[English] 日本語
Yorodumi
- PDB-6moj: Dimeric DARPin A_angle_R5 complex with EpoR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6moj
TitleDimeric DARPin A_angle_R5 complex with EpoR
Components
  • Dimeric DARPin ACR5 (A_angle_R5)
  • Erythropoietin receptor
KeywordsBIOSYNTHETIC PROTEIN / DARPin / complex / receptor
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
D(-)-TARTARIC ACID / Erythropoietin receptor
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.431 Å
AuthorsJude, K.M. / Mohan, K. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI51321 United States
CitationJournal: Science / Year: 2019
Title: Topological control of cytokine receptor signaling induces differential effects in hematopoiesis.
Authors: Mohan, K. / Ueda, G. / Kim, A.R. / Jude, K.M. / Fallas, J.A. / Guo, Y. / Hafer, M. / Miao, Y. / Saxton, R.A. / Piehler, J. / Sankaran, V.G. / Baker, D. / Garcia, K.C.
History
DepositionOct 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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: Dimeric DARPin ACR5 (A_angle_R5)
B: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1188
Polymers49,3912
Non-polymers7276
Water39622
1
A: Dimeric DARPin ACR5 (A_angle_R5)
B: Erythropoietin receptor
hetero molecules

A: Dimeric DARPin ACR5 (A_angle_R5)
B: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,23516
Polymers98,7824
Non-polymers1,45312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area8880 Å2
ΔGint-34 kcal/mol
Surface area37510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.418, 130.418, 293.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein Dimeric DARPin ACR5 (A_angle_R5)


Mass: 24261.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein Erythropoietin receptor / / EPO-R


Mass: 25129.424 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium potassium tartrate, 0.1 M bis-tris propane pH 8.5, 20% PEG 3350, 30% glycerol as cryoprotectant

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.431→48.739 Å / Num. obs: 25096 / % possible obs: 52.4 % / Redundancy: 26 % / Biso Wilson estimate: 44.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.273 / Rpim(I) all: 0.054 / Net I/σ(I): 11.04
Reflection shellResolution: 2.431→2.73 Å / Redundancy: 25.7 % / Rmerge(I) obs: 2.759 / Mean I/σ(I) obs: 0.46 / Num. unique obs: 1280 / CC1/2: 0.517 / Rpim(I) all: 0.551 / % possible all: 9.2

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSJan 26, 2018data reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted model, 1ERN

1ern


Resolution: 2.431→46.11 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.67
Details: Refined against elliptically truncated data 3.387 (a*) x 3.387 (b*) x 2.448 (c*)
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1278 5.1 %random
Rwork0.2103 ---
obs0.2123 25037 52.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.431→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 48 22 3366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033408
X-RAY DIFFRACTIONf_angle_d0.6034649
X-RAY DIFFRACTIONf_dihedral_angle_d14.0282007
X-RAY DIFFRACTIONf_chiral_restr0.038542
X-RAY DIFFRACTIONf_plane_restr0.004611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.431-2.52830.664670.4236131X-RAY DIFFRACTION3
2.5283-2.64330.5077290.3759544X-RAY DIFFRACTION11
2.6433-2.78270.3583410.3575871X-RAY DIFFRACTION17
2.7827-2.9570.3323830.33911230X-RAY DIFFRACTION25
2.957-3.18530.3251100.30641998X-RAY DIFFRACTION40
3.1853-3.50570.31861880.26973541X-RAY DIFFRACTION70
3.5057-4.01270.30762680.25285006X-RAY DIFFRACTION99
4.0127-5.05460.17142710.16115111X-RAY DIFFRACTION100
5.0546-46.1180.22072810.17055327X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.60373.9715-1.3874.613-2.69871.9817-0.203-0.30540.5394-0.19170.5139-0.6598-1.3415-0.8581-0.34161.22320.1223-0.00810.5185-0.27610.6567-63.2639-16.222427.2785
23.17040.9599-0.57628.11533.19541.55860.21270.05841.1345-1.2588-0.14990.116-1.1028-0.38220.24091.46330.21980.03910.3901-0.21960.5028-60.367-13.530224.9409
32.3162-1.2496-0.25125.05822.80811.65670.00090.24260.4396-1.20680.167-0.4017-1.07950.0801-0.12711.418-0.20310.08890.41-0.19680.5091-55.7001-16.08816.9703
42.8589-0.60240.97513.04791.41153.95920.22550.12860.7376-0.78360.0323-0.3102-1.21880.8625-0.30711.197-0.38280.14620.6362-0.25590.3999-43.6673-21.672216.8927
52.6463-1.7112-0.61413.3119-0.5413.21430.2433-0.17520.4006-0.6735-0.099-0.472-0.46611.54-0.2650.8125-0.30650.23781.2334-0.37070.417-33.1865-30.598712.2717
61.2092-0.417-1.35115.2342-5.22317.9587-0.1756-0.81330.1122-0.29260.1095-0.54370.09172.73260.00530.8165-0.21730.16291.8411-0.23590.5408-25.7456-34.230515.1686
79.0773-2.9026-3.99216.3861-1.58763.2605-0.1159-0.0349-0.658-0.57610.06420.04191.37642.11570.24851.16850.08860.08411.4093-0.35710.5056-29.1506-41.25296.9723
80.55130.73380.80057.22773.13921.9091-0.27270.4222-0.34-0.0783-0.2405-0.97431.71641.00730.46141.19270.58870.05352.0559-0.09860.6872-20.5264-44.301116.3199
91.6517-0.94852.12176.5569-0.36129.7921-0.2827-1.0294-0.54471.26130.5789-0.0071.39092.4057-0.42761.5590.5339-0.01071.6636-0.13481.0077-25.4007-51.56128.174
103.3633-0.1694-0.67756.22353.71749.0883-0.0229-0.0737-0.04470.05090.13670.0081-0.06490.1592-0.08850.452-0.0196-0.0020.3749-0.13010.2061-57.2825-41.09223.4904
110.68311.41641.63032.7493.13585.4149-0.2154-0.22390.21550.14790.02150.2323-0.54350.04630.10260.4811-0.00280.05610.4256-0.16010.2183-58.6327-39.121621.5486
125.1004-0.03740.23983.93160.31163.21830.10530.21150.7849-0.6194-0.00890.6389-0.3668-0.47670.14150.5520.0339-0.06230.2811-0.00910.1725-68.6151-47.5723-4.4054
135.0195-0.04780.11725.81711.53284.64660.06970.22340.2712-0.31570.1025-0.0839-0.4844-0.1825-0.14570.37280.0117-0.02740.2873-0.03980.1212-65.9344-47.1259-5.1638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 125 )
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 158 )
6X-RAY DIFFRACTION6chain 'A' and (resid 159 through 172 )
7X-RAY DIFFRACTION7chain 'A' and (resid 173 through 192 )
8X-RAY DIFFRACTION8chain 'A' and (resid 193 through 205 )
9X-RAY DIFFRACTION9chain 'A' and (resid 206 through 224 )
10X-RAY DIFFRACTION10chain 'B' and (resid 6 through 69 )
11X-RAY DIFFRACTION11chain 'B' and (resid 70 through 127 )
12X-RAY DIFFRACTION12chain 'B' and (resid 128 through 174 )
13X-RAY DIFFRACTION13chain 'B' and (resid 175 through 223 )

+
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