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- PDB-5y8v: Crystal structure of GAS41 -

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Basic information

Entry
Database: PDB / ID: 5y8v
TitleCrystal structure of GAS41
ComponentsYEATS domain-containing protein 4
KeywordsNUCLEAR PROTEIN / YEATS domain
Function / homology
Function and homology information


modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / lysine-acetylated histone binding / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle ...modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / lysine-acetylated histone binding / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle / HATs acetylate histones / histone binding / nuclear membrane / regulation of apoptotic process / regulation of cell cycle / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleoplasm / nucleus
Similarity search - Function
YEATS domain / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
YEATS domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsWang, Y. / Hao, Q.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
HK-RGCC7037-14G Hong Kong
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Identification of the YEATS domain of GAS41 as a pH-dependent reader of histone succinylation
Authors: Wang, Y. / Jin, J. / Chung, M.W.H. / Feng, L. / Sun, H. / Hao, Q.
History
DepositionAug 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: YEATS domain-containing protein 4
A: YEATS domain-containing protein 4
C: YEATS domain-containing protein 4
D: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3578
Polymers66,2604
Non-polymers974
Water1,58588
1
B: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5892
Polymers16,5651
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5892
Polymers16,5651
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5892
Polymers16,5651
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5892
Polymers16,5651
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.467, 57.212, 205.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
YEATS domain-containing protein 4 / Glioma-amplified sequence 41 / Gas41 / NuMA-binding protein 1 / NuBI1


Mass: 16565.041 Da / Num. of mol.: 4 / Fragment: UNP residues 21-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS4, GAS41
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: O95619
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6 / Details: 0.1M MES pH 6.5, 1.6M MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 19176 / % possible obs: 98.7 % / Redundancy: 3.5 % / Net I/σ(I): 9.51

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FK3

3fk3


Resolution: 2.61→31.495 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.9
RfactorNum. reflection% reflection
Rfree0.2795 858 4.48 %
Rwork0.237 --
obs0.239 19172 92.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.61→31.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4451 0 4 88 4543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134578
X-RAY DIFFRACTIONf_angle_d1.5016194
X-RAY DIFFRACTIONf_dihedral_angle_d14.3152728
X-RAY DIFFRACTIONf_chiral_restr0.076655
X-RAY DIFFRACTIONf_plane_restr0.009782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6101-2.77350.37011030.31482138X-RAY DIFFRACTION66
2.7735-2.98750.34281270.28853109X-RAY DIFFRACTION96
2.9875-3.28790.29721770.25763217X-RAY DIFFRACTION100
3.2879-3.7630.26181370.22753282X-RAY DIFFRACTION100
3.763-4.73840.25351520.19823281X-RAY DIFFRACTION99
4.7384-31.49750.27181620.24123287X-RAY DIFFRACTION95

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