PDB-9x8s: Crystal structure of the human GAS41 YEATS domain in complex with...

ID or keywords:

Entry

Database: PDB / ID: 9x8s

Title

Crystal structure of the human GAS41 YEATS domain in complex with an acetylated YFV capsid peptide (K4ac)

Components

YEATS domain-containing protein 4
Yellow Fever Virus Capsid Protein

Keywords

VIRAL PROTEIN / YEATS domain / histone mimic / lysine acetylation / viral peptide

Function / homology

Function and homology information

histone H3K18ac reader activity / histone H3K27ac reader activity / Activation of the TFAP2 (AP-2) family of transcription factors / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle ...
Similarity search - Function

Biological species

Homo sapiens (human)

Yellow fever virus

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.696 Å

Authors

Chen, S.D.C. / Kang, S.S.K.

Funding support

China, 2items

Citation

Journal: To Be Published
Title: The structure of the human GAS41 YEATS domain in complex with an acetylated YFV capsid peptide (K4ac)
Authors: Kang, S. / Li, X. / Chen, S.

History

Deposition	Oct 20, 2025	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Nov 26, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9x8s.cif.gz	235.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9x8s.ent.gz	189.3 KB	Display	PDB format
PDBx/mmJSON format	9x8s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9x8s_validation.pdf.gz	486 KB	Display	wwPDB validaton report
Full document	9x8s_full_validation.pdf.gz	496.7 KB	Display
Data in XML	9x8s_validation.xml.gz	33.8 KB	Display
Data in CIF	9x8s_validation.cif.gz	45.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x8/9x8s ftp://data.pdbj.org/pub/pdb/validation_reports/x8/9x8s	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (1)

Deposited unit

A: YEATS domain-containing protein 4

B: YEATS domain-containing protein 4

C: YEATS domain-containing protein 4

D: YEATS domain-containing protein 4

E: Yellow Fever Virus Capsid Protein

F: Yellow Fever Virus Capsid Protein

64.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	129.979, 80.575, 72.398
Angle α, β, γ (deg.)	90.00, 100.39, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-333- HOH

#1: Protein	YEATS domain-containing protein 4 / Glioma-amplified sequence 41 / Gas41 / NuMA-binding protein 1 / NuBI-1 / NuBI1 Mass: 15706.036 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Glioma Amplified Sequence 41(YEATS4) / Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS4, GAS41 / Production host: Escherichia coli (E. coli) / References: UniProt: O95619
#2: Protein/peptide	Yellow Fever Virus Capsid Protein Mass: 745.806 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Yellow Fever Virus Capsid Protein(1-7) / Source: (synth.) Yellow fever virus
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.03 Å³/Da / Density % sol: 59.44 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: Sodium sulfate , Bis-Tris propane (pH= 6.5), PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
Detector	Type: OXFORD ONYX CCD / Detector: CCD / Date: Oct 9, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.69→43.81 Å / Num. obs: 76703 / % possible obs: 94.24 % / Redundancy: 4.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.042 / Net I/σ(I): 34.3
Reflection shell	Resolution: 1.696→1.756 Å / Num. unique obs: 10276 / CC_1/2: 0.747

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PDB_EXTRACT		data extraction
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.696→40.288 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2056	2000	2.61 %
R_work	0.1863	-	-
obs	0.1868	76698	94.14 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.696→40.288 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4335	0	0	587	4922

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4456
X-RAY DIFFRACTION	f_angle_d	0.892	6025
X-RAY DIFFRACTION	f_dihedral_angle_d	9.342	2635
X-RAY DIFFRACTION	f_chiral_restr	0.061	638
X-RAY DIFFRACTION	f_plane_restr	0.006	758

