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- PDB-6moh: Dimeric DARPin C_R3 complex with EpoR -

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Basic information

Entry
Database: PDB / ID: 6moh
TitleDimeric DARPin C_R3 complex with EpoR
Components
  • Dimeric DARPin E2C (C_R3)
  • Erythropoietin receptor
KeywordsBIOSYNTHETIC PROTEIN / Complex / Receptor / DARPin
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 / Ankyrin repeat-containing domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III ...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 / Ankyrin repeat-containing domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Erythropoietin receptor
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dimeric DARPin E2C (C_R3)
B: Dimeric DARPin E2C (C_R3)
C: Erythropoietin receptor
D: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,07712
Polymers85,3894
Non-polymers6888
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-89 kcal/mol
Surface area32490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.193, 96.193, 286.401
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Dimeric DARPin E2C (C_R3)


Mass: 17565.109 Da / Num. of mol.: 2
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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.1 M HEPES pH 7.3, 1.4 M sodium potassium phosphate, 24% glycerol cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999924 Å / Relative weight: 1
ReflectionResolution: 3.2→68.02 Å / Num. obs: 18878 / % possible obs: 79.96 % / Redundancy: 11.2 % / Biso Wilson estimate: 29.34 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.8886 / Rpim(I) all: 0.2813 / Net I/σ(I): 3.07
Reflection shellResolution: 3.2→3.315 Å / Redundancy: 11.3 % / Rmerge(I) obs: 5.596 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 944 / CC1/2: 0.552 / Rpim(I) all: 1.771 / % possible all: 17.52

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSJune 1, 2017data reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MOG, 1ERN

