[English] 日本語
Yorodumi
- PDB-8u7e: Structure of Sts-1 HP domain with rebamipide derivative -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u7e
TitleStructure of Sts-1 HP domain with rebamipide derivative
ComponentsUbiquitin-associated and SH3 domain-containing protein B
KeywordsHYDROLASE / Sts-1 / histidine phosphatase / inhibitor / UBASH3B / TULA-2 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


regulation of osteoclast differentiation / collagen-activated tyrosine kinase receptor signaling pathway / negative regulation of platelet aggregation / regulation of release of sequestered calcium ion into cytosol / negative regulation of bone resorption / negative regulation of osteoclast differentiation / negative regulation of signal transduction / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / phosphoprotein binding ...regulation of osteoclast differentiation / collagen-activated tyrosine kinase receptor signaling pathway / negative regulation of platelet aggregation / regulation of release of sequestered calcium ion into cytosol / negative regulation of bone resorption / negative regulation of osteoclast differentiation / negative regulation of signal transduction / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / phosphoprotein binding / platelet aggregation / ubiquitin protein ligase binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
UBASH3B, SH3 domain / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / UBA/TS-N domain / Variant SH3 domain / Ubiquitin associated domain / Histidine phosphatase superfamily / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily ...UBASH3B, SH3 domain / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / UBA/TS-N domain / Variant SH3 domain / Ubiquitin associated domain / Histidine phosphatase superfamily / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
: / Ubiquitin-associated and SH3 domain-containing protein B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsAziz, F. / Dey, R. / French, J.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI141592 United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Rebamipide and Derivatives are Potent, Selective Inhibitors of Histidine Phosphatase Activity of the Suppressor of T Cell Receptor Signaling Proteins.
Authors: Aziz, F. / Reddy, K. / Fernandez Vega, V. / Dey, R. / Hicks, K.A. / Rao, S. / Jordan, L.O. / Smith, E. / Shumate, J. / Scampavia, L. / Carpino, N. / Spicer, T.P. / French, J.B.
History
DepositionSep 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-associated and SH3 domain-containing protein B
B: Ubiquitin-associated and SH3 domain-containing protein B
C: Ubiquitin-associated and SH3 domain-containing protein B
D: Ubiquitin-associated and SH3 domain-containing protein B
E: Ubiquitin-associated and SH3 domain-containing protein B
F: Ubiquitin-associated and SH3 domain-containing protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,6809
Polymers192,5876
Non-polymers1,0933
Water1,54986
1
A: Ubiquitin-associated and SH3 domain-containing protein B
F: Ubiquitin-associated and SH3 domain-containing protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5603
Polymers64,1962
Non-polymers3641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-21 kcal/mol
Surface area21430 Å2
MethodPISA
2
B: Ubiquitin-associated and SH3 domain-containing protein B
E: Ubiquitin-associated and SH3 domain-containing protein B


Theoretical massNumber of molelcules
Total (without water)64,1962
Polymers64,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-23 kcal/mol
Surface area22010 Å2
MethodPISA
3
C: Ubiquitin-associated and SH3 domain-containing protein B
hetero molecules

D: Ubiquitin-associated and SH3 domain-containing protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9244
Polymers64,1962
Non-polymers7292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area2720 Å2
ΔGint-23 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.777, 122.701, 99.945
Angle α, β, γ (deg.)90.00, 112.62, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Ubiquitin-associated and SH3 domain-containing protein B


Mass: 32097.750 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBASH3B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TF42
#2: Chemical ChemComp-VXE / N-(4-ethylbenzoyl)-3-(2-oxo-1,2-dihydroquinolin-4-yl)-L-alanine


Mass: 364.395 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H20N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Hepes 10% Ethylene glycol 0.3 M magnesium chloride 20% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.63→122.7 Å / Num. obs: 52513 / % possible obs: 95.9 % / Redundancy: 2.4 % / CC1/2: 0.979 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.136 / Rrim(I) all: 0.221 / Net I/σ(I): 7.2 / Num. measured all: 126932
Reflection shellResolution: 2.63→2.71 Å / % possible obs: 95.3 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.787 / Num. measured all: 11153 / Num. unique obs: 4513 / CC1/2: 0.735 / Rpim(I) all: 0.639 / Rrim(I) all: 1.019 / Net I/σ(I) obs: 1.2

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W5G

5w5g


Resolution: 2.63→92.26 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2983 2485 4.75 %0
Rwork0.2153 ---
obs0.2192 52358 95.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→92.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11216 0 81 86 11383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511585
X-RAY DIFFRACTIONf_angle_d1.72815846
X-RAY DIFFRACTIONf_dihedral_angle_d9.7011636
X-RAY DIFFRACTIONf_chiral_restr0.0741819
X-RAY DIFFRACTIONf_plane_restr0.0122038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.680.43941460.31882736X-RAY DIFFRACTION95
2.68-2.740.42031170.3162739X-RAY DIFFRACTION95
2.74-2.790.39381410.30092739X-RAY DIFFRACTION94
2.79-2.860.3681470.27892675X-RAY DIFFRACTION92
2.86-2.930.34231430.26752573X-RAY DIFFRACTION90
2.93-3.010.3991210.26022816X-RAY DIFFRACTION97
3.01-3.10.41841250.25852808X-RAY DIFFRACTION97
3.1-3.20.34431310.27092803X-RAY DIFFRACTION97
3.2-3.310.37641450.25582804X-RAY DIFFRACTION96
3.31-3.450.3241470.23412780X-RAY DIFFRACTION97
3.45-3.60.30461260.21442815X-RAY DIFFRACTION97
3.6-3.790.28521170.20082817X-RAY DIFFRACTION97
3.79-4.030.32751270.18822750X-RAY DIFFRACTION95
4.03-4.340.27061530.18762676X-RAY DIFFRACTION92
4.34-4.780.2471330.16372851X-RAY DIFFRACTION98
4.78-5.470.24691500.18462844X-RAY DIFFRACTION98
5.47-6.890.29621620.22192848X-RAY DIFFRACTION98
6.89-92.260.2311540.20012799X-RAY DIFFRACTION95

+
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://pdbjlvh1.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