PDB-6q3m: Structure of CHD4 PHD2 - tandem chromodomains

ID or keywords:

Entry

Database: PDB / ID: 6q3m

Title

Structure of CHD4 PHD2 - tandem chromodomains

Components

Chromodomain-helicase-DNA-binding protein 4

Keywords

DNA BINDING PROTEIN / CHD5 / chromodomain / chromatin remodelling

Function / homology

Function and homology information

cerebellar granule cell to Purkinje cell synapse / terminal button organization / NuRD complex / regulation of cell fate specification / NGF-stimulated transcription / regulation of stem cell differentiation / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / site of DNA damage / RNA Polymerase I Transcription Initiation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.52 Å

Authors

Alt, A. / Mancini, E.J.

Citation

Journal: To Be Published
Title: Structure of histone readers
Authors: Mancini, E.J. / Alt, A.

History

Deposition	Dec 4, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 25, 2019	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6q3m.cif.gz	522.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6q3m.ent.gz	442.1 KB	Display	PDB format
PDBx/mmJSON format	6q3m.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/q3/6q3m ftp://data.pdbj.org/pub/pdb/validation_reports/q3/6q3m	HTTPS FTP

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Related structure data

Similar structure data	7by1-1 5xws-d 5aws-1 4az9-1 4az9-2 4url-1 2vpa-d 2w97-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#75 - Mar 2006 Tissue Factor similarity (1) #122 - Feb 2010 Enhanceosome similarity (2) #67 - Jul 2005 TATA-Binding Protein similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (2)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#75 - Mar 2006
Tissue Factor
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (2)
#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#61 - Jan 2005
Phenylalanine Hydroxylase
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#213 - Sep 2017
Sirtuins
similarity (1)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (2)

Deposited unit

A: Chromodomain-helicase-DNA-binding protein 4

B: Chromodomain-helicase-DNA-binding protein 4

C: Chromodomain-helicase-DNA-binding protein 4

D: Chromodomain-helicase-DNA-binding protein 4

hetero molecules

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

1

A: Chromodomain-helicase-DNA-binding protein 4

hetero molecules

defined by author&software
Evidence: SAXS
29.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Chromodomain-helicase-DNA-binding protein 4

hetero molecules

defined by author&software
29 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Chromodomain-helicase-DNA-binding protein 4

hetero molecules

defined by author&software
29.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Chromodomain-helicase-DNA-binding protein 4

hetero molecules

defined by author&software
28.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.731, 87.681, 129.257
Angle α, β, γ (deg.)	90.00, 93.57, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Chromodomain-helicase-DNA-binding protein 4 / CHD-4 / ATP-dependent helicase CHD4 / Mi-2 autoantigen 218 kDa protein / Mi2-beta Mass: 28357.270 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHD4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14839, DNA helicase

#1: Protein

Chromodomain-helicase-DNA-binding protein 4 / CHD-4 / ATP-dependent helicase CHD4 / Mi-2 autoantigen 218 kDa protein / Mi2-beta

Mass: 28357.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: CHD4 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q14839, DNA helicase

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Non-polymers , 5 types, 214 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.53 Å³/Da / Density % sol: 65.12 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion Details: 0.12M Diethyleneglycol, 0.12M Triethylene-glycol, 0.12M Tetraethyleneglycol, 0.12M Pentaethyleneglycol, 20% v/v Ethylene glycol, 10 % w/v PEG 8000, Sodium HEPES, MOPS pH = 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97793 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97793 Å / Relative weight: 1
Reflection	Resolution: 2.52→64.503 Å / Num. obs: 106090 / % possible obs: 99.31 % / Redundancy: 2 % / Net I/σ(I): 7.98
Reflection shell	Resolution: 2.52→2.61 Å / Num. unique obs: 5220

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.52→64.503 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.71

	R_factor	Num. reflection	% reflection
R_free	0.2626	4958	4.82 %
R_work	0.23	-	-
obs	0.2315	102862	98.26 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.52→64.503 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7120	0	160	177	7457

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7510
X-RAY DIFFRACTION	f_angle_d	0.801	10128
X-RAY DIFFRACTION	f_dihedral_angle_d	14.068	4480
X-RAY DIFFRACTION	f_chiral_restr	0.048	955
X-RAY DIFFRACTION	f_plane_restr	0.007	1309

