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- PDB-6p50: Crystal Structure of a Complex of human IL-7Ralpha with an anti-I... -

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Basic information

Entry
Database: PDB / ID: 6p50
TitleCrystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha Fab 4A10
Components
  • Interleukin-7 receptor subunit alpha
  • anti-IL-7R 4A10 Fab heavy chain
  • anti-IL-7R 4A10 Fab light chain
KeywordsIMMUNE SYSTEM / Interleukin-7 receptor extracellular dohmain / Antibody 4A10 Fab fragment / protein polymer
Function / homology
Function and homology information


interleukin-7 receptor activity / negative regulation of T cell mediated cytotoxicity / regulation of DNA recombination / positive regulation of T cell differentiation in thymus / positive regulation of receptor signaling pathway via STAT / interleukin-7-mediated signaling pathway / negative regulation of T cell apoptotic process / cellular homeostasis / cytokine receptor activity / regulation of cell size ...interleukin-7 receptor activity / negative regulation of T cell mediated cytotoxicity / regulation of DNA recombination / positive regulation of T cell differentiation in thymus / positive regulation of receptor signaling pathway via STAT / interleukin-7-mediated signaling pathway / negative regulation of T cell apoptotic process / cellular homeostasis / cytokine receptor activity / regulation of cell size / T cell homeostasis / B cell homeostasis / B cell proliferation / hemopoiesis / lymph node development / antigen binding / Interleukin-7 signaling / positive regulation of receptor signaling pathway via JAK-STAT / clathrin-coated endocytic vesicle membrane / T cell mediated cytotoxicity / cell morphogenesis / cytokine-mediated signaling pathway / Cargo recognition for clathrin-mediated endocytosis / T cell differentiation in thymus / Clathrin-mediated endocytosis / gene expression / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / extracellular region / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Immunoglobulin-like - #1870 / IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Fibronectin type III domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold ...Immunoglobulin-like - #1870 / IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Fibronectin type III domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-7 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWalsh, S.T.R. / Kashi, L. / Kohnhorst, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Leukemia / Year: 2020
Title: New anti-IL-7R alpha monoclonal antibodies show efficacy against T cell acute lymphoblastic leukemia in pre-clinical models.
Authors: Hixon, J.A. / Andrews, C. / Kashi, L. / Kohnhorst, C.L. / Senkevitch, E. / Czarra, K. / Barata, J.T. / Li, W. / Schneider, J.P. / Walsh, S.T.R. / Durum, S.K.
History
DepositionMay 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Feb 5, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Interleukin-7 receptor subunit alpha
H: anti-IL-7R 4A10 Fab heavy chain
L: anti-IL-7R 4A10 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8794
Polymers73,6573
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.113, 40.171, 105.097
Angle α, β, γ (deg.)90.000, 105.477, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Interleukin-7 receptor subunit alpha / IL-7RA / CDw127


Mass: 25691.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL7R / Production host: Drosophila melanogaster (fruit fly) / Variant (production host): Schneider S2 / References: UniProt: P16871
#2: Antibody anti-IL-7R 4A10 Fab heavy chain


Mass: 24360.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody anti-IL-7R 4A10 Fab light chain


Mass: 23606.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#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.: 1
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
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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 25% PEG 3350, 0.2 M sodium malonate pH 6.0, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.9→38.61 Å / Num. obs: 12886 / % possible obs: 96.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 56.77 Å2 / CC1/2: 0.969 / Rrim(I) all: 0.283 / Net I/σ(I): 3.63
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 1892 / CC1/2: 0.734 / Rrim(I) all: 1.14 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX1.16rc1_3535refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DI3 for IL-7R chain and 6P4Y for 4A10

