PDB-3qb0: Crystal structure of Actin-related protein Arp4 from S. cerevisia...

ID or keywords:

Entry

Database: PDB / ID: 3qb0

Title

Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP

Components

Actin-related protein 4

Keywords

STRUCTURAL PROTEIN / actin fold / ATP binding / Nucleus

Function / homology

Function and homology information

Swr1 complex / kinetochore assembly / Ino80 complex / SWI/SNF complex / NuA4 histone acetyltransferase complex / chromatin organization / histone binding / chromatin remodeling / DNA repair / DNA-templated transcription ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.404 Å

Authors

Fenn, S. / Breitsprecher, D. / Gerhold, C.B. / Witte, G. / Faix, J. / Hopfner, K.P.

Citation

Journal: Embo J. / Year: 2011
Title: Structural biochemistry of nuclear actin-related proteins 4 and 8 reveals their interaction with actin.
Authors: Fenn, S. / Breitsprecher, D. / Gerhold, C.B. / Witte, G. / Faix, J. / Hopfner, K.P.

History

Deposition	Jan 12, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 2, 2011	Group: Database references
Revision 1.3	Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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	3qb0.cif.gz	357.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3qb0.ent.gz	286 KB	Display	PDB format
PDBx/mmJSON format	3qb0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3qb0_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	3qb0_full_validation.pdf.gz	1.5 MB	Display
Data in XML	3qb0_validation.xml.gz	63.7 KB	Display
Data in CIF	3qb0_validation.cif.gz	82.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qb/3qb0 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/3qb0	HTTPS FTP

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Related structure data

Related structure data	1yagS S: Starting model for refinement
Similar structure data	4m0l-5 4ab5-d 3pas-2 4mpn-d 4mpe-d 6240 1ui5-d 4mp7-d 6wp9-3 5dsz-2 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

Related structure data

1yagS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#19 - Jul 2001 Actin similarity (5) #18 - Jun 2001 Myosin similarity (5) #241 - Jan 2020 Twenty Years of Molecules similarity (3)

Deposited unit

A: Actin-related protein 4

B: Actin-related protein 4

C: Actin-related protein 4

D: Actin-related protein 4

hetero molecules

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

1

A: Actin-related protein 4

hetero molecules

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

2

B: Actin-related protein 4

hetero molecules

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

3

C: Actin-related protein 4

hetero molecules

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

4

D: Actin-related protein 4

hetero molecules

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

Unit cell

Length a, b, c (Å)	118.810, 118.810, 395.660
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

#1: Protein	Actin-related protein 4 / Actin-like protein ARP4 / Actin-like protein 4 Mass: 56113.105 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ACT3, ARP4, J1012, YJL081C / Plasmid: pFBDM / Cell line (production host): HIGH FIVE / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P80428
#2: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.59 Å³/Da / Density % sol: 65.75 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 27 % PEG2000MME, 0.1 M HEPES-NaOH, 6 % D+-Trehalose, 50 mM Glycine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 9, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.4→50 Å / Num. all: 43229 / Num. obs: 43032 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.71 % / Net I/σ(I): 11.64
Reflection shell	Resolution: 3.4→3.61 Å / R_merge(I) obs: 0.563 / Mean I/σ(I) obs: 3.01 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.6.1_357)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1YAG

1yag

Resolution: 3.404→49.54 Å / SU ML: 0.44 / σ(F): 2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2207	2118	4.92 %	Random
R_work	0.1915	-	-	-
obs	0.1929	43013	99.89 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 28.45 Å² / k_sol: 0.315 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.6367 Å²	-0 Å²	-0 Å²
2-	-	6.6367 Å²	-0 Å²
3-	-	-	-13.2735 Å²

Refinement step

Cycle: LAST / Resolution: 3.404→49.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13657	0	128	0	13785

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	14539
X-RAY DIFFRACTION	f_angle_d	0.805	19144
X-RAY DIFFRACTION	f_dihedral_angle_d	11.863	5240
X-RAY DIFFRACTION	f_chiral_restr	0.09	2125
X-RAY DIFFRACTION	f_plane_restr	0.003	2432

