PDB-4am7: ADP-BOUND C-TERMINAL DOMAIN OF ACTIN-RELATED PROTEIN ARP8 FROM S....

ID or keywords:

Entry

Database: PDB / ID: 4am7

Title

ADP-BOUND 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 /

MOLECULAR REPLACEMENT / Resolution: 3.25 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
Revision 1.2	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 1.3	Dec 20, 2023	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 / pdbx_initial_refinement_model / 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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Download

PDBx/mmCIF format	4am7.cif.gz	521 KB	Display	PDBx/mmCIF format
PDB format	pdb4am7.ent.gz	434.6 KB	Display	PDB format
PDBx/mmJSON format	4am7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4am7_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	4am7_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4am7_validation.xml.gz	48 KB	Display
Data in CIF	4am7_validation.cif.gz	64 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/am/4am7 ftp://data.pdbj.org/pub/pdb/validation_reports/am/4am7	HTTPS FTP

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Related structure data

Related structure data	2224C 2225C 4am6SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4am6-1 4am6-2 5cfc-d 4g33-d 3pbp-2 6mzi-d 3juh-d 3pov-d 6t40-d 1e3p-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
75.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ACTIN-LIKE PROTEIN ARP8

hetero molecules

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

Unit cell

Length a, b, c (Å)	137.718, 89.795, 149.647
Angle α, β, γ (deg.)	90.00, 114.37, 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	TYR	TYR	THR	THR	6	A	A	490 - 498	264 - 272
2	7	TYR	TYR	THR	THR	6	B	B	490 - 498	264 - 272
1	8	CYS	CYS	SER	SER	4	A	A	499 - 555	273 - 329
2	8	CYS	CYS	SER	SER	4	B	B	499 - 555	273 - 329
1	9	LYS	LYS	PHE	PHE	5	A	A	556 - 584	330 - 358
2	9	LYS	LYS	PHE	PHE	5	B	B	556 - 584	330 - 358
1	10	MET	MET	GLU	GLU	6	A	A	585 - 594	359 - 368
2	10	MET	MET	GLU	GLU	6	B	B	585 - 594	359 - 368
1	11	LYS	LYS	GLN	GLN	5	A	A	595 - 686	369 - 460
2	11	LYS	LYS	GLN	GLN	5	B	B	595 - 686	369 - 460
1	12	ASP	ASP	LEU	LEU	6	A	A	687 - 696	461 - 470
2	12	ASP	ASP	LEU	LEU	6	B	B	687 - 696	461 - 470
1	13	LYS	LYS	SER	SER	5	A	A	697 - 759	471 - 533
2	13	LYS	LYS	SER	SER	5	B	B	697 - 759	471 - 533
1	14	SER	SER	HIS	HIS	6	A	A	760 - 823	534 - 597
2	14	SER	SER	HIS	HIS	6	B	B	760 - 823	534 - 597
1	15	ILE	ILE	ASN	ASN	6	A	A	824 - 837	598 - 611
2	15	ILE	ILE	ASN	ASN	6	B	B	824 - 837	598 - 611
1	16	PRO	PRO	TYR	TYR	5	A	A	838 - 881	612 - 655
2	16	PRO	PRO	TYR	TYR	5	B	B	838 - 881	612 - 655

NCS oper: (Code: given
Matrix: (0.67099, 0.08449, 0.73663), (0.72002, -0.31144, -0.62014), (0.17702, 0.9465, -0.26981)
Vector: -46.07872, 105.46299, -34.37724)

#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: ADP-BOUND STATE OF THE PROTEIN Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: W303-1A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / Variant (production host): PLYSS / References: UniProt: Q12386
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM

#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: ADP-BOUND STATE OF THE PROTEIN
Source: (gene. exp.)

SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: W303-1A / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / Variant (production host): PLYSS / References: UniProt: Q12386

#2: Chemical

ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE

Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM

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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: 19.5% W/V PEG 5000 MME, 0.32 M LI2SO4, 0.1 M MES PH 6.5, 0.002 M ADP, 0.005 M MGCL2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
Detector	Type: ADSC CCD / Detector: CCD / Date: Dec 2, 2009 / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 3.25→20 Å / Num. obs: 25357 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / B_iso Wilson estimate: 96.105 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 8.5
Reflection shell	Resolution: 3.25→3.43 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 2.5 / % possible all: 94.6

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AM6

4am6

Resolution: 3.25→19.81 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.874 / SU B: 63.316 / SU ML: 0.506 / Cross valid method: THROUGHOUT / ESU R: 1.863 / ESU R Free: 0.617 / 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	0.28417	1301	5.1 %	RANDOM
R_work	0.2192	-	-	-
obs	0.22259	24054	96.45 %	-

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: 121.118 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.61 Å²	0 Å²	0.62 Å²
2-	-	1.81 Å²	0 Å²
3-	-	-	0.31 Å²

Refinement step

Cycle: LAST / Resolution: 3.25→19.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10072	0	54	0	10126

