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- PDB-4y5y: Diabody 330 complex with EpoR -

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Basic information

Entry
Database: PDB / ID: 4y5y
TitleDiabody 330 complex with EpoR
Components
  • Erythropoietin receptor
  • diabody 330 VH domain
  • diabody 330 VL domain
Keywordsprotein binding/immune system / diabody complex / receptor / protein binding-immune system complex
Function / homology
Function and homology information


erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / erythropoietin-mediated signaling pathway / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / decidualization / Erythropoietin activates RAS / brain development ...erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / erythropoietin-mediated signaling pathway / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / decidualization / Erythropoietin activates RAS / brain development / cytokine-mediated signaling pathway / heart development / nuclear speck / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Erythropoietin receptor / Long hematopoietin receptor, single chain, conserved site / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Erythropoietin receptor / Long hematopoietin receptor, single chain, conserved site / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Fibronectin type III domain / Fibronectin type 3 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
Erythropoietin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMoraga, I. / Guo, F. / Ozkan, E. / Jude, K.M. / Garcia, K.C.
CitationJournal: Cell / Year: 2015
Title: Tuning Cytokine Receptor Signaling by Re-orienting Dimer Geometry with Surrogate Ligands.
Authors: Moraga, I. / Wernig, G. / Wilmes, S. / Gryshkova, V. / Richter, C.P. / Hong, W.J. / Sinha, R. / Guo, F. / Fabionar, H. / Wehrman, T.S. / Krutzik, P. / Demharter, S. / Plo, I. / Weissman, I.L. ...Authors: Moraga, I. / Wernig, G. / Wilmes, S. / Gryshkova, V. / Richter, C.P. / Hong, W.J. / Sinha, R. / Guo, F. / Fabionar, H. / Wehrman, T.S. / Krutzik, P. / Demharter, S. / Plo, I. / Weissman, I.L. / Minary, P. / Majeti, R. / Constantinescu, S.N. / Piehler, J. / Garcia, K.C.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly_auth_evidence ...entity_src_gen / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: diabody 330 VH domain
B: diabody 330 VL domain
C: Erythropoietin receptor
D: diabody 330 VH domain
E: diabody 330 VL domain
F: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4287
Polymers102,3366
Non-polymers921
Water59433
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, microscopy, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.141, 95.799, 144.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Detailsbiological unit is the same as asymmetric unit as confirmed by beta-gal complementation, signalling assay, superresolution microscopy, MALS

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Components

#1: Antibody diabody 330 VH domain


Mass: 13941.515 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody diabody 330 VL domain


Mass: 12016.095 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Protein Erythropoietin receptor / EPO-R


Mass: 25210.562 Da / Num. of mol.: 2 / Mutation: N76Q, N188Q, D247L, and L248D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPOR / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P19235
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: Magnesium chloride, Tris, PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→48.32 Å / Num. obs: 25898 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 62.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.054 / Net I/σ(I): 11.1 / Num. measured all: 110916
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.85-2.90484.50.7271.91679037590.7810.38399.9
9.01-48.323.70.02632.932899000.9990.01597.1

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S34, 1EER

3s34

1eer


Resolution: 2.85→43.146 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 2585 10 %random selection
Rwork0.2209 ---
obs-25846 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine analyzeLuzzati sigma a obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.85→43.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6492 0 6 33 6531
LS refinement shellResolution: 2.85→2.9048 Å /
RfactorNum. reflection
Rwork0.32 -
Rfree-142
all-1282
Refinement TLS params.Method: refined / Origin x: 11.7429 Å / Origin y: 22.1547 Å / Origin z: -53.5305 Å
111213212223313233
T0.4839 Å2-0.0432 Å2-0.0333 Å2-0.3765 Å20.0463 Å2--0.4387 Å2
L1.9757 °20.4471 °2-0.4288 °2-0.0617 °2-0.1695 °2--0.1168 °2
S0.1023 Å °-0.2126 Å °-0.0052 Å °0.033 Å °-0.074 Å °-0.0222 Å °0.0092 Å °0.0313 Å °-0.0256 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 204
2X-RAY DIFFRACTION1allC9 - 404
3X-RAY DIFFRACTION1allB1 - 201
4X-RAY DIFFRACTION1allE1 - 205
5X-RAY DIFFRACTION1allD1 - 209
6X-RAY DIFFRACTION1allF9 - 310

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