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- PDB-6moi: Dimeric DARPin C_angle_R5 complex with EpoR -

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Basic information

Entry
Database: PDB / ID: 6moi
TitleDimeric DARPin C_angle_R5 complex with EpoR
Components
  • Dimeric DARPing CCR5 (C_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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Erythropoietin receptor
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.065 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 21, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
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 1.5Nov 6, 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 DARPing CCR5 (C_angle_R5)
B: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,78519
Polymers49,4732
Non-polymers1,31217
Water61334
1
A: Dimeric DARPing CCR5 (C_angle_R5)
B: Erythropoietin receptor
hetero molecules

A: Dimeric DARPing CCR5 (C_angle_R5)
B: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,57038
Polymers98,9464
Non-polymers2,62434
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Unit cell
Length a, b, c (Å)112.748, 112.748, 280.793
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Dimeric DARPing CCR5 (C_angle_R5)


Mass: 24343.793 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

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Non-polymers , 7 types, 51 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 7
Details: 0.3 M magnesium sulfate, 0.1 M bis-tris propane pH 7, 22.5% PurePEGs cocktail (Anatrace), 30% ethylene glycol 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: Feb 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.065→48.821 Å / Num. obs: 29498 / % possible obs: 45.01 % / Redundancy: 37.3 % / Biso Wilson estimate: 44.32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.4664 / Rpim(I) all: 0.08034 / Net I/σ(I): 9.4
Reflection shellResolution: 2.065→2.421 Å / Redundancy: 25.2 % / Rmerge(I) obs: 3.143 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1475 / CC1/2: 0.151 / Rpim(I) all: 6.339 / % possible all: 1.59

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSJan 26, 2018data reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted model; 1ERN

1ern


Resolution: 2.065→48.821 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.08
Details: Refined against elliptically truncated data 3.026 (0.894 a* - 0.447 b*) x 3.026 (b*) x 2.065 (c*)
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1573 5.33 %random
Rwork0.2145 ---
obs0.2164 29492 45.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.065→48.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3264 0 82 34 3380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023409
X-RAY DIFFRACTIONf_angle_d0.4774613
X-RAY DIFFRACTIONf_dihedral_angle_d11.332029
X-RAY DIFFRACTIONf_chiral_restr0.036529
X-RAY DIFFRACTIONf_plane_restr0.003593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0655-2.13210.080250.377684X-RAY DIFFRACTION2
2.1321-2.20830.443990.4173166X-RAY DIFFRACTION3
2.2083-2.29680.4838200.4012337X-RAY DIFFRACTION6
2.2968-2.40130.5483370.3651647X-RAY DIFFRACTION12
2.4013-2.52790.4131600.36941130X-RAY DIFFRACTION20
2.5279-2.68630.3098870.31851577X-RAY DIFFRACTION28
2.6863-2.89360.32591350.29932306X-RAY DIFFRACTION41
2.8936-3.18480.3362340.29044174X-RAY DIFFRACTION74
3.1848-3.64550.28653190.23045687X-RAY DIFFRACTION100
3.6455-4.59240.21253250.17575731X-RAY DIFFRACTION100
4.5924-48.83490.21773420.19146080X-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)
15.36820.79443.39178.3379-3.1537.34420.6083-0.61840.51020.8129-0.2973-0.3694-0.8660.9093-0.3440.5325-0.24080.11460.5915-0.10750.382217.7134-36.057816.2284
25.6710.06593.6111.2138-0.98844.45850.285-1.14540.62560.3852-0.23630.1942-0.3346-0.7124-0.07320.6297-0.04420.35160.4114-0.06550.41517.7987-35.935913.8475
33.9993.8955-0.76024.55190.11533.32060.4516-0.0602-0.27540.1613-0.2978-0.24710.13350.441-0.0170.3930.03780.17970.3760.01190.203315.3937-44.84119.0151
41.66260.1214-1.14820.2116-0.33572.52460.0263-0.012-0.00360.3563-0.01560.13620.04390.08080.13140.66020.0490.37650.25970.05840.23193.8453-42.64278.3445
55.32713.49260.46836.1884-0.19978.1731-0.11730.4836-0.30250.49150.2411-0.53810.61240.83770.05380.46870.11390.23120.3386-0.01250.178411.4179-49.49421.1372
61.30550.97351.2093.6819-2.34294.69430.08750.2677-0.05360.30290.34790.70570.0039-0.2978-0.3850.46160.040.22120.35660.04520.1996-0.0711-47.59270.8774
76.66164.6997-1.51443.3747-1.63175.58750.41750.04820.13340.007-0.3066-0.03420.20830.3496-0.24710.41610.1120.08970.3841-0.04350.16997.5091-51.8092-7.3157
86.5604-1.73341.18363.65591.93812.2374-0.08890.1692-0.11560.2523-0.07530.41760.5376-0.92320.13070.53710.02390.14660.4532-0.0150.27-2.9916-51.0574-8.3123
92.32610.17652.81856.22362.16324.3974-0.01440.61120.22110.06540.2989-0.29030.21720.2171-0.34840.43220.09470.0780.51680.00010.18185.2245-53.4297-16.518
103.176-1.2068-0.36895.99072.85077.25990.29770.60760.1891-0.5826-0.38290.2985-0.6006-0.52460.10740.42380.0188-0.00940.52050.01960.1628-0.2879-51.8778-22.9471
115.7426-0.3925-2.38586.9481-0.62136.69680.13031.21960.6995-1.2877-0.16550.5272-1.1663-0.89510.03040.82340.1894-0.08170.95780.04730.3915-2.7885-47.9162-32.3977
124.25124.02471.64435.26890.71434.5420.01221.06190.1257-0.44250.2415-0.2772-0.03950.0837-0.21490.70710.08690.28770.47580.05810.586114.6228-28.6398-12.6328
136.981.7867-4.78160.4624-1.28773.4850.291-0.030.70080.0108-0.11770.3823-0.69230.0187-0.24070.78170.08550.23780.29480.08690.502314.673-26.9851-6.8995
143.4043-0.6013-1.06943.58910.45286.3922-0.0058-0.04010.04020.5470.1160.04460.64920.3048-0.04850.40890.07260.03120.30930.10620.184842.53-29.9094-23.6352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 73 )
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 92 )
6X-RAY DIFFRACTION6chain 'A' and (resid 93 through 106 )
7X-RAY DIFFRACTION7chain 'A' and (resid 107 through 125 )
8X-RAY DIFFRACTION8chain 'A' and (resid 126 through 139 )
9X-RAY DIFFRACTION9chain 'A' and (resid 140 through 158 )
10X-RAY DIFFRACTION10chain 'A' and (resid 159 through 191 )
11X-RAY DIFFRACTION11chain 'A' and (resid 192 through 223 )
12X-RAY DIFFRACTION12chain 'B' and (resid 9 through 59 )
13X-RAY DIFFRACTION13chain 'B' and (resid 60 through 127 )
14X-RAY DIFFRACTION14chain 'B' and (resid 128 through 223 )

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