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 (%)
2.52-2.5486	0.4017	171	0.4112	3200	X-RAY DIFFRACTION	97
2.5486-2.5786	0.4789	154	0.4007	3233	X-RAY DIFFRACTION	97
2.5786-2.6101	0.3639	151	0.4032	3236	X-RAY DIFFRACTION	97
2.6101-2.6431	0.3932	144	0.3986	3204	X-RAY DIFFRACTION	96
2.6431-2.6779	0.3937	194	0.3799	3079	X-RAY DIFFRACTION	96
2.6779-2.7146	0.4087	164	0.3729	3219	X-RAY DIFFRACTION	96
2.7146-2.7533	0.3567	179	0.3553	3260	X-RAY DIFFRACTION	97
2.7533-2.7944	0.3373	166	0.3402	3226	X-RAY DIFFRACTION	98
2.7944-2.8381	0.3425	174	0.3292	3273	X-RAY DIFFRACTION	98
2.8381-2.8846	0.3472	144	0.3283	3232	X-RAY DIFFRACTION	98
2.8846-2.9344	0.3697	182	0.3183	3292	X-RAY DIFFRACTION	98
2.9344-2.9877	0.3364	124	0.3127	3252	X-RAY DIFFRACTION	98
2.9877-3.0452	0.3567	176	0.3001	3292	X-RAY DIFFRACTION	98
3.0452-3.1074	0.2924	187	0.2759	3234	X-RAY DIFFRACTION	98
3.1074-3.1749	0.2657	189	0.2604	3219	X-RAY DIFFRACTION	99
3.1749-3.2488	0.2989	177	0.2574	3322	X-RAY DIFFRACTION	99
3.2488-3.33	0.2808	134	0.2601	3313	X-RAY DIFFRACTION	99
3.33-3.42	0.283	172	0.245	3266	X-RAY DIFFRACTION	99
3.42-3.5207	0.2836	176	0.234	3303	X-RAY DIFFRACTION	99
3.5207-3.6343	0.2522	153	0.223	3301	X-RAY DIFFRACTION	99
3.6343-3.7642	0.2464	158	0.2164	3286	X-RAY DIFFRACTION	99
3.7642-3.9149	0.2531	194	0.2005	3265	X-RAY DIFFRACTION	99
3.9149-4.093	0.22	142	0.1886	3315	X-RAY DIFFRACTION	99
4.093-4.3088	0.2186	183	0.1792	3272	X-RAY DIFFRACTION	99
4.3088-4.5787	0.2	198	0.164	3257	X-RAY DIFFRACTION	99
4.5787-4.9321	0.1503	143	0.1589	3345	X-RAY DIFFRACTION	99
4.9321-5.4282	0.1889	153	0.172	3340	X-RAY DIFFRACTION	100
5.4282-6.2131	0.2509	141	0.2001	3325	X-RAY DIFFRACTION	99
6.2131-7.8257	0.285	171	0.2112	3261	X-RAY DIFFRACTION	99
7.8257-64.5242	0.2278	164	0.1932	3282	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	0.7883	-0.2061	-0.1715	1.0815	-0.4305	0.3692	-0.1534	0.2713	0.7563	-0.1946	0.1418	0.1712	-0.0163	-0.3047	-0.0004	0.5428	0.03	-0.0072	0.7495	0.17	0.7007	0.5264	23.6459	36.1828
2	1.7397	-0.1721	1.2093	1.901	-0.4908	1.2247	-0.27	0.4192	0.2635	-0.4239	0.1927	-0.1481	0.3226	0.3652	-0.0001	0.4045	-0.0058	0.0678	0.4805	0.0643	0.5581	5.9989	13.752	40.2652
3	2.903	0.9851	-0.5464	0.6132	0.1768	0.522	0.0808	0.3446	0.6122	-0.1631	0.0336	0.1715	0.0125	0.0876	0.0002	0.3613	0.0107	0.0101	0.4213	0.0543	0.4861	7.9967	10.795	50.8654
4	1.4153	0.6135	-0.1187	1.0625	-0.9223	1.119	0.1589	-0.3497	0.0355	0.7239	-0.3549	-0.8217	-0.0696	0.2863	-0.0001	0.5123	-0.0363	-0.0948	0.53	0.0494	0.5572	5.7845	-2.4077	65.5669
5	2.9823	0.4462	1.0991	3.9894	-0.7983	1.8466	-0.0877	-0.0609	-0.2401	-0.1042	-0.1898	-0.2901	0.125	0.5806	0.0001	0.4517	0.0461	0.0084	0.3103	0.0973	0.4385	-0.681	-20.3032	55.8282
6	0.1352	-0.0667	0.2636	0.2565	-0.1128	0.6958	0.0065	0.3757	-1.0344	-0.1258	0.0422	-0.8034	1.099	0.6753	0.0005	0.6113	0.0627	-0.0243	0.4284	0.0173	0.6806	-0.2152	-30.7682	59.293
7	1.0264	-0.4236	-0.1283	1.094	-1.1789	2.9773	-0.2603	-0.3566	-0.1091	0.0605	0.5359	0.357	0.2994	-0.4577	0.0001	0.3579	-0.0153	-0.0564	0.5159	0.0154	0.6164	-23.5002	10.3669	51.2223
8	1.5465	-0.0497	-1.1764	1.1986	-1.0279	1.4607	0.0395	-0.142	0.287	-0.2103	-0.0852	0.0021	0.1164	0.0375	-0	0.4169	-0.0243	-0.0105	0.6438	0.0367	0.5503	-25.8274	20.2616	37.1352
9	2.8364	0.1359	-0.443	2.1134	-1.0871	2.8435	0.18	0.4404	0.5384	-0.4635	-0.2166	0.3551	-0.8452	-0.826	-0.0244	0.5246	0.0762	-0.0337	0.7109	0.1832	0.5834	-21.8782	28.6561	15.3032
10	0.8965	-0.4508	-0.5528	1.6834	0.7442	0.4823	0.0851	0.0405	-0.11	-0.5278	0.2313	0.7029	-0.69	-1.0338	-0	0.8804	0.0828	-0.0452	0.789	0.2164	0.6066	-19.2145	25.9288	3.5685
11	1.8662	0.6989	1.2504	1.9711	-0.5775	3.412	-0.2168	0.1743	-0.1511	-0.2331	0.101	0.043	0.0555	-0.5987	0	0.5895	-0.0399	-0.0202	0.6222	-0.0912	0.479	-24.5561	-7.2784	16.0736
12	1.0774	-1.3517	1.3457	1.7032	-1.5787	2.5413	0.0162	0.0521	-0.1068	-0.3117	0.1181	0.0125	0.4307	-0.4972	-0.0003	0.726	-0.1823	-0.0511	0.607	-0.0076	0.6019	-25.5944	-21.0327	30.8868
13	3.2506	0.6327	0.3483	2.2742	0.572	3.6214	-0.0127	-0.0409	0.0433	-0.1456	0.0414	0.4411	0.3009	-0.7548	0	0.4546	-0.0346	-0.0339	0.5512	0.1092	0.5969	-22.9474	-18.0406	58.821
