PDB-8jg4: Crystal Structure of YAF9A YEATS bound to H3K27cr peptide

ID or keywords:

Entry

Database: PDB / ID: 8jg4

Title

Crystal Structure of YAF9A YEATS bound to H3K27cr peptide

Components

Histone H3.1Histone H3
Transcription initiation factor TFIID subunit 14b

Keywords

TRANSCRIPTION /

YEATS domain

Function / homology

Function and homology information

: /

: / regulation of timing of transition from vegetative to reproductive phase /

regulation of photoperiodism, flowering /

regulation of flower development /

flower development / chromocenter / Swr1 complex /

plastid /

NuA4 histone acetyltransferase complex ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Li, H.T. / Liu, W.Q.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of YAF9A YEATS bound to H3K27cr peptide
Authors: Li, H.T. / Liu, W.Q.

History

Deposition	May 19, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	May 22, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8jg4.cif.gz	148.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8jg4.ent.gz	114.6 KB	Display	PDB format
PDBx/mmJSON format	8jg4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jg/8jg4 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/8jg4	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	#7 - Jul 2000 Nucleosome similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Transcription initiation factor TFIID subunit 14b

B: Transcription initiation factor TFIID subunit 14b

C: Histone H3.1

D: Histone H3.1

44.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Transcription initiation factor TFIID subunit 14b

D: Histone H3.1

defined by author
Evidence: gel filtration
22.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Transcription initiation factor TFIID subunit 14b

C: Histone H3.1

defined by author
22.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.331, 117.700, 59.053
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Transcription initiation factor TFIID subunit 14b / GAS 41-like protein / Protein AF-9 homolog a / TBP-associated factor 14b / AtTAF14b Mass: 21277.209 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TAF14B, GAS41, YAF9A, At5g45600, K2N11.8 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FH40
#2: Protein/peptide	Histone H3.1 / Histone H3 Mass: 839.960 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.61 Å³/Da / Density % sol: 52.79 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 0.2 M Li2SO4, 25% PEG 3350

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Data collection

Diffraction

Mean temperature: 110 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U1 / Wavelength: 0.9792 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2020

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 21078 / % possible obs: 99 % / Redundancy: 10.3 % / CC_1/2: 0.992 / CC star: 0.998 / R_merge(I) obs: 0.132 / R_pim(I) all: 0.043 / R_rim(I) all: 0.139 / Χ²: 0.872 / Net I/σ(I): 5 / Num. measured all: 216550

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.3-2.34	8.8	0.897	1038	0.77	0.933	0.314	0.953	0.491	98.6
2.34-2.38	9.6	0.71	1023	0.857	0.961	0.24	0.751	0.53	98.2
2.38-2.43	10.5	0.664	1034	0.893	0.971	0.214	0.699	0.523	99.8
2.43-2.48	10.6	0.603	1024	0.886	0.969	0.195	0.635	0.54	98.7
2.48-2.53	10.7	0.519	1038	0.931	0.982	0.166	0.545	0.553	99
2.53-2.59	10.5	0.495	1039	0.931	0.982	0.161	0.521	0.591	98.8
2.59-2.66	10.3	0.438	1017	0.928	0.981	0.145	0.462	0.61	97.9
2.66-2.73	10.1	0.37	1034	0.959	0.99	0.123	0.391	0.608	99
2.73-2.81	10.7	0.329	1030	0.966	0.991	0.105	0.346	0.68	97.5
2.81-2.9	10.6	0.284	1022	0.98	0.995	0.092	0.299	0.684	98.2
2.9-3	10.5	0.231	1039	0.983	0.996	0.075	0.243	0.801	98.4
3-3.12	10.1	0.178	1035	0.983	0.996	0.059	0.188	0.946	98
3.12-3.26	10.4	0.152	1053	0.993	0.998	0.049	0.16	1.091	99.3
3.26-3.44	10.6	0.125	1056	0.994	0.998	0.04	0.132	1.222	99.7
3.44-3.65	9.9	0.111	1062	0.993	0.998	0.036	0.117	1.326	99.7
3.65-3.93	10.2	0.096	1078	0.996	0.999	0.031	0.101	1.342	100
3.93-4.33	11	0.084	1069	0.997	0.999	0.027	0.088	1.393	100
4.33-4.95	10.3	0.071	1101	0.997	0.999	0.023	0.074	1.484	99.9
4.95-6.24	10.7	0.064	1094	0.998	1	0.021	0.067	0.984	100
6.24-50	9.4	0.052	1192	0.998	1	0.017	0.055	0.849	99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→44.11 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 2.05 / Phase error: 21.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2118	1591	7.57 %
R_work	0.1715	-	-
obs	0.1747	21018	98.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→44.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2564	0	0	175	2739

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2646
X-RAY DIFFRACTION	f_angle_d	0.91	3603
X-RAY DIFFRACTION	f_dihedral_angle_d	24.492	959
X-RAY DIFFRACTION	f_chiral_restr	0.054	387
X-RAY DIFFRACTION	f_plane_restr	0.006	462

