[English] 日本語
Yorodumi
- PDB-1cn4: ERYTHROPOIETIN COMPLEXED WITH EXTRACELLULAR DOMAINS OF ERYTHROPOI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cn4
TitleERYTHROPOIETIN COMPLEXED WITH EXTRACELLULAR DOMAINS OF ERYTHROPOIETIN RECEPTOR
Components
  • PROTEIN (ERYTHROPOIETIN RECEPTOR)
  • PROTEIN (ERYTHROPOIETIN)
KeywordsHEMATOPOIETIC CYTOKINE / CYTOKINE RECEPTOR
Function / homology
Function and homology information


nucleate erythrocyte development / negative regulation of erythrocyte apoptotic process / erythropoietin receptor binding / erythropoietin receptor activity / negative regulation of cation channel activity / erythropoietin-mediated signaling pathway / 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 ...nucleate erythrocyte development / negative regulation of erythrocyte apoptotic process / erythropoietin receptor binding / erythropoietin receptor activity / negative regulation of cation channel activity / erythropoietin-mediated signaling pathway / 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) / cellular hyperosmotic response / response to vitamin A / positive regulation of Ras protein signal transduction / blood circulation / Regulation of gene expression by Hypoxia-inducible Factor / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / response to testosterone / protein kinase activator activity / response to dexamethasone / positive regulation of activated T cell proliferation / erythrocyte maturation / hemopoiesis / decidualization / response to axon injury / response to hyperoxia / response to electrical stimulus / Erythropoietin activates RAS / positive regulation of tyrosine phosphorylation of STAT protein / response to salt stress / embryo implantation / positive regulation of neuron differentiation / response to interleukin-1 / erythrocyte differentiation / cytokine activity / acute-phase response / brain development / hormone activity / cytokine-mediated signaling pathway / positive regulation of neuron projection development / response to estrogen / heart development / cell body / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / SIR / Resolution: 2.8 Å
AuthorsStroud, R.M. / Reid, S.W.
Citation
Journal: 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.
#1: Journal: Protein Eng. / Year: 1999
Title: Engineering a Soluble Extracellular Erythropoietin Receptor (EPObp) in Pichia pastoris to Eliminate Microheterogeneity, and its Complex with Erythropoietin
Authors: Zhan, H. / Liu, B. / Reid, S.W. / Aoki, K.H. / Li, C. / Syed, R.S. / Karkaria, C. / Koe, G. / Sitney, K. / Hayenga, K. / Mistry, F. / Savel, L. / Dreyer, M. / Katz, B. / Schreurs, J. / ...Authors: Zhan, H. / Liu, B. / Reid, S.W. / Aoki, K.H. / Li, C. / Syed, R.S. / Karkaria, C. / Koe, G. / Sitney, K. / Hayenga, K. / Mistry, F. / Savel, L. / Dreyer, M. / Katz, B. / Schreurs, J. / Matthews, D.J. / Cheetham, J.C. / Egrie, J. / Giebel, L.B. / Stroud, R.M.
History
DepositionMay 25, 1999Deposition site: BNL / Processing site: RCSB
SupersessionAug 11, 1999ID: 1BLW
Revision 1.0Aug 11, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 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 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (ERYTHROPOIETIN RECEPTOR)
B: PROTEIN (ERYTHROPOIETIN RECEPTOR)
C: PROTEIN (ERYTHROPOIETIN)


Theoretical massNumber of molelcules
Total (without water)69,0113
Polymers69,0113
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.340, 80.340, 134.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PROTEIN (ERYTHROPOIETIN RECEPTOR)


Mass: 25273.570 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR LIGAND BINDING DOMAINS / 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
#2: Protein PROTEIN (ERYTHROPOIETIN)


Mass: 18464.338 Da / Num. of mol.: 1 / Mutation: N24K, N38K, N83K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01588
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 %PEG40001reservoir
20.2 M1reservoirCaCl2
30.1 MMES1reservoirpH6.5-7.0

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 20677 / % possible obs: 91.6 % / Redundancy: 4.3 % / Biso Wilson estimate: -0.2 Å2 / Rsym value: 0.122 / Net I/σ(I): 8.6
Reflection shellResolution: 2.8→2.9 Å / Rsym value: 0.374 / % possible all: 89
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % possible obs: 91.6 % / Num. measured all: 88794 / Rmerge(I) obs: 0.122
Reflection shell
*PLUS
% possible obs: 89.2 % / Rmerge(I) obs: 0.374

-
Processing

Software
NameVersionClassification
bioteXdata collection
bioteXdata reduction
MLPHAREphasing
SOLOMONphasing
CNS0.4refinement
bioteXdata scaling
RefinementMethod to determine structure: SIR / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high rms absF: 2899584.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.336 1146 6.8 %RANDOM
Rwork0.28 ---
obs0.28 16861 83.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.168 e/Å3
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2---0.66 Å20 Å2
3----0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a1.27 Å1.13 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4589 0 0 15 4604
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 61 2.9 %
Rwork0.431 2057 -
obs--64.2 %
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:PROTEIN_REP.PARA / Topol file: CNS_TOPPAR:PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 80 Å / Num. reflection obs: 18797 / Rfactor obs: 0.19 / Rfactor Rwork: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
LS refinement shell
*PLUS
Rfactor Rfree: 0.406 / Rfactor Rwork: 0.431

+
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