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- PDB-6moe: Monomeric DARPin E2 complex with EpoR -

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Basic information

Entry
Database: PDB / ID: 6moe
TitleMonomeric DARPin E2 complex with EpoR
Components
  • E2 DARPin
  • 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: 2.091 Å
AuthorsJude, K.M. / Mohan, K. / Garcia, K.C.
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 1.2Oct 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: E2 DARPin
B: E2 DARPin
C: Erythropoietin receptor
D: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,40716
Polymers86,1894
Non-polymers1,21712
Water8,071448
1
A: E2 DARPin
D: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6328
Polymers43,0952
Non-polymers5376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E2 DARPin
C: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7758
Polymers43,0952
Non-polymers6806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.250, 122.160, 132.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein E2 DARPin


Mass: 17965.291 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

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Non-polymers , 4 types, 460 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.6
Details: 1 M sodium potassium phosphate pH 5.6 Cryoprotected in 25% ethylene glycol

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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 PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 2.091→29.765 Å / Num. obs: 67078 / % possible obs: 99.4 % / Redundancy: 13.6 % / Biso Wilson estimate: 52.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1322 / Rpim(I) all: 0.03702 / Net I/σ(I): 12.15
Reflection shellResolution: 2.091→2.166 Å / Redundancy: 13.8 % / Rmerge(I) obs: 2.671 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 6559 / CC1/2: 0.693 / Rpim(I) all: 0.7394 / % possible all: 96.63

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSJun 1, 2017data reduction
XDSJun 1, 2017data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ern

