PDB-4am6: C-TERMINAL DOMAIN OF ACTIN-RELATED PROTEIN ARP8 FROM S. CEREVISIAE

ID or keywords:

Entry

Database: PDB / ID: 4am6

Title

C-TERMINAL DOMAIN OF ACTIN-RELATED PROTEIN ARP8 FROM S. CEREVISIAE

Components

ACTIN-LIKE PROTEIN ARP8

Keywords

NUCLEAR PROTEIN / CHROMATIN REMODELLING COMPLEX / ATP-BINDING PROTEIN / NUCLEAR ACTIN-RELATED PROTEIN / TRANSCRIPTION REGULATION / DNA REPAIR

Function / homology

Function and homology information

Ino80 complex / mitotic recombination / double-strand break repair / cytoskeleton / chromatin remodeling / DNA repair / mRNA binding / DNA damage response / regulation of DNA-templated transcription / ATP binding ...
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.7 Å

Authors

Wuerges, J. / Saravanan, M. / Bose, D. / Cook, N.J. / Zhang, X. / Wigley, D.B.

Citation

Journal: Proc Natl Acad Sci U S A / Year: 2012
Title: Interactions between the nucleosome histone core and Arp8 in the INO80 chromatin remodeling complex.
Authors: Matheshwaran Saravanan / Jochen Wuerges / Daniel Bose / Elizabeth A McCormack / Nicola J Cook / Xiaodong Zhang / Dale B Wigley /

Abstract: Actin-related protein Arp8 is a component of the INO80 chromatin remodeling complex. Yeast Arp8 (yArp8) comprises two domains: a 25-KDa N-terminal domain, found only in yeast, and a 75-KDa C-terminal ...

History

Deposition	Mar 7, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 12, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 16, 2013	Group: Database references / Structure summary
Revision 1.2	Mar 6, 2013	Group: Data collection
Revision 1.3	Nov 13, 2019	Group: Data collection / Database references / Other / Category: pdbx_database_related / pdbx_database_status Item: _pdbx_database_related.content_type / _pdbx_database_status.status_code_sf
Revision 1.4	May 8, 2024	Group: 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 / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4am6.cif.gz	519.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4am6_validation.pdf.gz	466.2 KB	Display	wwPDB validaton report
Full document	4am6_full_validation.pdf.gz	522 KB	Display
Data in XML	4am6_validation.xml.gz	48.8 KB	Display
Data in CIF	4am6_validation.cif.gz	65.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/am/4am6 ftp://data.pdbj.org/pub/pdb/validation_reports/am/4am6	HTTPS FTP

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Related structure data

Related structure data	2224C 2225C 4am7C C: citing same article (ref.)
Similar structure data	4am7-1 5cfc-d 4am7-2 7r1r-1 3pbp-2 6ezt-1 5cfd-d 6ezr-2 6mzi-d 4amb-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) 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	#19 - Jul 2001 Actin similarity (3) #18 - Jun 2001 Myosin similarity (3) #241 - Jan 2020 Twenty Years of Molecules similarity (3)