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.696-1.7373	0.2538	97	0.2392	3607	X-RAY DIFFRACTION	64
1.7373-1.7843	0.2349	116	0.2341	4373	X-RAY DIFFRACTION	78
1.7843-1.8368	0.2643	132	0.2222	4905	X-RAY DIFFRACTION	87
1.8368-1.8961	0.2311	144	0.2048	5396	X-RAY DIFFRACTION	95
1.8961-1.9638	0.2033	150	0.1937	5587	X-RAY DIFFRACTION	99
1.9638-2.0425	0.2139	150	0.1849	5585	X-RAY DIFFRACTION	99
2.0425-2.1354	0.1896	151	0.1834	5642	X-RAY DIFFRACTION	99
2.1354-2.248	0.2139	150	0.1876	5646	X-RAY DIFFRACTION	100
2.248-2.3888	0.2109	151	0.1938	5635	X-RAY DIFFRACTION	100
2.3888-2.5732	0.2019	151	0.1974	5623	X-RAY DIFFRACTION	99
2.5732-2.8321	0.2572	151	0.2067	5621	X-RAY DIFFRACTION	99
2.8321-3.2418	0.2087	152	0.1843	5676	X-RAY DIFFRACTION	100
3.2418-4.0837	0.1915	151	0.1639	5645	X-RAY DIFFRACTION	99
4.0837-40.288	0.165	154	0.1645	5757	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.0034	0.0035	-0.0045	0.0065	-0.0024	0.0144	0.0107	-0.004	0.0008	-0.0013	-0.0059	-0.0293	-0.004	0.0121	0.0108	0.0201	-0.03	0.0059	0.0832	-0.0173	0.0644	0.1984	-110.0142	71.2975
2	0.015	0.019	-0.0042	0.0285	-0.0108	0.006	0.0121	-0.0008	0.0203	-0.0106	0.0264	-0.0418	-0.0223	0.0251	0.0302	0.011	-0.0217	0.031	0.0767	-0.0326	0.0937	22.5323	-105.1261	74.8951
3	0.0027	-0.0002	0.0027	0.0013	0.0022	0.0075	0.0136	-0.0077	-0.0002	0.009	0.0059	0.0167	0.002	-0.0108	-0.0002	0.0468	0.0097	0.0165	0.0426	-0.0051	0.0943	-0.7976	-118.1164	76.4879
4	0.0656	0.0311	-0.0146	0.0143	-0.0064	0.0031	0.0141	0.0111	0.0167	-0.0262	0.0022	-0.0229	-0.0189	-0.0107	0.0199	0.0826	-0.0376	0.0682	0.0781	-0.0034	0.0774	13.3635	-108.3563	63.1035
5	0.0028	0.0005	-0.002	0.0008	-0.0036	0.0153	0.0017	0.0057	-0.0012	-0.0063	0.0019	-0.0042	0.0009	0.0023	0.014	0.105	0.004	0.0502	0.1214	-0.0507	0.1207	11.5304	-116.5745	66.5134
6	0.04	-0.0101	-0.0274	0.0221	-0.0011	0.0224	0.0045	0.0315	0.0288	-0.0234	0.0189	-0.0249	-0.0074	-0.0013	0.0388	0.0415	-0.0388	0.0356	0.104	-0.0179	0.0872	12.2727	-106.6548	68.4094
7	0.0302	0.0019	0.0101	0.0079	0.0019	0.0035	0.0035	0.006	-0.0067	-0.0042	-0.0045	-0.0014	0.007	-0.0016	-0.0153	0.1546	-0.0418	-0.0798	0.2302	-0.0384	0.1671	-3.7918	-116.2648	59.5553
8	0.001	-0.0003	0.0008	0.0058	-0.0004	0.0015	0.0195	0.006	0.0191	-0.0038	0.0143	0.0083	-0.026	-0.0025	0.0116	0.071	-0.0228	0.0119	0.0793	-0.0171	0.0768	10.9156	-99.7689	73.3988
9	0.0048	-0.0014	-0.0005	0.0004	0.0002	0.0001	0.0127	-0.0053	0.002	0.0078	0.0082	-0.0076	-0.0072	0.0071	0.005	0.2596	-0.041	-0.0066	0.1193	-0.0545	0.138	17.704	-96.1026	90.319
10	0.0013	-0.0027	0.0018	0.0065	-0.004	0.0021	0.0112	0.0403	-0.0032	-0.0144	-0.0187	0.0027	0.006	-0.0295	-0.0004	0.0375	-0.0164	-0.0098	0.0817	-0.0176	0.0711	-0.0338	-107.7358	74.3987
11	0.0071	0.0002	0.0093	0.0765	-0.0066	0.0187	-0.009	0.0143	0.0242	0.083	-0.0053	-0.0523	-0.0142	0.0224	-0.0016	0.0549	0.0235	-0.0382	0.0567	0.0137	0.0308	5.0394	-104.7942	99.9142
