[English] 日本語
Yorodumi
- PDB-4y5y: Diabody 330 complex with EpoR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y5y
TitleDiabody 330 complex with EpoR
Components
  • Erythropoietin receptor
  • diabody 330 VH domain
  • diabody 330 VL domain
Keywordsprotein binding/immune system / diabody complex / receptor / protein binding-immune system complex
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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Erythropoietin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMoraga, I. / Guo, F. / Ozkan, E. / Jude, K.M. / Garcia, K.C.
CitationJournal: Cell / Year: 2015
Title: Tuning Cytokine Receptor Signaling by Re-orienting Dimer Geometry with Surrogate Ligands.
Authors: Moraga, I. / Wernig, G. / Wilmes, S. / Gryshkova, V. / Richter, C.P. / Hong, W.J. / Sinha, R. / Guo, F. / Fabionar, H. / Wehrman, T.S. / Krutzik, P. / Demharter, S. / Plo, I. / Weissman, I.L. ...Authors: Moraga, I. / Wernig, G. / Wilmes, S. / Gryshkova, V. / Richter, C.P. / Hong, W.J. / Sinha, R. / Guo, F. / Fabionar, H. / Wehrman, T.S. / Krutzik, P. / Demharter, S. / Plo, I. / Weissman, I.L. / Minary, P. / Majeti, R. / Constantinescu, S.N. / Piehler, J. / Garcia, K.C.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly_auth_evidence ...entity_src_gen / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: diabody 330 VH domain
B: diabody 330 VL domain
C: Erythropoietin receptor
D: diabody 330 VH domain
E: diabody 330 VL domain
F: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4287
Polymers102,3366
Non-polymers921
Water59433
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, microscopy, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.141, 95.799, 144.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Detailsbiological unit is the same as asymmetric unit as confirmed by beta-gal complementation, signalling assay, superresolution microscopy, MALS

-
Components

#1: Antibody diabody 330 VH domain


Mass: 13941.515 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody diabody 330 VL domain


Mass: 12016.095 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Protein Erythropoietin receptor / EPO-R


Mass: 25210.562 Da / Num. of mol.: 2 / Mutation: N76Q, N188Q, D247L, and L248D
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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: Magnesium chloride, Tris, PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→48.32 Å / Num. obs: 25898 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 62.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.054 / Net I/σ(I): 11.1 / Num. measured all: 110916
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.85-2.90484.50.7271.91679037590.7810.38399.9
9.01-48.323.70.02632.932899000.9990.01597.1

-
Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S34, 1EER

3s34

1eer


Resolution: 2.85→43.146 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 2585 10 %random selection
Rwork0.2209 ---
obs-25846 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine analyzeLuzzati sigma a obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.85→43.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6492 0 6 33 6531
LS refinement shellResolution: 2.85→2.9048 Å /
RfactorNum. reflection
Rwork0.32 -
Rfree-142
all-1282
Refinement TLS params.Method: refined / Origin x: 11.7429 Å / Origin y: 22.1547 Å / Origin z: -53.5305 Å
111213212223313233
T0.4839 Å2-0.0432 Å2-0.0333 Å2-0.3765 Å20.0463 Å2--0.4387 Å2
L1.9757 °20.4471 °2-0.4288 °2-0.0617 °2-0.1695 °2--0.1168 °2
S0.1023 Å °-0.2126 Å °-0.0052 Å °0.033 Å °-0.074 Å °-0.0222 Å °0.0092 Å °0.0313 Å °-0.0256 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 204
2X-RAY DIFFRACTION1allC9 - 404
3X-RAY DIFFRACTION1allB1 - 201
4X-RAY DIFFRACTION1allE1 - 205
5X-RAY DIFFRACTION1allD1 - 209
6X-RAY DIFFRACTION1allF9 - 310

+
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