[English] 日本語
Yorodumi
- PDB-6ap0: Crystal structure of human FLASH N-terminal domain C54S/C83A (Cry... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ap0
TitleCrystal structure of human FLASH N-terminal domain C54S/C83A (Crystal form 2)
ComponentsCASP8-associated protein 2
KeywordsGENE REGULATION / coiled-coil
Function / homology
Function and homology information


Fas signaling pathway / SUMO polymer binding / peptidase activator activity involved in apoptotic process / death receptor binding / cysteine-type endopeptidase activator activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / SUMOylation of transcription cofactors / apoptotic signaling pathway / PML body / cellular response to mechanical stimulus ...Fas signaling pathway / SUMO polymer binding / peptidase activator activity involved in apoptotic process / death receptor binding / cysteine-type endopeptidase activator activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / SUMOylation of transcription cofactors / apoptotic signaling pathway / PML body / cellular response to mechanical stimulus / transcription corepressor activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / cell cycle / signal transduction / mitochondrion / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
CASP8-associated protein 2 / : / Myb-like DNA-binding domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
CASP8-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.581 Å
AuthorsAik, W.S. / Tong, L.
CitationJournal: PLoS ONE / Year: 2017
Title: The N-terminal domains of FLASH and Lsm11 form a 2:1 heterotrimer for histone pre-mRNA 3'-end processing.
Authors: Aik, W.S. / Lin, M.H. / Tan, D. / Tripathy, A. / Marzluff, W.F. / Dominski, Z. / Chou, C.Y. / Tong, L.
History
DepositionAug 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
B: CASP8-associated protein 2
A: CASP8-associated protein 2


Theoretical massNumber of molelcules
Total (without water)22,6682
Polymers22,6682
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-45 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.478, 44.346, 68.433
Angle α, β, γ (deg.)90.00, 98.65, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein CASP8-associated protein 2 / FLICE-associated huge protein


Mass: 11333.769 Da / Num. of mol.: 2 / Fragment: UNP residues 51-137 / Mutation: C54S, C83A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP8AP2, FLASH, KIAA1315, RIP25 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKL3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium formate, 15% (w/v) PEG 3350, 3% (v/v) 1,6-hexanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.58→36.216 Å / Num. obs: 11542 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.42
Reflection shellResolution: 2.58→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 3.82 / Num. unique obs: 1848 / CC1/2: 0.898 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ANO

6ano


Resolution: 2.581→36.216 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27
RfactorNum. reflection% reflection
Rfree0.2487 575 4.98 %
Rwork0.2138 --
obs0.2156 11536 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.581→36.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 0 10 1399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031412
X-RAY DIFFRACTIONf_angle_d0.5341890
X-RAY DIFFRACTIONf_dihedral_angle_d15.973562
X-RAY DIFFRACTIONf_chiral_restr0.021216
X-RAY DIFFRACTIONf_plane_restr0.002244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5808-2.84050.34261440.27992699X-RAY DIFFRACTION99
2.8405-3.25130.27181470.26592776X-RAY DIFFRACTION100
3.2513-4.09530.28281420.19982738X-RAY DIFFRACTION100
4.0953-36.21970.18891420.18692748X-RAY DIFFRACTION99
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)
10.9372.513-1.78529.0412-6.22625.431-0.19730.032-0.0713-0.6055-0.092-0.24420.19080.14490.26730.27740.0494-0.030.42830.0050.4468126.617113.9151142.616
27.4551-0.406-1.4747.05264.1454.4350.3723-0.2417-0.6144-0.39450.2448-0.3692-0.22562.2772-0.55491.02050.0486-0.05620.9769-0.33040.7829137.775351.954111.0051
30.25921.3287-0.9266.1801-5.33724.3818-0.08250.2767-0.07270.53870.3368-0.0222-0.1672-0.4085-0.35660.4312-0.040.04780.3879-0.00620.3498120.24774.7849149.0035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 52 through 139 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 140 )

+
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