Deposited unit

A: ACTIN-LIKE PROTEIN ARP8

B: ACTIN-LIKE PROTEIN ARP8

hetero molecules

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

1

A: ACTIN-LIKE PROTEIN ARP8

hetero molecules

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

2

B: ACTIN-LIKE PROTEIN ARP8

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

Unit cell

Length a, b, c (Å)	138.200, 87.859, 149.370
Angle α, β, γ (deg.)	90.00, 115.40, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASN	ASN	TRP	TRP	5	A	A	263 - 301	37 - 75
2	1	ASN	ASN	TRP	TRP	5	B	B	263 - 301	37 - 75
1	2	LEU	LEU	GLU	GLU	6	A	A	302 - 318	76 - 92
2	2	LEU	LEU	GLU	GLU	6	B	B	302 - 318	76 - 92
1	3	GLN	GLN	MET	MET	5	A	A	319 - 338	93 - 112
2	3	GLN	GLN	MET	MET	5	B	B	319 - 338	93 - 112
1	4	ARG	ARG	ARG	ARG	6	A	A	339 - 391	113 - 165
2	4	ARG	ARG	ARG	ARG	6	B	B	339 - 391	113 - 165
1	5	CYS	CYS	PRO	PRO	5	A	A	392 - 442	166 - 216
2	5	CYS	CYS	PRO	PRO	5	B	B	392 - 442	166 - 216
1	6	THR	THR	CYS	CYS	4	A	A	443 - 489	217 - 263
2	6	THR	THR	CYS	CYS	4	B	B	443 - 489	217 - 263
1	7	CYS	CYS	SER	SER	4	A	A	499 - 555	273 - 329
2	7	CYS	CYS	SER	SER	4	B	B	499 - 555	273 - 329
1	8	LYS	LYS	PHE	PHE	5	A	A	556 - 584	330 - 358
2	8	LYS	LYS	PHE	PHE	5	B	B	556 - 584	330 - 358
1	9	MET	MET	GLU	GLU	6	A	A	585 - 594	359 - 368
2	9	MET	MET	GLU	GLU	6	B	B	585 - 594	359 - 368
1	10	LYS	LYS	GLN	GLN	5	A	A	595 - 686	369 - 460
2	10	LYS	LYS	GLN	GLN	5	B	B	595 - 686	369 - 460
1	11	ASP	ASP	LEU	LEU	6	A	A	687 - 696	461 - 470
2	11	ASP	ASP	LEU	LEU	6	B	B	687 - 696	461 - 470
1	12	LYS	LYS	SER	SER	5	A	A	697 - 759	471 - 533
2	12	LYS	LYS	SER	SER	5	B	B	697 - 759	471 - 533
1	13	SER	SER	HIS	HIS	6	A	A	760 - 823	534 - 597
2	13	SER	SER	HIS	HIS	6	B	B	760 - 823	534 - 597
1	14	ILE	ILE	ASN	ASN	6	A	A	824 - 837	598 - 611
2	14	ILE	ILE	ASN	ASN	6	B	B	824 - 837	598 - 611
1	15	PRO	PRO	TYR	TYR	5	A	A	838 - 881	612 - 655
2	15	PRO	PRO	TYR	TYR	5	B	B	838 - 881	612 - 655

NCS oper: (Code: given
Matrix: (0.67739, 0.08674, 0.7305), (0.71762, -0.29631, -0.63026), (0.16179, 0.95114, -0.26297)
Vector: -45.36862, 105.17695, -35.30404)

#1: Protein	ACTIN-LIKE PROTEIN ARP8 Mass: 74813.469 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 248-881 Source method: isolated from a genetically manipulated source Details: NUCLEOTIDE-FREE STATE OF THE PROTEIN Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: W303-1A / Plasmid: PET28A / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 / Variant (production host): PLYSS / References: UniProt: Q12386
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H₂O
Nonpolymer details	SULFATE ION (SO4): TWO SULPHATE IONS ARE LOCATED IN THE NUCLEOTIDE-BINDING SITE OF CHAIN A
Sequence details	THE CRYSTALLISED PROTEIN CONTAINS THE ARP8 C-TERMINAL DOMAIN FROM RESIDUE 248 TO 881 AND A N- ...THE CRYSTALLISED PROTEIN CONTAINS THE ARP8 C-TERMINAL DOMAIN FROM RESIDUE 248 TO 881 AND A N-TERMINAL EXPRESSION- TAG, COMPRISING RESIDUES MGSSHHHHHHSSGLVPRGSHM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 57 % / Description: NONE
Crystal grow	pH: 6.5 Details: 18% W/V PEG 5000 MME, 0.28 M LI2SO4, 0.1 M NA-CACODYLATE PH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
Detector	Type: ADSC CCD / Detector: CCD / Date: Mar 12, 2010 / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.7→29 Å / Num. obs: 44062 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / B_iso Wilson estimate: 83.265 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 20.7
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.35 / Mean I/σ(I) obs: 3.5 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0088	refinement
MOSFLM		data reduction
SCALA		data scaling
SHARP		phasing

