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- PDB-1eba: COMPLEX BETWEEN THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) ... -

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Basic information

Entry
Database: PDB / ID: 1eba
TitleCOMPLEX BETWEEN THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) RECEPTOR [EBP] AND AN INACTIVE PEPTIDE [EMP33] CONTAINS 3,5-DIBROMOTYROSINE IN POSITION 4 (DENOTED DBY)
Components
  • PROTEIN (EPO MIMETICS PEPTIDE 33)
  • PROTEIN (ERYTHROPOIETIN RECEPTOR)
KeywordsSIGNALING PROTEIN / ERYTHROPOIETIN RECEPTOR / SIGNAL TRANSDUCTION / PROTEIN MINIMIZATION / DRUG DESIGN / CYTOKINE RECEPTOR CLASS 1 / COMPLEX (CYTOKINE RECEPTOR-PEPTIDE)
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLivnah, O. / Stura, E.A. / Wilson, I.A.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: An antagonist peptide-EPO receptor complex suggests that receptor dimerization is not sufficient for activation.
Authors: Livnah, O. / Johnson, D.L. / Stura, E.A. / Farrell, F.X. / Barbone, F.P. / You, Y. / Liu, K.D. / Goldsmith, M.A. / He, W. / Krause, C.D. / Pestka, S. / Jolliffe, L.K. / Wilson, I.A.
#1: Journal: Science / Year: 1996
Title: Functional Mimicry of a Protein Hormone by a Peptide Agonist: The Epo Receptor Complex at 2.8 A
Authors: Livnah, O. / Stura, E.A. / Johnson, D.L. / Middleton, S.A. / Mulcahy, L.S. / Wrighton, N.C. / Dower, W.J. / Jolliffe, L.K. / Wilson, I.A.
History
DepositionOct 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ERYTHROPOIETIN RECEPTOR)
B: PROTEIN (ERYTHROPOIETIN RECEPTOR)
C: PROTEIN (EPO MIMETICS PEPTIDE 33)
D: PROTEIN (EPO MIMETICS PEPTIDE 33)


Theoretical massNumber of molelcules
Total (without water)51,9904
Polymers51,9904
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-25 kcal/mol
Surface area24720 Å2
MethodPISA
2
A: PROTEIN (ERYTHROPOIETIN RECEPTOR)

B: PROTEIN (ERYTHROPOIETIN RECEPTOR)
C: PROTEIN (EPO MIMETICS PEPTIDE 33)
D: PROTEIN (EPO MIMETICS PEPTIDE 33)


Theoretical massNumber of molelcules
Total (without water)51,9904
Polymers51,9904
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation4_654-x+1,-y+1/2,z-1/21
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-35 kcal/mol
Surface area22150 Å2
MethodPISA
3
B: PROTEIN (ERYTHROPOIETIN RECEPTOR)

A: PROTEIN (ERYTHROPOIETIN RECEPTOR)
C: PROTEIN (EPO MIMETICS PEPTIDE 33)
D: PROTEIN (EPO MIMETICS PEPTIDE 33)


Theoretical massNumber of molelcules
Total (without water)51,9904
Polymers51,9904
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation4_655-x+1,-y+1/2,z+1/21
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-33 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.890, 75.009, 130.527
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein PROTEIN (ERYTHROPOIETIN RECEPTOR) / EBP / EPO-R


Mass: 23739.908 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P19235
#2: Protein/peptide PROTEIN (EPO MIMETICS PEPTIDE 33) / EMP33 /


Mass: 2255.168 Da / Num. of mol.: 2 / Source method: obtained synthetically

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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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 %mPEG50001reservoir
20.100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 99999 / % possible obs: 99 % / Redundancy: 3.3 % / Rsym value: 0.089 / Net I/σ(I): 19.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.3 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 16100 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoRE(CCP4)phasing
X-PLOR3.8refinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EBP MONOMER

1ebp


Resolution: 2.7→50 Å / Cross valid method: THROUGHT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.299 -10 %RANDOM
Rwork0.2 ---
obs0.2 16100 99 %-
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 0 0 3536
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARHCSDX
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 50 Å / σ(F): 1 / Num. reflection Rfree: 1498 / % reflection Rfree: 10 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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