3di3

6p4y

4a10


Resolution: 2.9→38.61 Å / SU ML: 0.4937 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.0274
RfactorNum. reflection% reflectionSelection details
Rfree0.3298 641 5 %RANDOM
Rwork0.2855 ---
obs0.2879 12872 96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 70.59 Å2
Refinement stepCycle: LAST / Resolution: 2.9→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 14 0 3990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00184084
X-RAY DIFFRACTIONf_angle_d0.50525560
X-RAY DIFFRACTIONf_chiral_restr0.0425639
X-RAY DIFFRACTIONf_plane_restr0.0035699
X-RAY DIFFRACTIONf_dihedral_angle_d9.11162451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.120.41041180.38872257X-RAY DIFFRACTION89.69
3.12-3.440.39961270.36162377X-RAY DIFFRACTION95.83
3.44-3.940.40151260.33032447X-RAY DIFFRACTION96.73
3.94-4.960.3361330.25062500X-RAY DIFFRACTION98.54
4.96-38.610.2431370.23122604X-RAY DIFFRACTION99.06
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)
10.511972693318-0.0505222060575-0.2100422139330.005081661738170.01992431842160.08871260578930.14563902406-0.5501287676370.4066762414520.1003133376930.188215154750.05540844107860.2536327850040.2739038553550.007475351516641.21350360687-0.0142465121513-0.2162933274430.396207175138-0.06381702850450.5620636468451.50112727668-24.3213203819108.695015698
20.1298566789020.0716473079156-0.01851345895950.0540816262926-0.1135970979231.64478270378-0.203302932169-0.193719470070.0579623877107-0.152622576716-0.0416556974496-0.0213694584908-0.223312827016-0.0840013508601-1.843651500141.42166692593-0.0691840220355-0.7233752121350.490791347847-0.04914566910380.412688243933-5.91998608503-24.5132380669106.48736285
30.0644821489937-0.0659721183147-0.04854358786150.04768999046570.05238585393990.0414150260011-0.1530253334790.153815373834-0.434162219740.0989028302369-0.559645390335-0.4130475217610.0428609557968-0.0890650683557-0.002559129530560.878136838108-0.136916678454-0.05270645454380.5583342272360.01824382950210.6130617796664.54414568595-25.8451034744101.07474407
40.133837410758-0.0211995874458-0.036001030120.0400789551215-0.02559232393510.05380324584710.211085951042-0.37246702081-0.122208388026-0.1269804570560.006482026936760.305312212763-0.331235086811-0.1770808073770.0001447775154871.33981565387-0.0520248952733-0.2941656662030.6319321973360.04150229505770.831248678182-27.4316227989-58.6559742698161.206531156
50.349918238927-0.1353884852050.6397217670630.317019915355-0.07365304599711.283675193240.222790198569-0.0216606371728-0.2431149385090.1761695539740.275791051027-0.02230652021620.03076369761240.2010800138510.5537103106741.4795801249-0.00148876416377-0.5166831383950.265026106104-0.2463176497350.631263046083-23.3540003487-61.6198526144164.440348741
60.191855238995-0.00172734725506-0.08093579762810.01284624180390.07675365210691.040756811090.183893668523-0.16036017745-0.109697573513-0.1215254111770.2684504781620.0423070922995-0.294755760513-0.3227196855860.3587407742251.590592012360.108973082149-0.4198883798750.6006768130530.1770758694130.267148173145-26.7019003304-52.9399646362158.557461385
70.3854221941810.183703060059-0.2128534567160.0944482929358-0.1048404545810.1125671383490.08021566945070.144795845730.09265292060960.150133748644-0.04888364302520.255230850091-0.195639174417-0.3859581330962.31053738319E-50.864311634599-0.041498976772-0.2257959984920.612310652132-0.140689512480.200284215903-28.226686581-39.8251100395126.801247214
80.7368529391760.2855281020640.1565703530250.431093440316-0.1971101771660.3262370751440.0549826216380.072392309422-0.166917348192-0.1769971726290.0841839596183-0.05438755614540.070844449085-0.2237809425230.5637640246920.210178512708-0.1590796160640.1640421132270.237104821310.1183881709490.139539799908-25.7784936975-46.5643474853135.220373514
90.019980445992-0.0754256827207-0.0744104010130.2990247250490.2966987670540.2968372922190.006064172183810.0703221072430.0746521579047-0.1075805101410.174015488635-0.114959136835-0.09620331184380.113401623270.8364200183760.177547284519-0.1593826173830.2248678299770.442601487690.08788216310040.319834841729-19.4546691782-39.1619665053138.711759489
100.981464009784-0.0754171040746-0.7049091802240.363489146490.4754636987481.00422178847-0.05377648250510.0991082660265-0.2614529221390.104634973231-0.2821387657590.1800192262950.204312312979-0.266518589018-0.3090456460211.20481201117-0.0696768331627-0.3961391449460.247676835138-0.08343379710790.588308837972-27.1707626321-38.8284756134145.036377334
110.0462409597654-0.145676069161-0.03497827188120.444029481902-0.2945685152830.638326867850.0722911977103-0.142738069219-0.0358807959284-0.09743967474670.2862047332510.391088928146-0.0290857432662-0.6242737901210.04853411666311.20902456718-0.0352128594521-0.3529427174830.4037898198860.06203669980020.43014305165-25.0014486632-40.8290516122133.911341456
120.7850720895860.231463178850.1662639083911.82007393670.2114184486160.06081767244540.07471597581710.313421266853-0.0487656984151-0.3269785973860.00210930489034-0.260325013359-0.116243723463-0.04839800462180.3048504397631.26288392058-0.0314260465753-0.3310292126760.2527686068330.1739296391230.374584071823-15.6838767392-33.777439967103.17775495
130.511968142882-0.00612540487252-0.02611815594410.186334428491-0.3325565411750.562085661482-0.06252084463910.0879472385754-0.0546997324186-0.0482804238628-0.140308229935-0.038573110873-0.221179640841-0.0895749159265-0.9327214606451.131489165250.0205716282631-0.5077895233310.5000670753990.02571731694280.299960919476-12.8896964885-36.3737531185104.30184987
140.0880581754959-0.08163771145240.05095034903250.0738182762943-0.05089731974930.03057243039550.08168444335160.07856801523860.111583812115-0.0003164985756930.0405351430057-0.05703019917560.037787708330.1047520811160.1763123211190.09101987266160.336350686577-0.08125381401490.2508887491560.005373771707650.231804870599-24.8921628473-36.1067915358107.392820476
151.05024938398-0.08996774273420.2818738937521.292567377360.04198622473590.07799831536070.17255173523-0.07629892049850.375564420547-0.279997024699-0.175575658689-0.134592713903-0.124972836796-0.257147589944-0.01558877877720.02989926866170.09580872424620.1821153327670.1352107703260.0222371660360.377867654863-21.0828189031-34.625623663596.5019370393
160.06242633965950.08373167310950.06711683317090.4784404702050.02904463553890.08385919434620.2226590095980.2274951268130.259469404037-0.120112514467-0.0115345443473-0.181211711478-0.0484685533303-0.4184314759770.1114547676770.013822240837-0.2526777237870.2758368269030.1717359350020.172779923135-0.0371035364024-3.78262743631-44.0196081946136.761526334
170.307538223958-0.37692613359-0.06669723484430.4927030498360.0814292907980.0165933243123-0.08797102809870.02569035256840.440701258456-0.0746441863592-0.0434756095842-0.3634864798250.05966940278280.177921357848-0.04937554276320.5821582527380.06335696279780.1796120676380.3039077766320.0004771176674620.225771585303-2.29456908793-52.3010651197139.110698531
180.7070791847810.18677885168-0.2137452825090.1585536371910.02060775369111.09223785862-0.4662376175550.05293939080380.26908924867-0.008850889300930.0571092007108-0.1121123320820.03684107451210.469451967423-0.1950863635061.255524197760.155575996898-0.3024702811850.3195583615390.06226154313940.459205487861-5.99394256784-44.7645023532134.815294658
190.5248217303190.351797979817-0.8466963607410.586431300933-0.3106643039721.52807018798-0.2673536435110.09905617372740.0964585253033-0.252430432492-0.3463509351090.148272567444-0.2102981637650.141672117735-1.668749195821.345019196010.0816449863593-0.6770139764240.1849589797180.2446251884150.299460358938-5.54745915085-30.7292031454105.352033986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 137 through 154 )
2X-RAY DIFFRACTION2chain 'L' and (resid 155 through 195 )
3X-RAY DIFFRACTION3chain 'L' and (resid 196 through 211 )
4X-RAY DIFFRACTION4chain 'C' and (resid 17 through 61 )
5X-RAY DIFFRACTION5chain 'C' and (resid 62 through 75 )
6X-RAY DIFFRACTION6chain 'C' and (resid 76 through 109 )
7X-RAY DIFFRACTION7chain 'H' and (resid 1 through 17 )
8X-RAY DIFFRACTION8chain 'H' and (resid 18 through 40 )
9X-RAY DIFFRACTION9chain 'H' and (resid 41 through 52 )
10X-RAY DIFFRACTION10chain 'H' and (resid 53 through 69 )
11X-RAY DIFFRACTION11chain 'H' and (resid 70 through 127 )
12X-RAY DIFFRACTION12chain 'H' and (resid 128 through 166 )
13X-RAY DIFFRACTION13chain 'H' and (resid 167 through 202 )
14X-RAY DIFFRACTION14chain 'H' and (resid 203 through 211 )
15X-RAY DIFFRACTION15chain 'H' and (resid 212 through 223 )
16X-RAY DIFFRACTION16chain 'L' and (resid 1 through 48 )
17X-RAY DIFFRACTION17chain 'L' and (resid 49 through 75 )
18X-RAY DIFFRACTION18chain 'L' and (resid 76 through 101 )
19X-RAY DIFFRACTION19chain 'L' and (resid 102 through 136 )

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