[English] 日本語
Yorodumi
- PDB-2xer: Human PatL1 C-terminal domain (loop variant with sulfates) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xer
TitleHuman PatL1 C-terminal domain (loop variant with sulfates)
ComponentsPAT1 HOMOLOG 1
KeywordsRNA BINDING PROTEIN / MRNA DECAPPING / P-BODIES
Function / homology
Function and homology information


poly(G) binding / mRNA decay by 5' to 3' exoribonuclease / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body assembly / poly(U) RNA binding / P-body / PML body / cytoplasmic ribonucleoprotein granule / nuclear speck / RNA binding / cytosol
Similarity search - Function
mRNA decay factor PAT1 domain / Pat1-like / Topoisomerase II-associated protein PAT1
Similarity search - Domain/homology
Protein PAT1 homolog 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsTritschler, F. / Weichenrieder, O.
CitationJournal: Embo J. / Year: 2010
Title: The C-Terminal Alpha-Alpha Superhelix of Pat is Required for Mrna Decapping in Metazoa.
Authors: Braun, J.E. / Tritschler, F. / Haas, G. / Igreja, C. / Truffault, V. / Weichenrieder, O. / Izaurralde, E.
History
DepositionMay 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PAT1 HOMOLOG 1
B: PAT1 HOMOLOG 1
C: PAT1 HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6817
Polymers85,2973
Non-polymers3844
Water79344
1
A: PAT1 HOMOLOG 1


Theoretical massNumber of molelcules
Total (without water)28,4321
Polymers28,4321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PAT1 HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5282
Polymers28,4321
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PAT1 HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7204
Polymers28,4321
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.000, 100.100, 141.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein PAT1 HOMOLOG 1 / PAT1-LIKE PROTEIN 1 / PATL1


Mass: 28432.215 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN, RESIDUES 517-767 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HELA / Plasmid: MODIFIED PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q86TB9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 664 TO GLY ENGINEERED RESIDUE IN CHAIN B, GLN 664 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, GLN 664 TO GLY ENGINEERED RESIDUE IN CHAIN B, GLN 664 TO GLY ENGINEERED RESIDUE IN CHAIN C, GLN 664 TO GLY
Sequence detailsTHE FIRST 5 AMINO ACIDS GPQDP RESULT FROM THE 5' CLONING SITE. RESIDUES 664-673 (QSAATPALSN) HAVE ...THE FIRST 5 AMINO ACIDS GPQDP RESULT FROM THE 5' CLONING SITE. RESIDUES 664-673 (QSAATPALSN) HAVE BEEN REPLACED BY G664 AND S665

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS, PH 8.5, 1.15 M AMMONIUM SULFATE, 0.15 M LITHIUM SULFATE, 8% GLYCEROL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→47.2 Å / Num. obs: 18701 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 42.86 Å2 / Rsym value: 0.12 / Net I/σ(I): 11.1
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.59 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XES

2xes


Resolution: 2.95→47.189 Å / SU ML: 0.42 / σ(F): 1.99 / Phase error: 28.8 / Stereochemistry target values: ML
Details: RESIDUES 512-516 AND 573-577 AND 704-708 AND 767 OF CHAIN A ARE DISORDERED. RESIDUES 512- -516 AND 573-577 AND 701-710 AND 767 OF CHAIN B ARE DISORDERED. RESIDUES 512-514 AND 574-577 AND 701- ...Details: RESIDUES 512-516 AND 573-577 AND 704-708 AND 767 OF CHAIN A ARE DISORDERED. RESIDUES 512- -516 AND 573-577 AND 701-710 AND 767 OF CHAIN B ARE DISORDERED. RESIDUES 512-514 AND 574-577 AND 701-709 AND 765-767 OF CHAIN C ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2888 950 5.1 %
Rwork0.2471 --
obs0.2492 18674 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.225 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso mean: 50.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.0384 Å20 Å20 Å2
2--4.6914 Å20 Å2
3----3.6529 Å2
Refinement stepCycle: LAST / Resolution: 2.95→47.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5523 0 20 44 5587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075622
X-RAY DIFFRACTIONf_angle_d0.7677587
X-RAY DIFFRACTIONf_dihedral_angle_d14.7232184
X-RAY DIFFRACTIONf_chiral_restr0.052904
X-RAY DIFFRACTIONf_plane_restr0.005946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9501-3.10560.34911440.31912448X-RAY DIFFRACTION99
3.1056-3.30010.39351230.29962507X-RAY DIFFRACTION99
3.3001-3.55480.32111440.2862520X-RAY DIFFRACTION99
3.5548-3.91240.28651440.24672506X-RAY DIFFRACTION99
3.9124-4.47820.25111230.21292532X-RAY DIFFRACTION99
4.4782-5.64050.26211280.21872578X-RAY DIFFRACTION99
5.6405-47.1950.23671440.21742633X-RAY DIFFRACTION97

+
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