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- PDB-6mof: Monomeric DARPin G2 complex with EpoR -

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Basic information

Entry
Database: PDB / ID: 6mof
TitleMonomeric DARPin G2 complex with EpoR
Components
  • Erythropoietin receptor
  • G2 DARPin
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-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. / 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 / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Long hematopoietin receptor, single chain family signature. / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Erythropoietin receptor
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.894 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 1.2Nov 20, 2019Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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: G2 DARPin
B: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9383
Polymers42,8762
Non-polymers621
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-2 kcal/mol
Surface area17980 Å2
Unit cell
Length a, b, c (Å)108.834, 108.834, 96.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein G2 DARPin


Mass: 17746.170 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


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

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: 0.2 M Magnesium chloride, 0.1 M Tris pH 7.0, 10% PEG 8000, 25% ethylene glycol as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.894→36.053 Å / Num. obs: 13260 / % possible obs: 98.72 % / Redundancy: 12.2 % / Biso Wilson estimate: 102.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.3095 / Rpim(I) all: 0.0886 / Net I/σ(I): 18.83
Reflection shellResolution: 2.894→2.998 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.172 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 1269 / CC1/2: 0.375 / Rpim(I) all: 0.3532 / % possible all: 96.87

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSJun 1, 2017data reduction
XDSJun 1, 2017data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ern, predicted model of G2

1ern


Resolution: 2.894→36.053 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.49
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 1328 10.02 %random
Rwork0.2237 ---
obs0.2279 13254 98.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.894→36.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 4 6 2832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012886
X-RAY DIFFRACTIONf_angle_d0.4413938
X-RAY DIFFRACTIONf_dihedral_angle_d11.6951714
X-RAY DIFFRACTIONf_chiral_restr0.035459
X-RAY DIFFRACTIONf_plane_restr0.003513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8936-3.00940.36791420.34391274X-RAY DIFFRACTION96
3.0094-3.14630.37781420.3171273X-RAY DIFFRACTION98
3.1463-3.31210.40441460.3031313X-RAY DIFFRACTION99
3.3121-3.51940.33381440.26641304X-RAY DIFFRACTION99
3.5194-3.79090.27281470.241304X-RAY DIFFRACTION99
3.7909-4.17190.23831470.22021331X-RAY DIFFRACTION99
4.1719-4.77440.23621510.20091339X-RAY DIFFRACTION100
4.7744-6.01070.26721500.2111350X-RAY DIFFRACTION99
6.0107-36.05550.23751590.20191438X-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)
18.55581.98824.33812.07370.28758.6547-0.3220.1803-1.3784-1.29491.13620.0220.2013-0.2811-0.82110.7723-0.16150.01091.0191-0.18691.00879.1661-23.7738-17.4211
24.6871-1.02032.09133.3710.42085.0402-0.3712-1.8436-0.46380.08630.3780.3691-0.2289-1.1180.01050.58330.17120.05541.28920.16010.72797.4589-20.1877-1.1413
37.21363.6666-2.23594.4031-0.8384.6945-0.3931-1.85860.3581-0.0427-0.13710.1493-0.843-1.24620.45430.95390.542-0.03492.424-0.38461.00383.1846-10.824510.1286
47.4536-0.8737-3.38755.76630.82083.4033-0.503-2.3963-0.0601-0.2252-0.03150.26270.2565-1.04590.3151.22060.3019-0.09142.3157-0.21151.07158.3216-8.739318.7724
56.1551-2.34863.27553.05861.11924.4414-0.8541-0.3124-0.39471.94430.55831.0094-2.00520.0399-0.26932.19530.22370.29930.6753-0.12931.542227.13025.6413-3.1367
65.6266-2.4960.98896.9389-3.68397.5378-0.1818-0.88640.38520.15220.0342-0.4228-1.4481-0.06510.08180.8565-0.0876-0.03910.8529-0.0140.723826.8582-8.0047-3.6659
70.62640.9923-1.25098.6588-3.61621.14330.1245-0.4020.36880.08730.22930.4646-0.25950.1424-0.34160.8021-0.0960.0310.773-0.06660.924322.83239.5092-14.4016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:27)
2X-RAY DIFFRACTION2(chain A and resid 28:111)
3X-RAY DIFFRACTION3(chain A and resid 112:130)
4X-RAY DIFFRACTION4(chain A and resid 131:162)
5X-RAY DIFFRACTION5(chain B and resid 8:22)
6X-RAY DIFFRACTION6(chain B and resid 23:62)
7X-RAY DIFFRACTION7(chain B and resid 63:224)

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