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- PDB-6ano: Crystal structure of human FLASH N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6ano
TitleCrystal structure of human FLASH N-terminal domain
ComponentsCASP8-associated protein 2
KeywordsGENE REGULATION / coiled-coil
Function / homology
Function and homology information


SUMO polymer binding / Fas signaling pathway / 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 / cellular response to mechanical stimulus / PML body ...SUMO polymer binding / Fas signaling pathway / 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 / cellular response to mechanical stimulus / PML body / transcription corepressor activity / 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 / SAD / Resolution: 2.61 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 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: CASP8-associated protein 2
A: CASP8-associated protein 2


Theoretical massNumber of molelcules
Total (without water)23,0452
Polymers23,0452
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-42 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.800, 43.750, 65.000
Angle α, β, γ (deg.)90.00, 114.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 11522.583 Da / Num. of mol.: 2 / Fragment: UNP residues 51-137
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


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM Tris (pH 8.0), 18% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.6→35.508 Å / Num. obs: 10151 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.24
Reflection shellResolution: 2.61→2.77 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.72 / Num. unique all: 1620 / CC1/2: 0.846 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.61→35.508 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 500 4.93 %random 5%
Rwork0.1993 ---
obs0.2021 10144 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.61→35.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 0 6 1206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041214
X-RAY DIFFRACTIONf_angle_d0.6511621
X-RAY DIFFRACTIONf_dihedral_angle_d17.034478
X-RAY DIFFRACTIONf_chiral_restr0.026179
X-RAY DIFFRACTIONf_plane_restr0.002210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6102-2.87270.31871240.25212393X-RAY DIFFRACTION99
2.8727-3.28820.3721250.2522414X-RAY DIFFRACTION100
3.2882-4.14170.28251220.19252420X-RAY DIFFRACTION100
4.1417-35.51130.19311290.17792417X-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)
12.33284.225-3.0945.8677-5.58595.6422-0.62930.1331-0.5763-0.62640.0258-1.35390.9159-0.10520.36070.55930.02770.06070.53390.15770.690419.3929-4.766914.1153
21.0711.8578-1.72367.6269-6.02775.4422-0.0995-0.0883-0.30410.4717-0.143-0.4056-0.0255-0.09980.18480.4981-0.07910.01410.42270.03340.403814.3284-7.48118.5717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 70 through 139 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 145 )

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