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- PDB-6p67: Crystal Structure of a Complex of human IL-7Ralpha with an anti-I... -

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Basic information

Entry
Database: PDB / ID: 6p67
TitleCrystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha 2B8 Fab
Components
  • Anti-IL-7R 2B8 Fab heavy chain
  • Interleukin-7 receptor subunit alpha
  • anti-IL-7R 2B8 Fab light chain
KeywordsIMMUNE SYSTEM / Interleukin-7 receptor extracellular dohmain / antibody 2B8 Fab fragment / protein polymer
Function / homology
Function and homology information


interleukin-7 receptor activity / positive regulation of receptor signaling pathway via STAT / negative regulation of T cell mediated cytotoxicity / regulation of DNA recombination / positive regulation of T cell differentiation in thymus / negative regulation of T cell apoptotic process / cytokine receptor activity / regulation of cell size / B cell proliferation / T cell homeostasis ...interleukin-7 receptor activity / positive regulation of receptor signaling pathway via STAT / negative regulation of T cell mediated cytotoxicity / regulation of DNA recombination / positive regulation of T cell differentiation in thymus / negative regulation of T cell apoptotic process / cytokine receptor activity / regulation of cell size / B cell proliferation / T cell homeostasis / B cell homeostasis / hemopoiesis / lymph node development / antigen binding / Interleukin-7 signaling / clathrin-coated endocytic vesicle membrane / positive regulation of receptor signaling pathway via JAK-STAT / cell morphogenesis / T cell mediated cytotoxicity / cytokine-mediated signaling pathway / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / T cell differentiation in thymus / 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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / Interleukin-7 receptor subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
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
DepositionJun 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 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 2.2Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-IL-7R 2B8 Fab heavy chain
B: anti-IL-7R 2B8 Fab light chain
C: Anti-IL-7R 2B8 Fab heavy chain
D: anti-IL-7R 2B8 Fab light chain
E: Anti-IL-7R 2B8 Fab heavy chain
F: anti-IL-7R 2B8 Fab light chain
G: Interleukin-7 receptor subunit alpha
H: Anti-IL-7R 2B8 Fab heavy chain
I: Interleukin-7 receptor subunit alpha
J: Interleukin-7 receptor subunit alpha
K: Interleukin-7 receptor subunit alpha
L: anti-IL-7R 2B8 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,90820
Polymers294,26212
Non-polymers2,6468
Water0
1
A: Anti-IL-7R 2B8 Fab heavy chain
B: anti-IL-7R 2B8 Fab light chain
K: Interleukin-7 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7874
Polymers73,5653
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Anti-IL-7R 2B8 Fab heavy chain
D: anti-IL-7R 2B8 Fab light chain
J: Interleukin-7 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2115
Polymers73,5653
Non-polymers6462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Anti-IL-7R 2B8 Fab heavy chain
F: anti-IL-7R 2B8 Fab light chain
I: Interleukin-7 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3735
Polymers73,5653
Non-polymers8082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Interleukin-7 receptor subunit alpha
H: Anti-IL-7R 2B8 Fab heavy chain
L: anti-IL-7R 2B8 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5376
Polymers73,5653
Non-polymers9723
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.900, 219.680, 90.350
Angle α, β, γ (deg.)90.000, 104.328, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 1 through 42 or (resid 43...A1 - 135
121(chain 'A' and (resid 1 through 42 or (resid 43...A140 - 223
211(chain 'C' and ((resid 1 and (name N or name...C1 - 135
221(chain 'C' and ((resid 1 and (name N or name...C140 - 223
311(chain 'E' and (resid 1 through 12 or (resid 13...E1 - 135
321(chain 'E' and (resid 1 through 12 or (resid 13...E140 - 223
411(chain 'H' and (resid 1 through 12 or (resid 13...H1 - 135
421(chain 'H' and (resid 1 through 12 or (resid 13...H140 - 223
112(chain 'B' and (resid 1 through 212 or (resid 213...B1 - 212
212(chain 'D' and (resid 1 through 212 or (resid 213...D1 - 212
312chain 'F'F1 - 212
412(chain 'L' and (resid 1 through 212 or (resid 213...L1 - 212
113(chain 'G' and ((resid 17 and (name N or name...G17 - 44
123(chain 'G' and ((resid 17 and (name N or name...G51 - 89
133(chain 'G' and ((resid 17 and (name N or name...G95 - 210
143(chain 'G' and ((resid 17 and (name N or name...G328
213(chain 'I' and ((resid 17 and (name N or name...I17 - 44
223(chain 'I' and ((resid 17 and (name N or name...I51 - 89
233(chain 'I' and ((resid 17 and (name N or name...I95 - 210
243(chain 'I' and ((resid 17 and (name N or name...I316
313(chain 'J' and (resid 17 through 18 or (resid 19...J17 - 44
323(chain 'J' and (resid 17 through 18 or (resid 19...J51 - 89
333(chain 'J' and (resid 17 through 18 or (resid 19...J95 - 210
343(chain 'J' and (resid 17 through 18 or (resid 19...J315
413(chain 'K' and (resid 17 through 18 or (resid 19...K17 - 44
423(chain 'K' and (resid 17 through 18 or (resid 19...K51 - 89
433(chain 'K' and (resid 17 through 18 or (resid 19...K95 - 210
443(chain 'K' and (resid 17 through 18 or (resid 19...K312

