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

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Basic information

Entry
Database: PDB / ID: 3qb0
TitleCrystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP
ComponentsActin-related protein 4
KeywordsSTRUCTURAL PROTEIN / actin fold / ATP binding / Nucleus
Function / homology
Function and homology information


Swr1 complex / Ino80 complex / kinetochore assembly / SWI/SNF complex / NuA4 histone acetyltransferase complex / chromatin organization / histone binding / chromatin remodeling / DNA repair / DNA-templated transcription ...Swr1 complex / Ino80 complex / kinetochore assembly / SWI/SNF complex / NuA4 histone acetyltransferase complex / chromatin organization / histone binding / chromatin remodeling / DNA repair / DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 ...ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin-related protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.404 Å
AuthorsFenn, S. / Breitsprecher, D. / Gerhold, C.B. / Witte, G. / Faix, J. / Hopfner, K.P.
CitationJournal: 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
DepositionJan 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin-related protein 4
B: Actin-related protein 4
C: Actin-related protein 4
D: Actin-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,64112
Polymers224,4524
Non-polymers2,1898
Water0
1
A: Actin-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6603
Polymers56,1131
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Actin-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6603
Polymers56,1131
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Actin-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6603
Polymers56,1131
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Actin-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6603
Polymers56,1131
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22D
13B
23C
14B
24C
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B
110C
210A
111C
211A
112C
212A
113C
213A
114C
214A
115D
215C
116D
216C
117D
217C
118D
218C
119D
219C
120B
220D
121B
221D
122B
222D
123B
223D
124B
224D
125A
225D
126B
226C
127A
227B
128C
228A
129D
229C
130B
230D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A resid 10:325A0
211chain D resid 10:325D0
112chain A resid 382:489A0
212chain D resid 382:489D0
113chain B resid 8:326B0
213chain C resid 8:326C0
114chain B resid 382:489B0
214chain C resid 382:489C0
115chain A resid 12:294A0
215chain B resid 12:294B0
116chain A resid 311:326A0
216chain B resid 311:326B0
117chain A resid 383:440A0
217chain B resid 383:440B0
118chain A resid 446:464A0
218chain B resid 446:464B0
119chain A resid 466:489A0
219chain B resid 466:489B0
1110chain C resid 12:294C0
2110chain A resid 12:294A0
1111chain C resid 311:326C0
2111chain A resid 311:326A0
1112chain C resid 383:440C0
2112chain A resid 383:440A0
1113chain C resid 446:464C0
2113chain A resid 446:464A0
1114chain C resid 466:489C0
2114chain A resid 466:489A0
1115chain D resid 12:294D0
2115chain C resid 12:294C0
1116chain D resid 311:326D0
2116chain C resid 311:326C0
1117chain D resid 383:440D0
2117chain C resid 383:440C0
1118chain D resid 446:464D0
2118chain C resid 446:464C0
1119chain D resid 466:489D0
2119chain C resid 466:489C0
1120chain B resid 12:294B0
2120chain D resid 12:294D0
1121chain B resid 311:326B0
2121chain D resid 311:326D0
1122chain B resid 383:440B0
2122chain D resid 383:440D0
1123chain B resid 446:464B0
2123chain D resid 446:464D0
1124chain B resid 466:489B0
2124chain D resid 466:489D0
1125chain AE0
2125chain DK0
1126chain BG0
2126chain CI0
1127chain AE0
2127chain BG0
1128chain CI0
2128chain AE0
1129chain DK0
2129chain CI0
1130chain BG0
2130chain DK0