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	10356
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.566	1.963	14058
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.281	5	1244
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.102	25.412	510
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	23.055	15	1838
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.025	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	1566
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	7840
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	0.577	1.5	6250
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.088	2	10196
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.222	3	4106
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.159	4.5	3862
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	0.37	0.5
2	B	2173	medium positional	0.37	0.5
1	A	2830	loose positional	1.34	5
2	B	2830	loose positional	1.34	5
1	A	2173	medium thermal	4.17	2
2	B	2173	medium thermal	4.17	2
1	A	2830	loose thermal	3.45	10
2	B	2830	loose thermal	3.45	10

LS refinement shell

Resolution: 3.25→3.332 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.333	87	-
R_work	0.284	1611	-
obs	-	-	89.89 %

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	4.5968	-1.2268	-0.0351	3.9748	0.2897	3.91	0.1739	-0.0753	0.1497	-0.0428	-0.4143	0.3213	-0.002	-0.2361	0.2404	0.011	0.0009	-0.0082	0.0758	-0.1035	0.2317	-115.94	7.9272	-9.2815
2	3.6602	-0.5129	-0.4776	5.5995	-0.617	4.6187	0.1387	0.57	-0.2882	-0.4708	0.1289	0.3062	0.3093	-0.09	-0.2676	0.225	0.1903	-0.0609	0.3292	-0.0182	0.0874	-129.9586	24.9787	-44.972
3	0.3342	0.9391	1.0915	5.3386	-0.0686	9.0453	0.0438	0.0681	0.027	-0.377	-0.3369	0.027	0.3042	0.2615	0.2931	0.2088	0.2421	-0.0381	0.2983	-0.057	0.2405	-113.312	3.7301	-33.9293
4	9.5123	-0.8758	-1.3354	2.9228	-1.5624	1.3952	0.0834	0.4987	0.2534	0.0383	0.1493	0.413	-0.1795	-0.1966	-0.2328	0.2941	0.2133	0.0678	0.3198	0.2228	0.2268	-145.972	44.4025	-40.9163
5	6.3502	-2.883	-0.0032	3.0802	-0.0546	3.816	-0.0703	-0.3585	-0.2307	0.3221	-0.2446	0.1365	0.1885	0.2224	0.315	0.0662	-0.0644	0.0014	0.1646	0.1063	0.2131	-93.7639	-4.4049	-1.5198
6	3.8393	0.8693	-0.5309	7.6439	-0.8517	3.0049	-0.1653	0.8962	0.0349	-0.8244	0.1769	-0.7755	0.0148	0.2496	-0.0116	0.3915	0.1957	0.1983	0.6574	0.0593	0.1347	-110.4843	39.9475	-55.1302
7	3.8872	0.9031	1.0083	6.3898	0.583	4.2773	0.1664	0.7933	-0.5715	-0.5669	-0.2764	0.0803	0.1012	0.1091	0.1099	0.2194	0.1896	0.0789	0.2811	-0.0539	0.2664	-97.1448	-14.6265	-26.8138
8	5.4397	0.3305	2.0101	2.2378	-0.9186	3.5001	-0.1116	1.0034	1.1387	-0.4527	0.196	0.3524	-0.3511	-0.0631	-0.0844	0.6201	0.2424	0.0943	0.7001	0.4983	0.4347	-132.3498	56.9903	-58.518
9	5.3003	0.1724	3.4635	2.2014	-1.0122	5.665	0.2093	0.413	-0.6462	-0.7217	-0.357	-0.2074	0.2622	0.0781	0.1477	0.4448	0.2496	0.1135	0.1984	-0.0701	0.3446	-95.5903	-14.9124	-28.2492
10	9.0366	2.7632	-1.1713	2.337	-0.4821	2.1029	-0.0842	0.5485	0.0015	-0.5182	0.0643	0.1885	-0.6573	0.0987	0.0199	0.7677	0.2999	0.1065	0.573	0.3711	0.6418	-132.4376	58.9605	-57.9273
11	1.8428	-1.8215	-0.1094	3.6067	0.5837	1.3584	0.2208	0.3141	0.6147	-0.3866	-0.5445	-0.6085	-0.6602	0.5384	0.3237	0.3766	-0.2437	-0.0371	0.4202	0.2255	0.5855	-89.2289	13.537	-8.1554
12	4.7944	0.1076	-2.0382	1.9002	-0.0578	1.116	0.2527	-0.7828	0.6226	0.7544	-0.0073	-0.5095	-0.2902	0.6166	-0.2454	0.7053	0.0357	-0.0769	0.7416	-0.0097	0.3672	-110.8528	41.8178	-35.3126
13	9.3541	1.714	-1.6131	8.9833	-0.9969	6.9434	-0.1572	-1.095	0.6261	1.1279	0.2804	-0.545	-0.1478	1.0419	-0.1232	0.2704	-0.1179	-0.2842	0.7632	0.0763	0.4864	-74.2277	8.5304	16.4896
14	1.2594	3.0732	0.7324	7.7231	1.8126	0.4335	0.3007	0.2463	-0.3895	0.8616	-0.0914	-0.9427	0.2435	0.0992	-0.2093	0.6856	0.2191	0.1402	2.1027	0.3644	1.3038	-83.2816	39.6853	-42.7209

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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