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- PDB-6mok: Dimeric DARPin A_distance_R7 complex with EpoR -

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Basic information

Entry
Database: PDB / ID: 6mok
TitleDimeric DARPin A_distance_R7 complex with EpoR
Components
  • Dimeric DARPin ANR7 (A_distance_r7)
  • Erythropoietin receptor
KeywordsBIOSYNTHETIC PROTEIN / DARPin / complex / receptor
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) / decidualization / Erythropoietin activates RAS / brain development / cytokine-mediated signaling pathway ...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) / 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 / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Long hematopoietin receptor, single chain family signature. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Erythropoietin receptor
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.101 Å
AuthorsJude, K.M. / Mohan, K. / Garcia, K.C. / Guo, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI51321 United States
CitationJournal: Science / Year: 2019
Title: Topological control of cytokine receptor signaling induces differential effects in hematopoiesis.
Authors: Mohan, K. / Ueda, G. / Kim, A.R. / Jude, K.M. / Fallas, J.A. / Guo, Y. / Hafer, M. / Miao, Y. / Saxton, R.A. / Piehler, J. / Sankaran, V.G. / Baker, D. / Garcia, K.C.
History
DepositionOct 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 17, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
Revision 1.5Oct 23, 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
A: Dimeric DARPin ANR7 (A_distance_r7)
B: Erythropoietin receptor


Theoretical massNumber of molelcules
Total (without water)55,8662
Polymers55,8662
Non-polymers00
Water00
1
A: Dimeric DARPin ANR7 (A_distance_r7)
B: Erythropoietin receptor

A: Dimeric DARPin ANR7 (A_distance_r7)
B: Erythropoietin receptor


Theoretical massNumber of molelcules
Total (without water)111,7334
Polymers111,7334
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)117.090, 117.090, 233.587
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Dimeric DARPin ANR7 (A_distance_r7)


Mass: 30736.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein Erythropoietin receptor / EPO-R


Mass: 25129.424 Da / Num. of mol.: 1
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
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: 4.14 Å3/Da / Density % sol: 70.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M NaCl, 0.1 M Tris pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00001 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 5.101→46.79 Å / Num. obs: 4205 / % possible obs: 98.38 % / Redundancy: 9.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.03905 / Rrim(I) all: 0.123 / Net I/σ(I): 9.92
Reflection shellResolution: 5.101→5.283 Å / Redundancy: 10.4 % / Rmerge(I) obs: 2.75 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 395 / CC1/2: 0.585 / Rpim(I) all: 0.884 / % possible all: 98.74

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSJan 26, 2018data reduction
XDSJan 26, 2018data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted model, 1ERN

1ern


Resolution: 5.101→46.79 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.893 / SU B: 146.123 / SU ML: 1.434 / Cross valid method: FREE R-VALUE / ESU R Free: 1.576
RfactorNum. reflection% reflectionSelection details
Rfree0.2989 421 10 %RANDOM
Rwork0.225 ---
obs0.23254 3786 98.62 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 434.475 Å2
Baniso -1Baniso -2Baniso -3
1-3.95 Å21.97 Å20 Å2
2--3.95 Å2-0 Å2
3----12.81 Å2
Refinement stepCycle: 1 / Resolution: 5.101→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3728 0 0 0 3728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123815
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.6215201
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3465498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.8822.446184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80915592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.851523
X-RAY DIFFRACTIONr_chiral_restr0.0950.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022873
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it38.4741.751998
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it60.0862.5692494
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it55.48644.6441815
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined15897
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 5.099→5.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.502 29 -
Rwork0.475 261 -
obs--98.98 %

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