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

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Components

#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 / Adenosine 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.75 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 3.4→3.61 Å / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3.01 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YAG
Resolution: 3.404→49.54 Å / SU ML: 0.44 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 2118 4.92 %Random
Rwork0.1915 ---
obs0.1929 43013 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.45 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.6367 Å2-0 Å2-0 Å2
2--6.6367 Å2-0 Å2
3----13.2735 Å2
Refinement stepCycle: LAST / Resolution: 3.404→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13657 0 128 0 13785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614539
X-RAY DIFFRACTIONf_angle_d0.80519144
X-RAY DIFFRACTIONf_dihedral_angle_d11.8635240
X-RAY DIFFRACTIONf_chiral_restr0.092125
X-RAY DIFFRACTIONf_plane_restr0.0032432
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2522X-RAY DIFFRACTIONPOSITIONAL0.007
12D2522X-RAY DIFFRACTIONPOSITIONAL0.007
21A848X-RAY DIFFRACTIONPOSITIONAL0.03
22D848X-RAY DIFFRACTIONPOSITIONAL0.03
31B2548X-RAY DIFFRACTIONPOSITIONAL0.011
32C2548X-RAY DIFFRACTIONPOSITIONAL0.011
41B848X-RAY DIFFRACTIONPOSITIONAL0.031
42C848X-RAY DIFFRACTIONPOSITIONAL0.031
51A2257X-RAY DIFFRACTIONPOSITIONAL0.009
52B2257X-RAY DIFFRACTIONPOSITIONAL0.009
61A141X-RAY DIFFRACTIONPOSITIONAL0.009
62B141X-RAY DIFFRACTIONPOSITIONAL0.009
71A434X-RAY DIFFRACTIONPOSITIONAL0.008
72B434X-RAY DIFFRACTIONPOSITIONAL0.008
81A148X-RAY DIFFRACTIONPOSITIONAL0.007
82B148X-RAY DIFFRACTIONPOSITIONAL0.007
91A212X-RAY DIFFRACTIONPOSITIONAL0.052
92B212X-RAY DIFFRACTIONPOSITIONAL0.052
101C2257X-RAY DIFFRACTIONPOSITIONAL0.013
102A2257X-RAY DIFFRACTIONPOSITIONAL0.013
111C141X-RAY DIFFRACTIONPOSITIONAL0.009
112A141X-RAY DIFFRACTIONPOSITIONAL0.009
121C434X-RAY DIFFRACTIONPOSITIONAL0.025
122A434X-RAY DIFFRACTIONPOSITIONAL0.025
131C148X-RAY DIFFRACTIONPOSITIONAL0.008
132A148X-RAY DIFFRACTIONPOSITIONAL0.008
141C212X-RAY DIFFRACTIONPOSITIONAL0.008
142A212X-RAY DIFFRACTIONPOSITIONAL0.008
151D2257X-RAY DIFFRACTIONPOSITIONAL0.013
152C2257X-RAY DIFFRACTIONPOSITIONAL0.013
161D141X-RAY DIFFRACTIONPOSITIONAL0.01
162C141X-RAY DIFFRACTIONPOSITIONAL0.01
171D434X-RAY DIFFRACTIONPOSITIONAL0.025
172C434X-RAY DIFFRACTIONPOSITIONAL0.025
181D148X-RAY DIFFRACTIONPOSITIONAL0.008
182C148X-RAY DIFFRACTIONPOSITIONAL0.008
191D212X-RAY DIFFRACTIONPOSITIONAL0.039
192C212X-RAY DIFFRACTIONPOSITIONAL0.039
201B2257X-RAY DIFFRACTIONPOSITIONAL0.008
202D2257X-RAY DIFFRACTIONPOSITIONAL0.008
211B141X-RAY DIFFRACTIONPOSITIONAL0.01
212D141X-RAY DIFFRACTIONPOSITIONAL0.01
221B434X-RAY DIFFRACTIONPOSITIONAL0.008
222D434X-RAY DIFFRACTIONPOSITIONAL0.008
231B148X-RAY DIFFRACTIONPOSITIONAL0.008
232D148X-RAY DIFFRACTIONPOSITIONAL0.008
241B212X-RAY DIFFRACTIONPOSITIONAL0.034
242D212X-RAY DIFFRACTIONPOSITIONAL0.034
251A31X-RAY DIFFRACTIONPOSITIONAL0.007
252D31X-RAY DIFFRACTIONPOSITIONAL0.007
261B31X-RAY DIFFRACTIONPOSITIONAL0.006
262C31X-RAY DIFFRACTIONPOSITIONAL0.006
271A31X-RAY DIFFRACTIONPOSITIONAL0.007
272B31X-RAY DIFFRACTIONPOSITIONAL0.007
281C31X-RAY DIFFRACTIONPOSITIONAL0.007
282A31X-RAY DIFFRACTIONPOSITIONAL0.007
291D31X-RAY DIFFRACTIONPOSITIONAL0.007
292C31X-RAY DIFFRACTIONPOSITIONAL0.007
301B31X-RAY DIFFRACTIONPOSITIONAL0.005
302D31X-RAY DIFFRACTIONPOSITIONAL0.005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4041-3.48330.34631110.28392755X-RAY DIFFRACTION100
3.4833-3.57030.28431380.24682714X-RAY DIFFRACTION100
3.5703-3.66680.25931450.23682701X-RAY DIFFRACTION100
3.6668-3.77470.25271450.21792716X-RAY DIFFRACTION100
3.7747-3.89650.26571440.20212718X-RAY DIFFRACTION100
3.8965-4.03570.20831410.18922741X-RAY DIFFRACTION100
4.0357-4.19720.20611430.17492729X-RAY DIFFRACTION100
4.1972-4.38810.19541450.14932731X-RAY DIFFRACTION100
4.3881-4.61930.17781410.14032706X-RAY DIFFRACTION100
4.6193-4.90850.15621470.15372739X-RAY DIFFRACTION100
4.9085-5.28710.20931410.16112717X-RAY DIFFRACTION100
5.2871-5.81840.21421440.18432722X-RAY DIFFRACTION100
5.8184-6.65860.20211450.18852745X-RAY DIFFRACTION100
6.6586-8.38250.21271430.18682727X-RAY DIFFRACTION100
8.3825-49.54530.17311450.17252734X-RAY DIFFRACTION99

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