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 (%)
2.3-2.37	0.3247	123	0.2427	1727	X-RAY DIFFRACTION	98
2.37-2.46	0.265	136	0.2105	1764	X-RAY DIFFRACTION	99
2.46-2.56	0.2375	143	0.1939	1718	X-RAY DIFFRACTION	99
2.56-2.67	0.247	140	0.2025	1727	X-RAY DIFFRACTION	99
2.67-2.81	0.2498	133	0.2087	1741	X-RAY DIFFRACTION	98
2.81-2.99	0.2747	146	0.2057	1734	X-RAY DIFFRACTION	98
2.99-3.22	0.2106	153	0.1776	1738	X-RAY DIFFRACTION	98
3.22-3.54	0.1975	146	0.1729	1783	X-RAY DIFFRACTION	100
3.54-4.06	0.1858	163	0.1505	1779	X-RAY DIFFRACTION	100
4.06-5.11	0.1629	151	0.1247	1817	X-RAY DIFFRACTION	100
5.11-44.11	0.2059	157	0.1668	1899	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	1.356	-0.5985	-0.5898	2.6488	2.0093	4.7073	-0.1643	-0.0656	0.0902	-0.0781	0.1505	0.0196	0.0653	0.2864	0.1011	0.2398	-0.0309	0.0034	0.2263	-0.0349	0.2916	-5.8798	-25.6971	-29.1562
2	1.943	-0.5453	0.2925	1.87	0.8812	1.8065	0.0026	0.124	0.1692	0.0106	0.0486	-0.1589	-0.0558	0.166	-0.0358	0.1984	-0.0148	-0.0038	0.236	-0.0018	0.2394	-2.2711	-18.3985	-21.9362
3	2.756	2.3451	2.8483	1.9907	2.4181	2.9319	0.4048	-0.4441	-0.4851	0.3031	-0.3727	0.0178	0.7387	-0.85	0.0651	0.3841	-0.0862	0.0119	0.3885	-0.0239	0.3145	-9.9448	-37.3409	-32.1188
4	0.9876	-0.5891	0.0092	2.6319	0.6214	1.444	-0.2085	-0.0578	0.1687	0.333	0.1425	0.2742	-0.06	0.052	0.0541	0.2559	-0.0483	0.0184	0.2243	-0.0171	0.2382	-13.8882	-13.5994	-12.4251
5	2.8155	-0.6373	-1.1665	0.1558	0.264	0.485	0.1053	-0.9116	0.0819	0.1503	0.1522	0.3388	-0.2847	-1.1106	-0.1403	0.3567	0.0527	0.091	0.79	0.0222	0.4747	-26.5616	-8.3204	-9.9855
6	1.9922	1.0278	-1.9687	2.6509	-2.7041	4.2118	-0.2108	-0.0039	0.1261	-0.3184	0.1732	0.1062	0.59	-0.0674	-0.0042	0.2298	0.005	-0.0258	0.2706	-0.0225	0.2388	15.3778	-24.2669	-0.447
7	1.3945	0.4304	0.0939	1.8955	-0.6232	1.9792	0.0256	0.0287	0.0666	0.0151	0.0231	0.1239	0.0622	-0.1431	-0.044	0.1738	-0.0082	-0.0147	0.1826	-0.0148	0.1644	11.1954	-17.5751	-7.9605
8	3.7253	-3.3061	3.2778	3.0475	-3.0161	2.972	0.7347	0.591	-0.3164	-0.2207	-0.5649	0.0219	0.8699	0.4548	-0.1177	0.4542	0.0536	-0.0238	0.3747	0.0101	0.3168	20.0431	-35.6993	2.6808
9	1.349	-0.3343	-0.0611	2.3666	-0.9341	1.73	0.0287	0.1555	0.1967	-0.4743	-0.1444	-0.2962	0.0557	0.2059	0.0907	0.2021	-0.0154	0.0297	0.3287	-0.0005	0.2176	22.3494	-11.9443	-17.5014
10	5.6228	1.514	-2.9579	0.3984	-0.7997	1.5904	0.5193	0.3338	0.3826	-0.0414	-0.0399	0.1051	-0.2854	0.3801	-0.3825	0.3185	-0.0594	-0.0398	0.5572	0.0031	0.4596	35.5041	-6.3656	-20.4223
11	6.6519	-4.3301	-0.1116	7.9869	-0.9519	1.9604	0.0946	0.4364	-0.572	-0.4676	-0.1165	0.2878	0.4204	-0.0951	-0.0342	0.5431	-0.2227	-0.0679	0.3443	0.0355	0.4865	4.9589	-35.2373	-3.97
12	3.6224	1.9313	1.2	5.7482	1.0786	6.4917	-0.1142	-0.4199	-0.6553	0.3626	0.0025	-0.4502	0.7912	0.1053	0.1144	0.3881	0.1848	-0.0151	0.5498	-0.095	0.4457	5.7957	-35.1501	-25.9229

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 42 through 66 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 67 through 140 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 141 through 157 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 158 through 179 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 180 through 194 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 42 through 66 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 67 through 140 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 141 through 157 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 158 through 179 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 180 through 195 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 25 through 30 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 25 through 30 )

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