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	2522	X-RAY DIFFRACTION	POSITIONAL	0.007
1	2	D	2522	X-RAY DIFFRACTION	POSITIONAL	0.007
2	1	A	848	X-RAY DIFFRACTION	POSITIONAL	0.03
2	2	D	848	X-RAY DIFFRACTION	POSITIONAL	0.03
3	1	B	2548	X-RAY DIFFRACTION	POSITIONAL	0.011
3	2	C	2548	X-RAY DIFFRACTION	POSITIONAL	0.011
4	1	B	848	X-RAY DIFFRACTION	POSITIONAL	0.031
4	2	C	848	X-RAY DIFFRACTION	POSITIONAL	0.031
5	1	A	2257	X-RAY DIFFRACTION	POSITIONAL	0.009
5	2	B	2257	X-RAY DIFFRACTION	POSITIONAL	0.009
6	1	A	141	X-RAY DIFFRACTION	POSITIONAL	0.009
6	2	B	141	X-RAY DIFFRACTION	POSITIONAL	0.009
7	1	A	434	X-RAY DIFFRACTION	POSITIONAL	0.008
7	2	B	434	X-RAY DIFFRACTION	POSITIONAL	0.008
8	1	A	148	X-RAY DIFFRACTION	POSITIONAL	0.007
8	2	B	148	X-RAY DIFFRACTION	POSITIONAL	0.007
9	1	A	212	X-RAY DIFFRACTION	POSITIONAL	0.052
9	2	B	212	X-RAY DIFFRACTION	POSITIONAL	0.052
10	1	C	2257	X-RAY DIFFRACTION	POSITIONAL	0.013
10	2	A	2257	X-RAY DIFFRACTION	POSITIONAL	0.013
11	1	C	141	X-RAY DIFFRACTION	POSITIONAL	0.009
11	2	A	141	X-RAY DIFFRACTION	POSITIONAL	0.009
12	1	C	434	X-RAY DIFFRACTION	POSITIONAL	0.025
12	2	A	434	X-RAY DIFFRACTION	POSITIONAL	0.025
13	1	C	148	X-RAY DIFFRACTION	POSITIONAL	0.008
13	2	A	148	X-RAY DIFFRACTION	POSITIONAL	0.008
14	1	C	212	X-RAY DIFFRACTION	POSITIONAL	0.008
14	2	A	212	X-RAY DIFFRACTION	POSITIONAL	0.008
15	1	D	2257	X-RAY DIFFRACTION	POSITIONAL	0.013
15	2	C	2257	X-RAY DIFFRACTION	POSITIONAL	0.013
16	1	D	141	X-RAY DIFFRACTION	POSITIONAL	0.01
16	2	C	141	X-RAY DIFFRACTION	POSITIONAL	0.01
17	1	D	434	X-RAY DIFFRACTION	POSITIONAL	0.025
17	2	C	434	X-RAY DIFFRACTION	POSITIONAL	0.025
18	1	D	148	X-RAY DIFFRACTION	POSITIONAL	0.008
18	2	C	148	X-RAY DIFFRACTION	POSITIONAL	0.008
19	1	D	212	X-RAY DIFFRACTION	POSITIONAL	0.039
19	2	C	212	X-RAY DIFFRACTION	POSITIONAL	0.039
20	1	B	2257	X-RAY DIFFRACTION	POSITIONAL	0.008
20	2	D	2257	X-RAY DIFFRACTION	POSITIONAL	0.008
21	1	B	141	X-RAY DIFFRACTION	POSITIONAL	0.01
21	2	D	141	X-RAY DIFFRACTION	POSITIONAL	0.01
22	1	B	434	X-RAY DIFFRACTION	POSITIONAL	0.008
22	2	D	434	X-RAY DIFFRACTION	POSITIONAL	0.008
23	1	B	148	X-RAY DIFFRACTION	POSITIONAL	0.008
23	2	D	148	X-RAY DIFFRACTION	POSITIONAL	0.008
24	1	B	212	X-RAY DIFFRACTION	POSITIONAL	0.034
24	2	D	212	X-RAY DIFFRACTION	POSITIONAL	0.034
25	1	A	31	X-RAY DIFFRACTION	POSITIONAL	0.007
25	2	D	31	X-RAY DIFFRACTION	POSITIONAL	0.007
26	1	B	31	X-RAY DIFFRACTION	POSITIONAL	0.006
26	2	C	31	X-RAY DIFFRACTION	POSITIONAL	0.006
27	1	A	31	X-RAY DIFFRACTION	POSITIONAL	0.007
27	2	B	31	X-RAY DIFFRACTION	POSITIONAL	0.007
28	1	C	31	X-RAY DIFFRACTION	POSITIONAL	0.007
28	2	A	31	X-RAY DIFFRACTION	POSITIONAL	0.007
29	1	D	31	X-RAY DIFFRACTION	POSITIONAL	0.007
29	2	C	31	X-RAY DIFFRACTION	POSITIONAL	0.007
30	1	B	31	X-RAY DIFFRACTION	POSITIONAL	0.005
30	2	D	31	X-RAY DIFFRACTION	POSITIONAL	0.005

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 (%)
3.4041-3.4833	0.3463	111	0.2839	2755	X-RAY DIFFRACTION	100
3.4833-3.5703	0.2843	138	0.2468	2714	X-RAY DIFFRACTION	100
3.5703-3.6668	0.2593	145	0.2368	2701	X-RAY DIFFRACTION	100
3.6668-3.7747	0.2527	145	0.2179	2716	X-RAY DIFFRACTION	100
3.7747-3.8965	0.2657	144	0.2021	2718	X-RAY DIFFRACTION	100
3.8965-4.0357	0.2083	141	0.1892	2741	X-RAY DIFFRACTION	100
4.0357-4.1972	0.2061	143	0.1749	2729	X-RAY DIFFRACTION	100
4.1972-4.3881	0.1954	145	0.1493	2731	X-RAY DIFFRACTION	100
4.3881-4.6193	0.1778	141	0.1403	2706	X-RAY DIFFRACTION	100
4.6193-4.9085	0.1562	147	0.1537	2739	X-RAY DIFFRACTION	100
4.9085-5.2871	0.2093	141	0.1611	2717	X-RAY DIFFRACTION	100
5.2871-5.8184	0.2142	144	0.1843	2722	X-RAY DIFFRACTION	100
5.8184-6.6586	0.2021	145	0.1885	2745	X-RAY DIFFRACTION	100
6.6586-8.3825	0.2127	143	0.1868	2727	X-RAY DIFFRACTION	100
8.3825-49.5453	0.1731	145	0.1725	2734	X-RAY DIFFRACTION	99

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