PDB-5ix1: Crystal structure of mouse Morc3 ATPase-CW cassette in complex wi...

ID or keywords:

Entry

Database: PDB / ID: 5ix1

Title

Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and H3K4me3 peptide

Components

MORC family CW-type zinc finger protein 3
Peptide from Histone H3.1

Keywords

TRANSCRIPTION /

Morc3 /

ATPase / CW domain /

H3K4me3

Function / homology

Function and homology information

Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.6 Å

Authors

Li, S. / Du, J. / Patel, D.J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin
Authors: Li, S. / Yen, L. / Pastor, W.A. / Johnston, J.B. / Du, J. / Shew, C.J. / Liu, W. / Ho, J. / Stender, B. / Clark, A.T. / Burlingame, A.L. / Daxinger, L. / Patel, D.J. / Jacobsen, S.E.

History

Deposition	Mar 23, 2016	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Aug 17, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 14, 2016	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ix1.cif.gz	357.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5ix1.ent.gz	306.7 KB	Display	PDB format
PDBx/mmJSON format	5ix1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ix/5ix1 ftp://data.pdbj.org/pub/pdb/validation_reports/ix/5ix1	HTTPS FTP

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Related structure data

Related structure data	5ix2C C: citing same article (ref.)
Similar structure data	5ix2-d 4q4x-d 6k4l-1 6mcq-2 3t5t-d 1b8a-d 1wyd-d 6uj8-d 4yqx-d 1x55-1 Search similar-shape structures by Omokage search (details) 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	#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #87 - Mar 2007 Zinc Fingers similarity (2) #183 - Mar 2015 Phototropin similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #108 - Dec 2008 Hsp90 similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

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Related items in Molecule of the Month

#152 - Aug 2012
cAMP-dependent Protein Kinase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (2)
#183 - Mar 2015
Phototropin
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#108 - Dec 2008
Hsp90
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: MORC family CW-type zinc finger protein 3

B: MORC family CW-type zinc finger protein 3

P: Peptide from Histone H3.1

Q: Peptide from Histone H3.1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	111.353, 149.079, 173.473
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

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Protein / Protein/peptide , 2 types, 4 molecules ABPQ

#1: Protein	MORC family CW-type zinc finger protein 3 / Nuclear matrix protein 2 / Zinc finger CW-type coiled-coil domain protein 3 Mass: 51950.477 Da / Num. of mol.: 2 / Fragment: UNP residues 7-456 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Morc3 / Plasmid: pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: F7BJB9
#2: Protein/peptide	Peptide from Histone H3.1 / Mass: 1607.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P68433

#1: Protein

MORC family CW-type zinc finger protein 3 / Nuclear matrix protein 2 / Zinc finger CW-type coiled-coil domain protein 3

Mass: 51950.477 Da / Num. of mol.: 2 / Fragment: UNP residues 7-456
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Morc3 / Plasmid: pET-Sumo / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: F7BJB9

#2: Protein/peptide

Peptide from Histone H3.1 /

Mass: 1607.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.)

Mus musculus (house mouse) / References: UniProt: P68433

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Non-polymers , 4 types, 73 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.36 Å³/Da / Density % sol: 63.4 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 5% ethanol, 5% 2-Methyl-2,4-pentanediol (MPD), 0.1 M HEPES-Na

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.6→20 Å / Num. obs: 44534 / % possible obs: 99.7 % / Redundancy: 6.4 % / R_merge(I) obs: 0.085 / Net I/σ(I): 11.8
Reflection shell	Resolution: 2.6→2.74 Å / Redundancy: 5.9 % / R_merge(I) obs: 0.866 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.6→19.762 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 32.07

	R_factor	Num. reflection	% reflection
R_free	0.2296	2242	5.05 %
R_work	0.2176	-	-
obs	0.2182	44441	99.7 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.6→19.762 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6909	0	66	67	7042

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.02	7120
X-RAY DIFFRACTION	f_angle_d	1.79	9611
X-RAY DIFFRACTION	f_dihedral_angle_d	20.725	2683
X-RAY DIFFRACTION	f_chiral_restr	0.108	1043
X-RAY DIFFRACTION	f_plane_restr	0.006	1209

