07662688201-0.06830841405710.81559866868310.7030832599-11.7231165058-12.3660443895
132.57883286872-0.1256303277961.158919003556.25872500663-0.8959928964285.4283202950.2810125157210.1081440550590.0417918723798-0.135191241751-0.312812650275-0.185659304774-0.311346902484-0.346068490991-0.06294308923270.5969923966740.05262830225680.01024971394790.875973073661-0.0355552137520.3966470628667.50985216024-14.4201373531-19.4416193486
143.366238165080.992153517728-0.9727172528183.75037739447-5.197407209997.36797173270.0349173723740.3952088923350.115357632648-0.1854740671010.2070095583840.0843901203564-0.124873102666-0.365434439087-0.3370607498550.8514047990370.03975510836770.01177783407140.92249386501-0.02594232948680.5174255851297.08676491642-13.6136821756-28.0109416577
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 52 through 73 )AA52 - 731 - 22
22chain 'A' and (resid 74 through 91 )AA74 - 9123 - 40
33chain 'A' and (resid 92 through 121 )AA92 - 12141 - 70
44chain 'A' and (resid 122 through 160 )AA122 - 16071 - 109
55chain 'A' and (resid 161 through 173 )AA161 - 173110 - 122
66chain 'A' and (resid 174 through 202 )AA174 - 202123 - 151
77chain 'A' and (resid 203 through 218 )AA203 - 218152 - 167
88chain 'A' and (resid 219 through 246 )AA219 - 246168 - 195
99chain 'A' and (resid 247 through 248 )AA247 - 248196 - 197
1010chain 'B' and (resid 1 through 32 )BF1 - 321 - 32
1111chain 'B' and (resid 33 through 52 )BF33 - 5233 - 52
1212chain 'B' and (resid 53 through 70 )BF53 - 7053 - 70
1313chain 'B' and (resid 71 through 116 )BF71 - 11671 - 116
1414chain 'B' and (resid 117 through 136 )BF117 - 136117 - 136

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