6mog

1ern


Resolution: 3.2→68.019 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.27
Details: refined against elliptically truncated data 3.469 (a*) x 3.469 (b*) x 3.167 (c*)
RfactorNum. reflection% reflectionSelection details
Rfree0.2767 891 4.82 %random
Rwork0.2364 ---
obs0.2383 18483 79.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→68.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5468 0 36 6 5510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025613
X-RAY DIFFRACTIONf_angle_d0.617662
X-RAY DIFFRACTIONf_dihedral_angle_d15.3913336
X-RAY DIFFRACTIONf_chiral_restr0.039891
X-RAY DIFFRACTIONf_plane_restr0.005987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.40060.3526430.3183691X-RAY DIFFRACTION20
3.4006-3.66320.37131090.29292184X-RAY DIFFRACTION61
3.6632-4.03180.28541810.26543586X-RAY DIFFRACTION99
4.0318-4.61510.25371810.21323618X-RAY DIFFRACTION100
4.6151-5.8140.24771820.21033661X-RAY DIFFRACTION99
5.814-68.03410.25831950.21793852X-RAY DIFFRACTION98
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)
12.3820.25912.74214.315-0.40623.27240.06770.2874-0.1433-0.2499-0.0349-0.67730.22140.3438-0.0320.35570.18970.02680.2783-0.0110.24447.3403-66.0798.1953
24.1088-0.0379-0.48130.8371-0.84081.35730.1698-0.0373-0.22530.1293-0.0083-0.13030.30460.2868-0.21810.56610.2598-0.05380.420.0340.29988.8618-67.142117.8229
31.5992-0.09210.13750.12150.04231.5473-0.0391-0.042-0.09530.0031-0.0146-0.05380.08890.17910.19180.1714-0.01310.0830.15930.04930.13584.8707-58.15479.7305
40.1024-0.1420.13130.3087-0.24960.23070.05340.00630.0565-0.0518-0.0148-0.03440.0020.10620.00470.18010.05280.08850.1661-0.00560.14615.7017-53.161414.3265
50.8360.0420.6361.0207-0.13131.00970.0132-0.1108-0.12520.07560.06280.07490.0475-0.0812-0.01960.15840.06420.06930.09780.05320.1136-2.2566-49.88519.3416
60.62590.10561.43050.03280.26523.3068-0.04960.08820.0727-0.0381-0.01210.0198-0.41490.04730.05740.36280.08570.07860.29510.08950.1582-1.6517-41.02119.8281
73.63171.3446-1.46751.37790.85052.8006-0.03080.39740.204-0.1120.12990.1616-0.1288-0.4322-0.12020.27890.04180.12610.35030.09390.2111-11.5236-44.166115.0851
82.763-0.83820.97931.42781.01234.54990.0545-0.1973-0.14690.3567-0.03220.12790.1316-0.19290.00320.22390.05690.04330.21940.08740.1304-7.5772-41.709324.3002
93.167-0.09361.94543.19071.20923.28720.11380.48660.1678-1.0184-0.30990.238-0.7916-0.32820.19610.84190.35260.10860.54630.11230.518-9.2211-34.47829.9741
105.4638-1.1055-0.43871.60311.80342.2316-0.1021-0.02350.1744-0.2028-0.30870.5677-0.6171-0.9370.42260.80760.4796-0.04020.87430.01220.7836-18.4705-36.858118.3532
113.5638-1.99610.27153.2313-0.58042.44510.16640.28490.2303-0.2945-0.14090.0248-0.3877-0.23690.01460.37630.25070.0270.42880.02910.4846-24.6303-33.716545.8237
120.27640.19330.30260.2875-0.09570.9570.0464-0.10280.3160.0019-0.04250.1184-0.2893-0.1777-0.010.44860.18440.09630.2354-0.06320.2798-11.6526-36.981142.9266
130.6294-0.0914-0.04060.0317-0.12380.90750.05370.0010.15070.01210.027-0.0018-0.18430.12750.03330.1464-0.06980.06610.1342-0.02440.18441.1316-44.246943.1962
142.1729-2.0691-0.53333.62570.11151.78810.05650.1187-0.1128-0.2023-0.10310.13730.0728-0.00510.06580.22580.07290.03270.1106-0.02990.1669-0.2157-47.00531.6707
150.7028-0.7385-0.81861.22551.18751.1918-0.178-0.36140.03830.05660.0419-0.2240.57111.12960.17570.420.02430.20770.70340.00280.38289.664-45.959744.1909
166.1704-1.84441.92047.94161.32394.9653-0.04420.1712-0.35980.07590.01330.06550.75130.71050.01180.43670.2508-0.02710.5169-0.07790.25217.1825-56.229437.3323
177.04231.7121.6883.83381.65442.01430.3627-0.2983-0.59690.2867-0.0476-0.15710.4478-0.1503-0.16490.3365-0.0318-0.10030.2165-0.03290.2208-12.0397-62.119554.3596
180.7975-0.31880.00820.9815-0.1051.35770.10690.1282-0.2049-0.0189-0.1220.30480.1908-0.42690.330.24790.01250.03170.2914-0.11550.1661-17.9716-59.933653.8947
191.49073.28830.88947.68273.08423.5379-0.03140.9702-0.7513-0.822-0.16320.2836-0.017-0.13670.15980.59740.049-0.15840.6925-0.24340.6721-24.3092-76.129239.2738
204.770.7952-1.87484.6514-1.72733.37560.04060.29680.2503-0.12760.19610.4421-0.1759-0.5103-0.2130.6529-0.0950.27760.78470.11770.5174-22.3771-60.48183.861
211.10080.4518-0.83040.3614-0.17080.77660.0410.08830.00530.0338-0.05440.1040.0353-0.1609-0.12450.2893-0.05440.14830.32920.04310.197-17.4791-64.18824.959
222.07290.763-0.29591.7848-1.00392.0496-0.0312-0.06020.0823-0.1138-0.1247-0.2429-0.22840.5655-0.04410.4497-0.23950.14560.4415-0.1230.3324-34.182-72.01521.4751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 56 )
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 79 )
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 99 )
6X-RAY DIFFRACTION6chain 'A' and (resid 100 through 112 )
7X-RAY DIFFRACTION7chain 'A' and (resid 113 through 122 )
8X-RAY DIFFRACTION8chain 'A' and (resid 123 through 132 )
9X-RAY DIFFRACTION9chain 'A' and (resid 133 through 145 )
10X-RAY DIFFRACTION10chain 'A' and (resid 146 through 163 )
11X-RAY DIFFRACTION11chain 'B' and (resid 9 through 32 )
12X-RAY DIFFRACTION12chain 'B' and (resid 33 through 99 )
13X-RAY DIFFRACTION13chain 'B' and (resid 100 through 122 )
14X-RAY DIFFRACTION14chain 'B' and (resid 123 through 132 )
15X-RAY DIFFRACTION15chain 'B' and (resid 133 through 145 )
16X-RAY DIFFRACTION16chain 'B' and (resid 146 through 163 )
17X-RAY DIFFRACTION17chain 'C' and (resid 7 through 49 )
18X-RAY DIFFRACTION18chain 'C' and (resid 50 through 150 )
19X-RAY DIFFRACTION19chain 'C' and (resid 151 through 217 )
20X-RAY DIFFRACTION20chain 'D' and (resid 8 through 49 )
21X-RAY DIFFRACTION21chain 'D' and (resid 50 through 137 )
22X-RAY DIFFRACTION22chain 'D' and (resid 138 through 220 )

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