1ern


Resolution: 2.091→29.765 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.47
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 1995 2.99 %random
Rwork0.204 ---
obs0.2047 66809 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.091→29.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5733 0 68 448 6249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035916
X-RAY DIFFRACTIONf_angle_d0.6338068
X-RAY DIFFRACTIONf_dihedral_angle_d14.7853507
X-RAY DIFFRACTIONf_chiral_restr0.041917
X-RAY DIFFRACTIONf_plane_restr0.0041044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0912-2.14350.43681500.42024396X-RAY DIFFRACTION96
2.1435-2.20140.35861280.37224562X-RAY DIFFRACTION99
2.2014-2.26620.42511410.33244563X-RAY DIFFRACTION99
2.2662-2.33930.30781340.29784590X-RAY DIFFRACTION100
2.3393-2.42290.30561490.28174574X-RAY DIFFRACTION100
2.4229-2.51990.30541390.27164585X-RAY DIFFRACTION100
2.5199-2.63450.2591380.26434633X-RAY DIFFRACTION100
2.6345-2.77330.2871410.24074643X-RAY DIFFRACTION100
2.7733-2.94690.26461410.2334608X-RAY DIFFRACTION100
2.9469-3.17420.25431420.22584640X-RAY DIFFRACTION100
3.1742-3.49320.24681490.20924684X-RAY DIFFRACTION100
3.4932-3.99760.23171410.18054672X-RAY DIFFRACTION100
3.9976-5.03260.15711480.15444751X-RAY DIFFRACTION100
5.0326-29.76820.19291540.17044913X-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)
12.88761.08810.93964.89491.68015.85070.07631.02510.0672-0.60450.07570.2415-0.0263-0.1543-0.08390.8160.087-0.12750.8308-0.0420.504123.3806-5.4203-49.4624
22.553-0.281-0.18182.08830.55762.22830.03890.2303-0.4334-0.2569-0.04230.22410.1209-0.24610.02740.47440-0.06170.5183-0.08460.565323.9266-13.0674-35.9623
32.689-0.1820.35623.02320.49473.5620.024-0.6317-0.41330.4784-0.24950.09870.0874-0.22060.250.4708-0.0264-0.01940.64450.07410.523521.9692-13.867-17.643
49.625-6.60720.12364.6131-0.22698.7288-0.5585-1.0202-0.9460.95090.59021.81160.4778-0.539-0.10820.7118-0.1210.03210.96760.18770.738115.0238-17.1537-10.8429
51.96441.2410.90611.7906-0.50851.88550.43750.01411.45530.4465-0.216-0.1342-0.29360.0858-0.30190.7262-0.07640.13270.5342-0.12661.0305-11.419218.4786-29.5436
62.93031.36061.64784.83143.00074.88140.398-0.84451.15590.3964-0.47710.0142-0.3946-0.0209-0.08330.606-0.02460.07240.617-0.20140.6514-16.33111.3715-24.1851
75.4592-0.7005-0.90483.90820.8685.58410.05450.0270.66820.36-0.064-0.9575-0.42370.6958-0.02310.5513-0.05460.04720.5203-0.12990.8154-4.171410.1264-27.1052
82.05741.25911.36982.7070.44761.11640.0414-0.54960.3966-0.07370.1416-0.3588-0.2579-0.0605-0.06670.5546-0.0455-0.00510.6351-0.11440.6091-8.56191.5317-24.5887
95.9634-0.26630.62055.8517-0.8555.1881-0.4916-0.02920.42130.4013-0.083-1.5141-1.25121.3012-0.04340.5725-0.1115-0.14110.64250.01280.95542.5612.9045-23.635
100.88430.6070.16294.77030.82824.59140.2319-1.5406-0.06930.8565-0.3126-0.8160.5280.09470.0760.4683-0.04-0.05320.8706-0.05630.5679-8.188-5.4404-20.0509
114.5137-0.5289-0.15743.10881.4686.11410.36090.0528-0.4104-0.14610.0598-0.5130.0074-0.0134-0.58070.5232-0.0708-0.00480.5902-0.04580.7324-3.2228-9.7595-29.8848
129.2149-1.09312.06982.76222.19632.75170.0964-0.68230.18070.10410.0196-1.9292-0.35590.3226-0.65360.55920.0001-0.06590.6023-0.02020.81255.4516-7.2175-25.0449
131.9922-0.21770.46541.91480.5092.1111-0.087-0.2801-0.7778-0.05660.2168-0.0878-0.00790.2529-0.14720.499-0.0396-0.10820.70340.03720.8134-4.2128-16.8066-25.8236
143.5847-0.4653-2.50733.78510.98948.5771-0.47850.1354-1.02810.2382-0.39490.03270.2063-0.0970.72350.5341-0.0462-0.07230.72760.08970.93996.8488-19.129-25.9652
152.54860.7347-0.38361.30591.54355.18990.08390.53420.2057-0.35470.0834-0.5883-0.28860.2672-0.12080.58650.01080.10380.60560.00320.5559-11.9715-5.4571-50.0255
164.0243-1.9445-1.223.95572.67182.68160.15550.0444-0.12850.0459-0.26540.2504-0.244-0.33210.12520.4936-0.04380.0560.4179-0.04270.3335-20.9805-5.9827-42.1322
172.1986-0.7928-1.91420.38371.64964.58780.34420.03580.4391-0.32050.0409-0.0282-0.6576-0.226-0.40210.5782-0.02870.09910.45470.00050.538-13.30712.2517-44.8909
185.36171.029-1.67154.47580.88774.93620.22-0.270.25240.46470.0720.01010.15530.574-0.26370.57680.0354-0.00750.62040.03910.34517.6217-1.1535-64.666
191.91250.0911.0228.06831.38991.2311-0.3778-0.37460.4130.49610.31110.495-0.3413-0.25350.06820.64360.0740.02720.68-0.06070.66824.801713.3542-23.5672
203.8718-0.8297-3.58872.95072.36876.77690.3039-0.24680.0073-0.01590.2822-0.3130.27130.4169-0.5940.5226-0.0017-0.02260.4597-0.04510.504235.31385.4392-25.9717
211.5911-1.6475-0.74163.12181.90450.80940.16870.25780.1639-0.4734-0.18270.0572-0.35460.1075-0.01250.4227-0.0078-0.00920.4228-0.0010.458527.83718.8487-30.856
224.8557-1.1733-0.584.78530.84663.81660.08110.1307-0.44870.0267-0.12720.79280.453-0.47670.03950.5198-0.0813-0.07070.48140.09040.74816.813129.5274-24.0948
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 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 162 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 26 )
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 40 )
7X-RAY DIFFRACTION7chain 'B' and (resid 41 through 59 )
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 83 )
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 92 )
10X-RAY DIFFRACTION10chain 'B' and (resid 93 through 106 )
11X-RAY DIFFRACTION11chain 'B' and (resid 107 through 116 )
12X-RAY DIFFRACTION12chain 'B' and (resid 117 through 125 )
13X-RAY DIFFRACTION13chain 'B' and (resid 126 through 149 )
14X-RAY DIFFRACTION14chain 'B' and (resid 150 through 162 )
15X-RAY DIFFRACTION15chain 'C' and (resid 7 through 42 )
16X-RAY DIFFRACTION16chain 'C' and (resid 43 through 85 )
17X-RAY DIFFRACTION17chain 'C' and (resid 86 through 127 )
18X-RAY DIFFRACTION18chain 'C' and (resid 128 through 223 )
19X-RAY DIFFRACTION19chain 'D' and (resid 8 through 35 )
20X-RAY DIFFRACTION20chain 'D' and (resid 36 through 78 )
21X-RAY DIFFRACTION21chain 'D' and (resid 79 through 127 )
22X-RAY DIFFRACTION22chain 'D' and (resid 128 through 223 )

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