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 2.7→28.89 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.892 / SU B: 34.253 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R: 1.649 / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINAL TAG AND RESIDUES 248 TO 258 OF ARP8 HAVE NOT BEEN LOCATED IN THE ELECTRON DENSITY MAP.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28642	2190	5 %	RANDOM
R_work	0.2228	-	-	-
obs	0.226	41860	98.92 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 86.485 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.06 Å²	0 Å²	0.44 Å²
2-	-	2.53 Å²	0 Å²
3-	-	-	-1.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→28.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10072	0	10	32	10114

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	10306
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.841	1.958	13980
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.881	5	1244
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.944	25.412	510
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	23.675	15	1838
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.128	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.133	0.2	1558
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	7818
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.763	1.5	6250
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.433	2	10196
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.012	3	4056
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.257	4.5	3784
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	2173	medium positional	0.41	0.5
2	B	2173	medium positional	0.41	0.5
1	A	2771	loose positional	1.37	5
2	B	2771	loose positional	1.37	5
1	A	2173	medium thermal	3.37	2
2	B	2173	medium thermal	3.37	2
1	A	2771	loose thermal	3.48	10
2	B	2771	loose thermal	3.48	10

LS refinement shell

Resolution: 2.701→2.771 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.396	148	-
R_work	0.424	2901	-
obs	-	-	93.76 %

