[English] 日本語
Yorodumi
- PDB-1eba: COMPLEX BETWEEN THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) ... -

+
Open data


ID or keywords:

Loading...

-
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-mediated signaling pathway / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / decidualization / Erythropoietin activates RAS / brain development ...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) / 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more