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 (%)
2.6-2.6295	0.4354	130	0.3978	2721	X-RAY DIFFRACTION	99
2.6295-2.6604	0.4159	169	0.3716	2697	X-RAY DIFFRACTION	100
2.6604-2.6927	0.3783	139	0.3775	2634	X-RAY DIFFRACTION	100
2.6927-2.7267	0.3886	150	0.3582	2693	X-RAY DIFFRACTION	100
2.7267-2.7625	0.3908	172	0.3649	2722	X-RAY DIFFRACTION	99
2.7625-2.8002	0.3345	150	0.3518	2618	X-RAY DIFFRACTION	99
2.8002-2.8401	0.3519	139	0.3583	2708	X-RAY DIFFRACTION	100
2.8401-2.8824	0.3663	123	0.3249	2720	X-RAY DIFFRACTION	100
2.8824-2.9273	0.3019	146	0.324	2701	X-RAY DIFFRACTION	100
2.9273-2.9751	0.2855	167	0.3084	2715	X-RAY DIFFRACTION	100
2.9751-3.0263	0.3379	133	0.3005	2698	X-RAY DIFFRACTION	100
3.0263-3.0811	0.3194	139	0.298	2697	X-RAY DIFFRACTION	100
3.0811-3.1401	0.2888	124	0.2733	2698	X-RAY DIFFRACTION	100
3.1401-3.204	0.2549	134	0.2631	2744	X-RAY DIFFRACTION	100
3.204-3.2733	0.2859	151	0.2552	2720	X-RAY DIFFRACTION	100
3.2733-3.3491	0.2411	129	0.2549	2697	X-RAY DIFFRACTION	100
3.3491-3.4325	0.2236	167	0.2489	2688	X-RAY DIFFRACTION	100
3.4325-3.5248	0.2488	127	0.2246	2709	X-RAY DIFFRACTION	100
3.5248-3.6279	0.282	120	0.2045	2773	X-RAY DIFFRACTION	100
3.6279-3.7442	0.2422	166	0.2013	2666	X-RAY DIFFRACTION	100
3.7442-3.8771	0.2212	137	0.1918	2704	X-RAY DIFFRACTION	100
3.8771-4.031	0.2081	150	0.178	2681	X-RAY DIFFRACTION	100
4.031-4.2128	0.209	141	0.1743	2702	X-RAY DIFFRACTION	100
4.2128-4.4325	0.1594	170	0.1684	2688	X-RAY DIFFRACTION	100
4.4325-4.7067	0.1854	143	0.161	2738	X-RAY DIFFRACTION	100
4.7067-5.0645	0.1981	133	0.1666	2689	X-RAY DIFFRACTION	100
5.0645-5.5638	0.1995	143	0.1886	2719	X-RAY DIFFRACTION	100
5.5638-6.3455	0.2268	117	0.1987	2738	X-RAY DIFFRACTION	100
6.3455-7.9085	0.1657	148	0.195	2708	X-RAY DIFFRACTION	100
7.9085-19.7625	0.147	153	0.1658	2666	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	1.8815	0.0113	-0.1659	2.8077	0.1599	3.1617	-0.0325	0.2626	0.2674	-0.3658	0.0175	0.0747	-0.3819	-0.1241	-0.0042	0.8326	0.0411	-0.0229	0.6895	0.1554	0.3496	77.0545	71.3784	27.1166
2	3.3309	0.3545	-0.1859	2.482	0.2691	1.7156	-0.0336	-0.0607	-0.4161	-0.1099	-0.0859	-0.3612	0.3203	0.006	0.0708	0.9967	-0.0386	0.0184	0.7548	0.0812	0.4168	80.9659	49.5588	24.8348
3	3.5529	2.7909	-0.4767	4.2862	-1.076	0.9984	-0.0876	0.245	-0.3315	-0.3845	0.0796	-0.0032	0.3764	-0.4721	0.0018	0.6623	-0.0326	0.0053	0.672	0.0584	0.3945	64.7139	43.5231	33.2728
4	2.3223	1.1141	-1.0494	1.7346	-0.9624	1.6285	-0.2733	0.4582	-0.1476	-0.8974	0.1154	-0.041	0.5509	-0.0273	0.1367	1.0488	0.0168	-0.01	0.8155	0.0713	0.4724	73.5303	54.0119	14.2335
5	1.8158	-0.0311	-0.1511	2.6956	0.0194	2.6857	-0.0609	-0.4083	0.297	0.2671	-0.0184	0.0221	-0.5815	-0.1108	0.0691	0.7927	0.0026	-0.0164	0.6845	0.0277	0.3343	79.3906	71.4403	59.5782
6	2.5666	-0.043	-1.1602	3.2737	-0.0451	2.0203	-0.0093	-0.2519	-0.2943	0.3724	-0.1034	0.0955	0.296	-0.0452	0.0935	0.8761	0.0429	-0.0229	0.7562	0.1464	0.3858	78.7678	48.6957	63.1165
7	4.8804	-2.9723	0.7895	6.3339	1.4526	3.3068	-0.0358	0.0235	-0.5946	0.1011	0.0112	0.1136	0.4261	0.0867	-0.0118	0.6337	0.0091	0.0583	0.681	0.1319	0.4482	92.9692	41.0002	48.5755
8	1.2746	-0.6999	-1.3451	2.2022	1.2827	2.9198	0.0841	-0.4829	-0.0718	0.8737	-0.1283	-0.0446	-0.2654	-0.24	0.0918	1.0936	-0.0027	-0.0457	1.0463	0.0677	0.4556	78.632	60.9361	83.2873
9	4.3231	0.5419	-2.1789	5.5317	1.3618	1.6994	-0.6714	1.1232	-0.0092	-0.7336	-0.2074	0.1088	0.5867	-0.2681	0.8922	1.4502	-0.0483	-0.0553	0.9569	0.0107	0.5078	75.4343	53.9182	-0.1005
10	4.4816	1.3961	0.8808	6.1392	2.2186	4.3713	-0.3992	-0.6737	-0.2376	0.4809	-0.2421	-0.2668	0.6306	-0.9475	0.69	1.5808	-0.0268	0.0606	1.1941	0.0285	0.5641	80.619	53.1752	86.1916

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 199 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 200 through 264 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 265 through 364 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 365 through 455 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 8 through 199 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 200 through 283 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 284 through 384 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 385 through 454 )
9	X-RAY DIFFRACTION	9	chain 'P' and (resid 1 through 9 )
10	X-RAY DIFFRACTION	10	chain 'Q' and (resid 1 through 10 )

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