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 4 molecules GIJK

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


Mass: 25691.020 Da / Num. of mol.: 4
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

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Antibody , 2 types, 8 molecules ACEHBDFL

#1: Antibody
Anti-IL-7R 2B8 Fab heavy chain


Mass: 24269.068 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) / Variant (production host): Freestyle HEK293F
#2: Antibody
anti-IL-7R 2B8 Fab light chain


Mass: 23605.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) / Variant (production host): Freestyle HEK293F

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Sugars , 4 types, 8 molecules

#4: 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 / IL-7RA / CDw127


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
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
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / IL-7RA / CDw127


Type: oligosaccharide / Mass: 424.401 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
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
#6: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / IL-7RA / CDw127 / 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 17% PEG 3350, 10% MPD, 0.2 lithium sulfate, 0.1 M imidazole pH 6.5, 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→50 Å / Num. obs: 70309 / % possible obs: 99.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 73.25 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.196 / Net I/σ(I): 8.41
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.08 / Num. unique obs: 6971 / CC1/2: 0.482 / % possible all: 98.72

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Processing

Software
NameVersionClassification
phenix.refine1.16rc1_3535refinement
PHENIX1.16rc1_3535refinement
XDSdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3di3 for IL-7R and 6P4Y for 2B8

3di3

6p4y


Resolution: 2.9→43.77 Å / SU ML: 0.5116 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.7175
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2663 1985 2.83 %
Rwork0.2486 68235 -
obs0.2491 70220 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.44 Å2
Refinement stepCycle: LAST / Resolution: 2.9→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19325 0 0 0 19325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003119796
X-RAY DIFFRACTIONf_angle_d0.660226944
X-RAY DIFFRACTIONf_chiral_restr0.04673064
X-RAY DIFFRACTIONf_plane_restr0.00383407
X-RAY DIFFRACTIONf_dihedral_angle_d10.563711730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.47471430.44444825X-RAY DIFFRACTION98.81
2.97-3.050.42371260.39774839X-RAY DIFFRACTION98.83
3.05-3.140.381510.3494856X-RAY DIFFRACTION98.7
3.14-3.240.38151340.32724838X-RAY DIFFRACTION98.83
3.24-3.360.33691520.29794842X-RAY DIFFRACTION99.13
3.36-3.490.29381410.28854845X-RAY DIFFRACTION99.18
3.49-3.650.30921470.29284890X-RAY DIFFRACTION99.23
3.65-3.850.28821360.26284877X-RAY DIFFRACTION99.44
3.85-4.090.25781360.25034881X-RAY DIFFRACTION99.33
4.09-4.40.24351440.21064881X-RAY DIFFRACTION99.58
4.4-4.840.22611380.1984886X-RAY DIFFRACTION99.52
4.84-5.540.2491440.2094932X-RAY DIFFRACTION99.76
5.54-6.980.24581470.2344902X-RAY DIFFRACTION99.72
6.98-43.770.18671460.20744941X-RAY DIFFRACTION99.16

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