[English] 日本語
Yorodumi
- PDB-1eer: CRYSTAL STRUCTURE OF HUMAN ERYTHROPOIETIN COMPLEXED TO ITS RECEPT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eer
TitleCRYSTAL STRUCTURE OF HUMAN ERYTHROPOIETIN COMPLEXED TO ITS RECEPTOR AT 1.9 ANGSTROMS
Components
  • ERYTHROPOIETIN
  • ERYTHROPOIETIN RECEPTOR
KeywordsCOMPLEX (CYTOKINE/RECEPTOR) / ERYTHROPOIETIN / ERYTHROPOIETIN RECEPTOR / SIGNAL TRANSDUCTION / HEMATOPOIETIC CYTOKINE / CYTOKINE RECEPTOR CLASS 1 / COMPLEX (CYTOKINE-RECEPTOR) / COMPLEX (CYTOKINE-RECEPTOR) complex
Function / homology
Function and homology information


negative regulation of erythrocyte apoptotic process / erythropoietin receptor binding / erythropoietin receptor activity / negative regulation of cation channel activity / myeloid cell apoptotic process / hemoglobin biosynthetic process / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / negative regulation of calcium ion transport into cytosol / Signaling by Erythropoietin / Erythropoietin activates STAT5 ...negative regulation of erythrocyte apoptotic process / erythropoietin receptor binding / erythropoietin receptor activity / negative regulation of cation channel activity / myeloid cell apoptotic process / hemoglobin biosynthetic process / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / negative regulation of calcium ion transport into cytosol / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / erythropoietin-mediated signaling pathway / cellular hyperosmotic response / cell surface receptor signaling pathway via STAT / positive regulation of Ras protein signal transduction / response to vitamin A / blood circulation / Regulation of gene expression by Hypoxia-inducible Factor / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / erythrocyte maturation / positive regulation of activated T cell proliferation / response to dexamethasone / response to testosterone / decidualization / protein kinase activator activity / response to axon injury / response to hyperoxia / response to electrical stimulus / Erythropoietin activates RAS / response to salt stress / embryo implantation / response to interleukin-1 / positive regulation of neuron differentiation / erythrocyte differentiation / cytokine activity / acute-phase response / cytokine-mediated signaling pathway / brain development / hormone activity / positive regulation of neuron projection development / response to estrogen / heart development / cell body / response to lipopolysaccharide / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / nuclear speck / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Erythropoietin / Erythropoietin/thrombopoietin / Erythropoietin/thrombopoeitin, conserved site / Erythropoietin/thrombopoietin / Erythropoietin / thrombopoeitin signature. / 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 ...Erythropoietin / Erythropoietin/thrombopoietin / Erythropoietin/thrombopoeitin, conserved site / Erythropoietin/thrombopoietin / Erythropoietin / thrombopoeitin signature. / 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 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Erythropoietin / Erythropoietin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.9 Å
AuthorsSyed, R.S. / Li, C.
CitationJournal: Nature / Year: 1998
Title: Efficiency of signalling through cytokine receptors depends critically on receptor orientation.
Authors: Syed, R.S. / Reid, S.W. / Li, C. / Cheetham, J.C. / Aoki, K.H. / Liu, B. / Zhan, H. / Osslund, T.D. / Chirino, A.J. / Zhang, J. / Finer-Moore, J. / Elliott, S. / Sitney, K. / Katz, B.A. / ...Authors: Syed, R.S. / Reid, S.W. / Li, C. / Cheetham, J.C. / Aoki, K.H. / Liu, B. / Zhan, H. / Osslund, T.D. / Chirino, A.J. / Zhang, J. / Finer-Moore, J. / Elliott, S. / Sitney, K. / Katz, B.A. / Matthews, D.J. / Wendoloski, J.J. / Egrie, J. / Stroud, R.M.
History
DepositionJul 24, 1998Processing site: BNL
Revision 1.0Oct 1, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ERYTHROPOIETIN
B: ERYTHROPOIETIN RECEPTOR
C: ERYTHROPOIETIN RECEPTOR


Theoretical massNumber of molelcules
Total (without water)68,8443
Polymers68,8443
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.400, 79.300, 136.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ERYTHROPOIETIN


Mass: 18471.289 Da / Num. of mol.: 1 / Mutation: N24K, N38K, N83K, P121N, P122S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01588
#2: Protein ERYTHROPOIETIN RECEPTOR / EPOBP


Mass: 25186.449 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN / Mutation: N52Q, N164Q, A211E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P19235
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
132 %PEG15001reservoir
20.28 Mammonium sulfate1reservoir
30.1 MMES1reservoirpH6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 49480 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 23.5 Å2 / Rsym value: 0.044 / Net I/σ(I): 19.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.377 / % possible all: 82.9
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Num. measured all: 251681 / Rmerge(I) obs: 0.044 / Biso Wilson estimate: 23.5 Å2
Reflection shell
*PLUS
% possible obs: 82.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.5

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→50 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1329 3 %RANDOM
Rwork0.242 ---
obs0.242 44507 93.3 %-
Displacement parametersBiso mean: 34.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 0 298 4917
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.66
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
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3543 106 2.2 %
Rwork0.2428 3536 -
obs--73.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.66

+
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