14	0.3952	0.1375	0.0836	0.4701	-0.035	0.0813	-0.4173	0.1413	-0.8486	-0.0044	0.1983	0.7304	0.362	0.574	-0.0006	0.9106	0.0943	0.0431	0.8112	0.1619	0.9561	-0.5031	-19.8251	28.0798
15	0.0391	0.0128	-0.0811	0.1068	-0.1133	0.226	-0.2482	-0.0268	-0.4472	0.4786	-0.2808	-0.5861	0.7271	0.8037	-0.0006	0.8665	0.3164	0.0649	0.9347	0.3159	0.9021	8.2703	-16.9241	27.093
16	0.9539	0.4572	-0.5447	1.161	0.368	0.9364	0.1718	-0.3689	-0.1514	0.2403	0.2078	0.1246	-0.2162	0.3481	-0.0001	0.747	0.0388	-0.1047	0.622	0.0809	0.5359	5.0682	-2.8208	19.2848
17	0.049	-0.0549	0.0622	0.0586	-0.0651	0.0706	-0.5969	-1.6147	-0.9527	0.5328	-0.6047	-1.39	-0.0109	1.0497	-0.0037	0.7685	0.1596	0.019	1.0092	0.4097	1.1093	16.4209	-12.0137	15.9611
18	1.266	-0.2901	-0.2529	0.2085	-0.2657	0.7517	0.1367	-0.1006	-0.1523	0.567	-0.0445	-0.3456	-0.0438	-0.0941	0	0.6966	-0.007	-0.001	0.516	-0.0216	0.4751	4.1412	4.2109	12.4147
19	0.3793	0.0693	-0.2442	0.0974	0.0803	0.3242	0.0984	-0.3253	-0.8064	-0.1777	-0.5617	0.0146	-0.0702	-0.745	0	0.5744	0.0538	0.0411	0.7286	-0.0141	0.613	-5.2596	-4.4843	9.5435
20	1.777	0.5424	-0.3769	0.1921	-0.2502	0.5184	-0.1645	0.412	-0.8573	-1.1091	-0.4979	-0.8708	0.1871	0.0841	-0.1578	0.7427	-0.0124	0.1549	0.6064	0.1005	0.6258	8.9484	-1.1028	-1.6295
21	1.3531	0.3556	0.2248	2.8462	-0.3762	1.8374	0.1057	0.2997	0.0722	-0.1871	-0.1012	-0.4372	0.0607	0.3184	-0.0002	0.6663	-0.0446	0.0633	0.5097	0.0875	0.5139	7.1607	19.6782	6.0265
22	0.9798	-0.9342	-0.2928	1.1748	0.1127	0.5706	0.2605	0.363	-0.0221	0.076	-0.36	-0.5657	0.179	0.734	0.0002	0.7641	-0.1288	0.0553	0.6923	0.1067	0.5546	3.4996	22.1957	6.2615
23	0.0725	0.4586	0.2888	4.9759	0.7719	1.6421	-0.013	0.4354	0.5571	-0.8361	0.5396	-0.4448	-1.447	0.4248	0.4713	1.1151	-0.1763	0.1128	0.5343	0.1747	0.558	5.1476	34.4756	5.2935

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 446 through 465 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 466 through 505 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 506 through 577 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 578 through 622 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 623 through 663 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 664 through 676 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 446 through 485 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 486 through 577 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 578 through 644 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 645 through 675 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 445 through 525 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 526 through 622 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 623 through 678 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 445 through 464 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 465 through 484 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 485 through 510 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 511 through 540 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 541 through 566 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 567 through 577 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 578 through 602 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 603 through 644 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 645 through 663 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 664 through 674 )

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+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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Movie

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Structure viewers

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This page

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Open data

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Validation report

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Assembly

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Components

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 214 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi