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- PDB-6mol: Monoextended DARPin M_R12 complex with EpoR -

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Basic information

Entry
Database: PDB / ID: 6mol
TitleMonoextended DARPin M_R12 complex with EpoR
Components
  • Erythropoietin receptor
  • Monoextended DARPin R12 (M_R12)
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 activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / 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 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 speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.163 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 1.2Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monoextended DARPin R12 (M_R12)
B: Erythropoietin receptor
C: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5744
Polymers98,4823
Non-polymers921
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-10 kcal/mol
Surface area38910 Å2
Unit cell
Length a, b, c (Å)168.109, 168.109, 78.029
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Monoextended DARPin R12 (M_R12)


Mass: 48223.402 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.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Source detailsDARPin is a computationally designed protein.

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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: 3.24 Å3/Da / Density % sol: 61.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Seeded from 0.2 M NaCl, 0.1 M CAPS pH 10.5, 20% PEG 8000 into 0.2 M ammonium tartrate and 20% PEG 3350, with 10% glycerol, 10% ethylene glycol as cryoprotectant
PH range: 7.3-10.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 3.163→44.969 Å / Num. obs: 14501 / % possible obs: 66.63 % / Redundancy: 8.7 % / Biso Wilson estimate: 109.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.07 / Net I/σ(I): 6.22
Reflection shellResolution: 3.163→3.4 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.046 / Mean I/σ(I) obs: 0.24 / Num. unique obs: 724 / CC1/2: 0.491 / Rpim(I) all: 0.832 / % possible all: 17.3

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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: 3.163→44.969 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4
Details: Refined against elliptically truncated data 3.144 (0.894 a* - 0.447 b*) x 3.144 (b*) x 4.58 (c*)
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 1370 9.46 %random
Rwork0.2193 ---
obs0.2232 14484 66.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.163→44.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6511 0 6 2 6519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026661
X-RAY DIFFRACTIONf_angle_d0.4949112
X-RAY DIFFRACTIONf_dihedral_angle_d11.3643920
X-RAY DIFFRACTIONf_chiral_restr0.0361067
X-RAY DIFFRACTIONf_plane_restr0.0041189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1627-3.27570.4329110.4657123X-RAY DIFFRACTION6
3.2757-3.40680.4264570.3901569X-RAY DIFFRACTION30
3.4068-3.56180.383850.3264895X-RAY DIFFRACTION45
3.5618-3.74950.36861080.30831059X-RAY DIFFRACTION55
3.7495-3.98430.35271370.31191293X-RAY DIFFRACTION67
3.9843-4.29170.31651600.27261515X-RAY DIFFRACTION77
4.2917-4.72310.24241810.22351757X-RAY DIFFRACTION89
4.7231-5.40560.25732060.22341919X-RAY DIFFRACTION98
5.4056-6.80670.26872180.22531973X-RAY DIFFRACTION100
6.8067-44.97380.20082070.15172011X-RAY DIFFRACTION99
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)
13.8997-0.32490.04251.65661.33571.0653-0.1672-1.0355-1.06620.653-0.20641.29060.6474-0.36480.43371.0419-0.14010.42120.84040.12271.52452.180525.816328.3976
29.67833.2954-1.78012.8090.61471.1877-0.1453-0.6155-0.59380.701-0.07660.49670.2416-0.11480.14260.79230.1267-0.08920.48890.18960.56732.73330.822827.6386
32.03610.28380.21996.7512-3.24583.4882-0.14570.27790.15770.1477-0.1458-0.7663-0.1454-0.00760.16720.62920.0877-0.08480.61850.25160.480849.693142.562813.2675
44.24952.34461.20426.70732.27035.7372-0.20880.32520.1968-0.47670.2066-0.837-0.75510.78570.11570.7374-0.0357-0.01240.80020.34820.570952.400254.0634-4.2471
51.0589-0.55261.59675.94120.71032.8327-0.21530.78510.571-1.46810.1681-0.7843-0.98710.47960.66551.0013-0.02340.09651.1970.58080.649550.858959.3307-21.2435
61.1312-0.06551.09620.03480.18812.99210.02160.29060.06560.0072-0.06810.06710.119-0.69170.03531.6316-0.0191-0.08421.38850.3050.407546.417363.1274-34.9636
74.90876.4013-2.91159.2057-2.29397.2546-1.14590.3049-0.6091-2.679-0.14952.05970.4221-0.32521.12191.02860.2114-0.36940.9383-0.02821.421221.795249.3741-20.9037
83.9302-1.3375-2.42418.42382.81329.7010.40640.6866-0.0856-1.1106-0.4104-0.38631.6793-0.5486-0.19280.63150.1586-0.09560.8076-0.02021.055229.350247.6454-16.9437
95.0851-0.2615-0.77254.27450.65494.4046-0.78510.98380.8313-0.9756-0.6568-0.2332-0.53450.63140.68731.06830.0152-0.08540.6664-0.05150.697836.665739.8499-18.7568
104.1446-3.8571-2.4024.32720.75794.3681-1.12590.7066-0.1699-0.1089-0.1941.3020.1524-0.32520.3840.7362-0.243-0.16650.74410.21510.581131.077942.0353-13.1679
118.4414-1.2719-1.51157.28122.7512.1943-0.05270.8241-0.1562-0.5065-0.6422-0.2429-0.5808-1.46730.28930.64360.0829-0.02490.83410.16520.453240.303447.3327-15.1824
128.0634-1.47860.12992.7951-2.34273.7074-0.2245-0.66230.48030.4935-0.233-0.4548-0.3875-0.79310.48540.68390.0013-0.34961.0065-0.16960.65487.862859.7804-8.2136
133.55010.08742.11646.4127-4.00766.1106-0.6952-0.56421.8551-0.6437-0.3177-0.3137-0.2841-0.3510.67830.7957-0.1998-0.60920.7666-0.10751.423113.715866.1053-12.7191
145.7205-0.8922.17279.2751-1.89525.6977-0.4932-0.19331.22610.6789-0.35490.0985-0.70020.28590.73310.6542-0.0862-0.17431.0016-0.27910.748.963267.5652-11.476
152.38490.1947-1.66063.04180.17361.3549-0.4559-0.13570.58970.35640.1811-0.84340.04030.3163-0.12011.035-0.0088-0.32661.0045-0.38620.820512.573662.6327-12.8843
165.4644-2.34492.92394.5114-4.54174.8423-0.47160.48490.543-0.2249-0.8461-1.489-0.55130.03171.27051.0462-0.0175-0.02350.8759-0.35951.672515.551550.748117.8918
172.8607-0.04411.147.5123-2.97765.4338-0.9560.309-0.78250.991.0103-0.1727-0.4954-0.4257-0.19220.7401-0.03850.04280.8528-0.28560.966112.092642.871615.3566
188.6125-0.6943-6.87733.9731.97498.26050.16441.70680.27430.0653-0.15150.4846-0.5182-0.70410.23890.8936-0.1201-0.00460.7905-0.24030.98698.78537.73118.9935
193.3676-0.58620.08727.40591.75860.90320.2733-0.1391-0.21510.7991-0.86040.88920.2403-0.27770.51840.7219-0.07350.01730.83480.07950.81524.130249.694719.7475
202.45241.89062.37522.85082.02822.75620.573-0.372-0.5804-0.2610.9255-0.17960.35760.4793-1.06071.0694-0.0202-0.05870.9844-0.07180.97452.446267.699621.3615
216.30834.91361.00658.00772.64694.67711.85630.0730.67161.8196-0.46530.79591.59121.092-0.76211.0855-0.18510.03190.88690.02230.52784.558463.244428.0711
229.0350.6321-4.09057.00090.67295.84270.705-1.2890.49710.155-0.74620.47330.3766-0.4489-0.39431.0808-0.02340.05631.6245-0.02320.70369.999769.575234.6724
238.13071.35871.97188.36213.13632.81980.8044-0.7882-1.06741.07680.0626-2.05980.62040.6497-0.83280.9251-0.2601-0.02380.7466-0.01591.082812.329667.293828.8542
248.55684.89321.2858.33952.94644.1337-0.3194-0.2170.207-0.47130.17770.00980.09230.6020.32450.7598-0.0573-0.0230.9798-0.15620.54789.180864.213827.2099
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 124 )
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 223 )
3X-RAY DIFFRACTION3chain 'A' and (resid 224 through 299 )
4X-RAY DIFFRACTION4chain 'A' and (resid 300 through 352 )
5X-RAY DIFFRACTION5chain 'A' and (resid 353 through 417 )
6X-RAY DIFFRACTION6chain 'A' and (resid 418 through 454 )
7X-RAY DIFFRACTION7chain 'B' and (resid 8 through 21 )
8X-RAY DIFFRACTION8chain 'B' and (resid 22 through 42 )
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 77 )
10X-RAY DIFFRACTION10chain 'B' and (resid 78 through 94 )
11X-RAY DIFFRACTION11chain 'B' and (resid 95 through 117 )
12X-RAY DIFFRACTION12chain 'B' and (resid 118 through 150 )
13X-RAY DIFFRACTION13chain 'B' and (resid 151 through 174 )
14X-RAY DIFFRACTION14chain 'B' and (resid 175 through 200 )
15X-RAY DIFFRACTION15chain 'B' and (resid 201 through 223 )
16X-RAY DIFFRACTION16chain 'C' and (resid 10 through 21 )
17X-RAY DIFFRACTION17chain 'C' and (resid 22 through 47 )
18X-RAY DIFFRACTION18chain 'C' and (resid 50 through 84 )
19X-RAY DIFFRACTION19chain 'C' and (resid 85 through 137 )
20X-RAY DIFFRACTION20chain 'C' and (resid 138 through 150 )
21X-RAY DIFFRACTION21chain 'C' and (resid 151 through 161 )
22X-RAY DIFFRACTION22chain 'C' and (resid 162 through 189 )
23X-RAY DIFFRACTION23chain 'C' and (resid 190 through 200 )
24X-RAY DIFFRACTION24chain 'C' and (resid 201 through 222 )

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