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	3.381	-0.9779	0.4367	3.2985	-0.0647	3.0194	0.2323	-0.362	0.0427	0.1002	-0.4569	0.4481	-0.002	-0.3252	0.2247	0.0908	-0.0659	0.0417	0.1971	-0.1806	0.315	-116.2877	7.5903	-9.1342
2	3.4204	-0.2073	-0.2935	4.3455	-1.5844	4.2099	0.1088	0.5457	-0.2514	-0.3015	0.1963	0.3064	0.1262	-0.443	-0.305	0.2123	0.1953	-0.0662	0.3717	-0.051	0.1431	-129.9944	24.9404	-44.4944
3	5.3675	0.9208	1.7036	7.6145	-0.102	10.2002	0.3417	0.7846	0.0019	-0.6138	-0.4602	0.0251	0.1052	0.6643	0.1185	0.1782	0.1665	-0.0658	0.2376	-0.0887	0.1884	-113.666	3.5589	-33.657
4	9.2484	-3.6283	-2.4993	5.5453	1.952	3.0837	0.0158	0.6391	0.6712	0.1148	0.3815	0.1349	-0.4944	-0.7177	-0.3973	0.4465	0.4537	0.1422	0.6893	0.2541	0.318	-145.7344	44.3656	-40.4394
5	4.3395	-1.1333	0.2273	2.2184	0.4262	2.3069	0.1326	-0.5931	-0.2659	0.2236	-0.2712	0.0872	0.202	0.1424	0.1386	0.1762	-0.0777	0.0165	0.2856	0.1551	0.2527	-93.8361	-4.0985	-1.4436
6	3.6319	-0.1864	-1.7556	4.7258	-1.0484	4.4435	0.094	0.7008	-0.0164	-0.4284	-0.0394	-0.4788	-0.2528	0.1499	-0.0546	0.3418	0.1514	0.1097	0.4428	0.0111	0.1903	-110.3417	39.6253	-54.3951
7	5.6205	0.4899	0.941	4.1935	0.1986	3.7763	0.4781	0.5026	-0.6915	-0.6317	-0.5647	0.0182	0.3376	0.3861	0.0866	0.3932	0.2623	-0.0639	0.2051	-0.0438	0.3238	-96.9339	-14.095	-26.5622
8	7.2946	0.9649	-3.3764	1.368	-1.6559	4.6401	0.5299	1.3885	1.0685	-0.2693	0.2789	0.3454	-0.9015	-0.9547	-0.8088	0.9214	0.4968	0.2294	0.7769	0.5234	0.4856	-131.852	56.8699	-57.8972
9	9.1919	-0.28	4.6232	2.9117	-1.2023	6.5676	0.7438	0.5774	-0.9361	-0.8492	-0.8481	-0.0891	1.0429	0.6853	0.1042	0.5951	0.3988	0.048	0.3327	-0.0452	0.3378	-95.5146	-14.4341	-28.0633
10	9.751	3.2733	-3.1084	2.6487	-0.5847	3.0103	-0.0238	0.8166	0.2521	-0.1788	0.3124	0.1581	-0.685	-0.5909	-0.2886	1.0473	0.4751	0.2734	0.6693	0.4615	0.6885	-131.9578	58.8037	-57.3269
11	1.6252	-2.2694	0.1349	3.6021	0.5067	2.0409	0.2415	0.3766	0.7152	-0.3466	-0.6039	-0.7611	-0.4448	0.515	0.3625	0.3051	-0.241	0.0906	0.5275	0.1154	0.5945	-89.6868	13.8201	-7.8889
12	4.566	1.0404	-3.7677	2.2305	-1.7812	3.596	0.3701	-0.9265	0.5249	0.9589	-0.1445	-0.4302	-0.8271	0.8103	-0.2256	0.7664	-0.0007	-0.1042	0.5775	-0.1071	0.3828	-110.7935	41.4331	-34.6484
13	10.5112	1.2456	-0.814	6.6031	2.0399	6.28	0.2585	-0.6317	0.9058	1.1798	0.0473	-0.5031	-0.1393	0.8569	-0.3059	0.3274	-0.1856	-0.2006	0.6979	0.0458	0.3503	-74.6826	9.1337	16.609
14	2.9934	3.504	0.1745	6.7816	3.4812	4.4861	0.1638	-0.3373	-0.9998	0.6026	0.0758	-1.1645	0.2135	1.3994	-0.2396	0.4624	-0.0148	-0.052	1.4931	0.4294	1.1371	-83.2131	38.9266	-41.9368

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	259 - 293
2	X-RAY DIFFRACTION	1	A	403 - 494
3	X-RAY DIFFRACTION	1	A	836 - 881
4	X-RAY DIFFRACTION	2	B	259 - 293
5	X-RAY DIFFRACTION	2	B	403 - 494
6	X-RAY DIFFRACTION	2	B	836 - 881
7	X-RAY DIFFRACTION	3	A	294 - 305
8	X-RAY DIFFRACTION	3	A	381 - 402
9	X-RAY DIFFRACTION	4	B	294 - 305
10	X-RAY DIFFRACTION	4	B	381 - 402
11	X-RAY DIFFRACTION	5	A	495 - 529
12	X-RAY DIFFRACTION	5	A	700 - 759
13	X-RAY DIFFRACTION	5	A	824 - 835
14	X-RAY DIFFRACTION	6	B	495 - 529
15	X-RAY DIFFRACTION	6	B	700 - 759
16	X-RAY DIFFRACTION	6	B	824 - 835
17	X-RAY DIFFRACTION	7	A	530 - 619
18	X-RAY DIFFRACTION	8	B	530 - 619
19	X-RAY DIFFRACTION	9	A	306 - 380
20	X-RAY DIFFRACTION	10	B	306 - 380
21	X-RAY DIFFRACTION	11	A	620 - 699
22	X-RAY DIFFRACTION	12	B	620 - 699
23	X-RAY DIFFRACTION	13	A	760 - 823
24	X-RAY DIFFRACTION	14	B	760 - 823

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