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- PDB-6moj: Dimeric DARPin A_angle_R5 complex with EpoR -

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Basic information

Entry
Database: PDB / ID: 6moj
TitleDimeric DARPin A_angle_R5 complex with EpoR
Components
  • Dimeric DARPin ACR5 (A_angle_R5)
  • 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 ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Erythropoietin receptor
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.431 Å
AuthorsJude, K.M. / Mohan, K. / Garcia, K.C.
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 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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 1.4Nov 13, 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 ACR5 (A_angle_R5)
B: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1188
Polymers49,3912
Non-polymers7276
Water39622
1
A: Dimeric DARPin ACR5 (A_angle_R5)
B: Erythropoietin receptor
hetero molecules

A: Dimeric DARPin ACR5 (A_angle_R5)
B: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,23516
Polymers98,7824
Non-polymers1,45312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area8880 Å2
ΔGint-34 kcal/mol
Surface area37510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.418, 130.418, 293.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Dimeric DARPin ACR5 (A_angle_R5)


Mass: 24261.668 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
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium potassium tartrate, 0.1 M bis-tris propane pH 8.5, 20% PEG 3350, 30% glycerol as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.431→48.739 Å / Num. obs: 25096 / % possible obs: 52.4 % / Redundancy: 26 % / Biso Wilson estimate: 44.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.273 / Rpim(I) all: 0.054 / Net I/σ(I): 11.04
Reflection shellResolution: 2.431→2.73 Å / Redundancy: 25.7 % / Rmerge(I) obs: 2.759 / Mean I/σ(I) obs: 0.46 / Num. unique obs: 1280 / CC1/2: 0.517 / Rpim(I) all: 0.551 / % possible all: 9.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSJan 26, 2018data reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted model, 1ERN

1ern


Resolution: 2.431→46.11 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.67
Details: Refined against elliptically truncated data 3.387 (a*) x 3.387 (b*) x 2.448 (c*)
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1278 5.1 %random
Rwork0.2103 ---
obs0.2123 25037 52.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.431→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 48 22 3366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033408
X-RAY DIFFRACTIONf_angle_d0.6034649
X-RAY DIFFRACTIONf_dihedral_angle_d14.0282007
X-RAY DIFFRACTIONf_chiral_restr0.038542
X-RAY DIFFRACTIONf_plane_restr0.004611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.431-2.52830.664670.4236131X-RAY DIFFRACTION3
2.5283-2.64330.5077290.3759544X-RAY DIFFRACTION11
2.6433-2.78270.3583410.3575871X-RAY DIFFRACTION17
2.7827-2.9570.3323830.33911230X-RAY DIFFRACTION25
2.957-3.18530.3251100.30641998X-RAY DIFFRACTION40
3.1853-3.50570.31861880.26973541X-RAY DIFFRACTION70
3.5057-4.01270.30762680.25285006X-RAY DIFFRACTION99
4.0127-5.05460.17142710.16115111X-RAY DIFFRACTION100
5.0546-46.1180.22072810.17055327X-RAY DIFFRACTION100
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)
15.60373.9715-1.3874.613-2.69871.9817-0.203-0.30540.5394-0.19170.5139-0.6598-1.3415-0.8581-0.34161.22320.1223-0.00810.5185-0.27610.6567-63.2639-16.222427.2785
23.17040.9599-0.57628.11533.19541.55860.21270.05841.1345-1.2588-0.14990.116-1.1028-0.38220.24091.46330.21980.03910.3901-0.21960.5028-60.367-13.530224.9409
32.3162-1.2496-0.25125.05822.80811.65670.00090.24260.4396-1.20680.167-0.4017-1.07950.0801-0.12711.418-0.20310.08890.41-0.19680.5091-55.7001-16.08816.9703
42.8589-0.60240.97513.04791.41153.95920.22550.12860.7376-0.78360.0323-0.3102-1.21880.8625-0.30711.197-0.38280.14620.6362-0.25590.3999-43.6673-21.672216.8927
52.6463-1.7112-0.61413.3119-0.5413.21430.2433-0.17520.4006-0.6735-0.099-0.472-0.46611.54-0.2650.8125-0.30650.23781.2334-0.37070.417-33.1865-30.598712.2717
61.2092-0.417-1.35115.2342-5.22317.9587-0.1756-0.81330.1122-0.29260.1095-0.54370.09172.73260.00530.8165-0.21730.16291.8411-0.23590.5408-25.7456-34.230515.1686
79.0773-2.9026-3.99216.3861-1.58763.2605-0.1159-0.0349-0.658-0.57610.06420.04191.37642.11570.24851.16850.08860.08411.4093-0.35710.5056-29.1506-41.25296.9723
80.55130.73380.80057.22773.13921.9091-0.27270.4222-0.34-0.0783-0.2405-0.97431.71641.00730.46141.19270.58870.05352.0559-0.09860.6872-20.5264-44.301116.3199
91.6517-0.94852.12176.5569-0.36129.7921-0.2827-1.0294-0.54471.26130.5789-0.0071.39092.4057-0.42761.5590.5339-0.01071.6636-0.13481.0077-25.4007-51.56128.174
103.3633-0.1694-0.67756.22353.71749.0883-0.0229-0.0737-0.04470.05090.13670.0081-0.06490.1592-0.08850.452-0.0196-0.0020.3749-0.13010.2061-57.2825-41.09223.4904
110.68311.41641.63032.7493.13585.4149-0.2154-0.22390.21550.14790.02150.2323-0.54350.04630.10260.4811-0.00280.05610.4256-0.16010.2183-58.6327-39.121621.5486
125.1004-0.03740.23983.93160.31163.21830.10530.21150.7849-0.6194-0.00890.6389-0.3668-0.47670.14150.5520.0339-0.06230.2811-0.00910.1725-68.6151-47.5723-4.4054
135.0195-0.04780.11725.81711.53284.64660.06970.22340.2712-0.31570.1025-0.0839-0.4844-0.1825-0.14570.37280.0117-0.02740.2873-0.03980.1212-65.9344-47.1259-5.1638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 125 )
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 158 )
6X-RAY DIFFRACTION6chain 'A' and (resid 159 through 172 )
7X-RAY DIFFRACTION7chain 'A' and (resid 173 through 192 )
8X-RAY DIFFRACTION8chain 'A' and (resid 193 through 205 )
9X-RAY DIFFRACTION9chain 'A' and (resid 206 through 224 )
10X-RAY DIFFRACTION10chain 'B' and (resid 6 through 69 )
11X-RAY DIFFRACTION11chain 'B' and (resid 70 through 127 )
12X-RAY DIFFRACTION12chain 'B' and (resid 128 through 174 )
13X-RAY DIFFRACTION13chain 'B' and (resid 175 through 223 )

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