[English] 日本語
Yorodumi
- PDB-6f8d: Crystal structure of Human ARS2 residues 171-270 + 408-763 (P65 form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6f8d
TitleCrystal structure of Human ARS2 residues 171-270 + 408-763 (P65 form)
Components(Serrate RNA effector molecule homolog) x 2
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


mRNA cap binding complex binding / neuronal stem cell population maintenance / primary miRNA processing / response to arsenic-containing substance / positive regulation of neurogenesis / RNA polymerase II transcribes snRNA genes / mRNA Splicing - Major Pathway / protein-macromolecule adaptor activity / nuclear body / ribonucleoprotein complex ...mRNA cap binding complex binding / neuronal stem cell population maintenance / primary miRNA processing / response to arsenic-containing substance / positive regulation of neurogenesis / RNA polymerase II transcribes snRNA genes / mRNA Splicing - Major Pathway / protein-macromolecule adaptor activity / nuclear body / ribonucleoprotein complex / regulation of DNA-templated transcription / protein-containing complex / DNA binding / RNA binding / nucleoplasm / cytoplasm
Similarity search - Function
SERRATE/Ars2 , C-terminal / SERRATE/Ars2, N-terminal / SERRATE/Ars2 / Arsenite-resistance protein 2 / SERRATE/Ars2, N-terminal domain / RNA-binding domain superfamily
Similarity search - Domain/homology
Serrate RNA effector molecule homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.48 Å
AuthorsCusack, S. / Schulze, W.M.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council322586 France
CitationJournal: Nat Commun / Year: 2018
Title: Structural analysis of human ARS2 as a platform for co-transcriptional RNA sorting.
Authors: Schulze, W.M. / Stein, F. / Rettel, M. / Nanao, M. / Cusack, S.
History
DepositionDec 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Serrate RNA effector molecule homolog
C: Serrate RNA effector molecule homolog
B: Serrate RNA effector molecule homolog
D: Serrate RNA effector molecule homolog


Theoretical massNumber of molelcules
Total (without water)106,3944
Polymers106,3944
Non-polymers00
Water00
1
A: Serrate RNA effector molecule homolog
C: Serrate RNA effector molecule homolog


Theoretical massNumber of molelcules
Total (without water)53,1972
Polymers53,1972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-37 kcal/mol
Surface area24210 Å2
MethodPISA
2
B: Serrate RNA effector molecule homolog
D: Serrate RNA effector molecule homolog


Theoretical massNumber of molelcules
Total (without water)53,1972
Polymers53,1972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-34 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.210, 105.210, 267.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A176 - 761
2010B176 - 761

-
Components

#1: Protein Serrate RNA effector molecule homolog / Arsenite-resistance protein 2


Mass: 12027.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 271-407 were deleted.Residues 171-270 and 408-763 were co-expressed as separate pieces.
Source: (gene. exp.) Homo sapiens (human) / Gene: SRRT, ARS2, ASR2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q9BXP5
#2: Protein Serrate RNA effector molecule homolog / Arsenite-resistance protein 2


Mass: 41169.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 271-407 were deleted.Residues 171-270 and 408-763 were co-expressed as separate pieces.
Source: (gene. exp.) Homo sapiens (human) / Gene: SRRT, ARS2, ASR2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q9BXP5

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: Crystals of ARS2 were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution (6 mg/ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to ...Details: Crystals of ARS2 were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution (6 mg/ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to crystallisation solution. The crystallisation solution was 1.2 M sodium dihydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.2 M lithium sulphate, 0.1 M CAPS pH 10.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.48→91.11 Å / Num. obs: 20970 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.12 % / CC1/2: 0.997 / Rsym value: 0.114 / Net I/σ(I): 8.71
Reflection shellResolution: 3.48→3.57 Å / Redundancy: 2.98 % / Mean I/σ(I) obs: 0.8 / CC1/2: 0.253 / Rsym value: 1.617 / % possible all: 86.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F7J

6f7j


Resolution: 3.48→91.11 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.897 / SU B: 44.876 / SU ML: 0.614 / Cross valid method: THROUGHOUT / ESU R Free: 0.592 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29224 922 4.4 %RANDOM
Rwork0.26415 ---
obs0.26537 20048 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 160.658 Å2
Baniso -1Baniso -2Baniso -3
1-2.6 Å21.3 Å20 Å2
2--2.6 Å2-0 Å2
3----8.44 Å2
Refinement stepCycle: 1 / Resolution: 3.48→91.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6504 0 0 0 6504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196619
X-RAY DIFFRACTIONr_bond_other_d0.0010.026288
X-RAY DIFFRACTIONr_angle_refined_deg0.9621.9658903
X-RAY DIFFRACTIONr_angle_other_deg0.818314576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2835772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71823.588354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.475151272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7021572
X-RAY DIFFRACTIONr_chiral_restr0.0530.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021376
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.50916.2153118
X-RAY DIFFRACTIONr_mcbond_other3.50916.2153117
X-RAY DIFFRACTIONr_mcangle_it6.01124.3163880
X-RAY DIFFRACTIONr_mcangle_other6.01124.3173881
X-RAY DIFFRACTIONr_scbond_it2.90516.5183501
X-RAY DIFFRACTIONr_scbond_other2.90516.5183502
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.30924.6475024
X-RAY DIFFRACTIONr_long_range_B_refined9.2387187
X-RAY DIFFRACTIONr_long_range_B_other9.2387187
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 24180 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.479→3.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 60 -
Rwork0.446 1301 -
obs--86.03 %

+
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