12	-0.0007	-0.0011	-0.0014	-0.0002	0.001	0.0002	-0.0153	-0.0212	-0.0017	0.0206	0.0099	0.011	-0.012	-0.0211	-0.0305	0.04	0.0792	0.0177	0.0252	-0.0146	0.0055	-7.3309	-102.1095	98.7969
13	0.0259	-0.0117	-0.0488	0.0247	0.0179	0.0979	-0.0089	0.0481	-0.0364	0.0142	0.0192	0.0135	-0.0009	-0.0939	0.0089	0.0069	0.0547	-0.0023	0.076	0.0039	0.0447	-1.1766	-109.3455	96.0261
14	0.0024	0.0001	0.0018	0.0074	-0.0008	0.0079	0.0122	0.0012	-0.0099	-0.0034	0.0015	0.012	-0.0012	0.0009	0.0393	0.0919	-0.0091	-0.0487	0.0442	-0.0073	0.0919	5.8599	-88.7061	91.5194
15	0.0007	-0.0007	0.0026	0.0058	-0.0021	0.01	0.0147	-0.0047	-0.0052	0.009	0.0027	-0.0169	0.0109	0.0044	0.0021	0.1055	-0.0436	-0.0008	0.1707	-0.0825	0.172	29.7636	-80.4388	99.2136
16	0.005	0.0036	-0.0025	0.0028	-0.0014	0.0075	0.0083	-0.0003	-0.0064	-0.013	0.0064	0.0068	0.0084	0.0091	0.0043	0.0955	-0.029	-0.0192	0.0587	-0.0321	0.0662	13.7278	-86.6283	91.5936
17	0.0438	0.0202	-0.0273	0.0154	-0.0157	0.0189	-0.0265	0.009	-0.0029	-0.0228	-0.007	0.0079	-0.0219	0.0041	-0.0131	0.1124	-0.0081	-0.0202	0.0384	0.0055	0.0643	1.8864	-92.94	80.9739
18	0.013	-0.003	0.0017	0.014	-0.0012	0.0448	0.0199	-0.0004	0.0001	-0.0251	0.0118	0.0104	0.0006	-0.0024	0.0611	0.2245	-0.0833	-0.0236	0.0723	-0.0053	0.054	12.1637	-77.3303	84.8884
19	0.0185	0.0139	-0.0098	0.0724	0.0579	0.1115	0.0289	0.0072	0.0065	-0.0782	0.0321	0.0421	-0.0107	0.0028	0.1204	0.1763	-0.0363	-0.0557	0.048	-0.005	0.0812	7.048	-79.0171	87.0048
20	0.013	0.0003	-0.0075	0.0176	0.0211	0.03	0.0024	-0.0197	-0	0.0071	-0.0104	0.0188	0.0111	-0.0022	-0.0146	0.1837	-0.0185	-0.0471	0.0681	-0.0153	0.1056	10.0248	-84.6062	100.5709
21	0.0163	0.0006	0.0048	0.0083	0.0057	0.0057	0.0074	0.0046	0.0084	-0.0058	-0.0087	0.0117	-0.0152	-0.0073	-0.0132	0.1133	0.0028	-0.0566	0.0357	0.0101	0.0987	0.6817	-88.0434	91.4082
22	0.0547	-0.0146	-0.0168	0.0133	-0.0069	0.0379	-0.0065	-0.035	0.0036	0.03	0.0197	-0.0342	0.004	0.036	0.0098	0.0413	0.0138	-0.0375	0.0875	-0.0025	0.179	24.3321	-122.8177	90.9482
23	0.017	-0.008	0.0036	0.0059	0.0008	0.0036	0.0049	-0.0024	0.0026	0.008	0.0061	-0.011	-0.0071	0.0042	0.0053	0.0634	0.0522	-0.0162	0.0754	-0.0259	0.1182	19.4469	-122.2596	90.6064
24	0.0019	0.0001	0.0014	0.0033	-0.0036	0.0072	-0.0158	-0.0118	-0.0224	0.0134	0.0028	0.0122	0.0085	-0.0025	-0.0214	0.0717	0.0353	0.0324	0.0594	0.0131	0.068	2.4781	-120.7579	87.9337
25	0.0373	-0.0094	0.0157	0.007	0.0009	0.0134	0.0049	-0.0041	-0.0128	0.0401	0.0187	-0.0216	0.0305	0.0244	0.0158	0.1307	0.0718	0.0273	0.0889	0.0198	0.1643	18.265	-134.1429	94.4816
26	0.0002	0.0013	-0.0001	0.008	-0.001	0.0004	0.0003	-0.0005	0.0004	0.0265	0.0113	-0.0169	0.0083	0.0138	0.0073	0.1033	0.064	-0.0214	0.0939	-0.0121	0.1237	19.165	-127.3973	94.8865
27	0.0034	-0.0047	0.0009	0.0065	-0.0016	0.0021	-0.0016	0.0009	-0.0022	0.0132	0.0238	-0.0099	0.0102	0.0195	0.054	0.0766	0.0357	0.0685	0.0824	-0.0276	0.1985	13.791	-131.7456	86.1658
