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- PDB-3nfp: Crystal structure of the Fab fragment of therapeutic antibody dac... -

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Basic information

Entry
Database: PDB / ID: 3nfp
TitleCrystal structure of the Fab fragment of therapeutic antibody daclizumab in complex with IL-2Ra (CD25) ectodomain
Components
  • Heavy chain of Fab fragment of daclizumab
  • Interleukin-2 receptor subunit alphaIL-2 receptor
  • Light chain of Fab fragment of daclizumab
KeywordsImmune system/Cytokine / IL-2Ra / CD25 / Daclizumab / Zenapax / therapeutic antibody / immune system / Immune system-Cytokine complex
Function / homology
Function and homology information


regulation of T cell tolerance induction / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-2 binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / activation-induced cell death of T cells / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / interleukin-2-mediated signaling pathway / activated T cell proliferation ...regulation of T cell tolerance induction / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-2 binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / activation-induced cell death of T cells / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / interleukin-2-mediated signaling pathway / activated T cell proliferation / inflammatory response to antigenic stimulus / Interleukin-2 signaling / positive regulation of T cell differentiation / positive regulation of activated T cell proliferation / Interleukin receptor SHC signaling / Notch signaling pathway / negative regulation of T cell proliferation / negative regulation of inflammatory response / RAF/MAP kinase cascade / cell surface receptor signaling pathway / immune response / inflammatory response / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Rubrerythrin, domain 2 - #230 / Interleukin-2 receptor alpha / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Rubrerythrin, domain 2 ...Rubrerythrin, domain 2 - #230 / Interleukin-2 receptor alpha / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Rubrerythrin, domain 2 / Single Sheet / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-2 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsYang, H. / Wang, J. / Du, J. / Zhong, C. / Guo, Y. / Ding, J.
CitationJournal: Cell Res. / Year: 2010
Title: Structural basis of immunosuppression by the therapeutic antibody daclizumab
Authors: Yang, H. / Wang, J. / Du, J. / Zhong, C. / Zhang, D. / Guo, H. / Guo, Y. / Ding, J.
History
DepositionJun 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2013Group: Database references / Derived calculations
Revision 1.3Nov 1, 2023Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain of Fab fragment of daclizumab
B: Light chain of Fab fragment of daclizumab
H: Heavy chain of Fab fragment of daclizumab
L: Light chain of Fab fragment of daclizumab
I: Interleukin-2 receptor subunit alpha
K: Interleukin-2 receptor subunit alpha


Theoretical massNumber of molelcules
Total (without water)143,1156
Polymers143,1156
Non-polymers00
Water1,74797
1
A: Heavy chain of Fab fragment of daclizumab
B: Light chain of Fab fragment of daclizumab
K: Interleukin-2 receptor subunit alpha


Theoretical massNumber of molelcules
Total (without water)71,5583
Polymers71,5583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Heavy chain of Fab fragment of daclizumab
L: Light chain of Fab fragment of daclizumab
I: Interleukin-2 receptor subunit alpha


Theoretical massNumber of molelcules
Total (without water)71,5583
Polymers71,5583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.167, 114.973, 247.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody Heavy chain of Fab fragment of daclizumab


Mass: 23034.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: purchased from Roche, expressed in a mammalian expression system
#2: Antibody Light chain of Fab fragment of daclizumab


Mass: 23134.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: purchased from Roche, expressed in a mammalian expression system
#3: Protein Interleukin-2 receptor subunit alpha / IL-2 receptor / IL-2 receptor subunit alpha / IL-2R subunit alpha / IL-2-RA / IL2-RA / p55 / TAC antigen / CD_antigen=CD25


Mass: 25388.348 Da / Num. of mol.: 2 / Fragment: UNP residues 22-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RA / Cell line (production host): Hi-5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01589
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris-HCl, 0.2M MgCl2, 10% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 31671 / % possible obs: 95.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 7.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0066refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NFS

3nfs


Resolution: 2.86→50 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.857 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1599 5 %RANDOM
Rwork0.253 ---
obs0.255 31669 93.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 187.67 Å2 / Biso mean: 69.528 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20 Å2
2---2.44 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.86→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8324 0 0 97 8421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228540
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.94811613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.88951072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65424.373343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.662151372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0851531
X-RAY DIFFRACTIONr_chiral_restr0.0670.21285
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216437
X-RAY DIFFRACTIONr_mcbond_it3.1461.55405
X-RAY DIFFRACTIONr_mcangle_it4.9228751
X-RAY DIFFRACTIONr_scbond_it3.90233135
X-RAY DIFFRACTIONr_scangle_it4.8274.52862
X-RAY DIFFRACTIONr_rigid_bond_restr4.54238540
X-RAY DIFFRACTIONr_sphericity_free1.457397
X-RAY DIFFRACTIONr_sphericity_bonded1.55938326
LS refinement shellResolution: 2.863→2.937 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 83 -
Rwork0.342 1503 -
all-1586 -
obs--64.58 %

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