28	0.0006	-0.0009	-0.0011	0.0014	0.0014	0.0033	0.0007	0.002	0.0006	0.0001	0.0007	-0.0004	-0.002	0.0013	0	0.8273	-0.0084	0.0105	0.8236	-0.0026	0.8354	31.262	-111.1457	80.2714
29	0.0373	-0.0349	-0.0077	0.0473	0.0051	0.025	0.0181	-0.002	-0.0138	-0.0058	0.0169	0.0065	-0.0004	-0.0009	0.0314	0.0809	-0.0029	0.0441	0.101	-0.0384	0.1599	10.8645	-124.8311	81.0333
30	0.0156	0.0094	0.0013	0.0062	0.0025	0.0072	-0.0017	0.0025	0.0065	0.0006	-0.0017	0.0002	-0.0039	-0.0002	-0.0009	0.13	-0.0673	0.0566	0.1934	0.0168	0.1797	19.6625	-93.4773	67.4288
31	0.0031	-0.0015	-0.0026	0.0127	0.0063	0.0042	-0.0022	-0.0009	-0.0004	-0.0049	0.0018	-0.0019	0.0039	0.0018	0.0006	0.4069	0.0569	-0.0162	0.4513	-0.0129	0.483	31.7163	-132.9098	87.0047

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 through 33 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 53 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 54 through 62 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 63 through 77 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 78 through 85 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 86 through 104 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 105 through 111 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 112 through 123 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 124 through 132 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 133 through 146 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 19 through 53 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 54 through 85 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 86 through 145 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 20 through 33 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 34 through 44 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 45 through 53 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 54 through 62 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 63 through 85 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 86 through 111 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 112 through 132 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 133 through 145 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 20 through 44 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 45 through 53 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 54 through 62 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 63 through 77 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 78 through 96 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 97 through 123 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 124 through 132 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 133 through 145 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 1 through 7 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 3 through 6 )

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