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- PDB-4wyb: Structure of the Bud6 flank domain in complex with actin -

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Basic information

Entry
Database: PDB / ID: 4wyb
TitleStructure of the Bud6 flank domain in complex with actin
Components
  • Actin, alpha skeletal muscle
  • Bud site selection protein 6
KeywordsCONTRACTILE PROTEIN/PROTEIN BINDING / nucleation promoting factor WH2 Domain / Formin / CONTRACTILE PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


cytoskeletal regulatory protein binding / positive regulation of formin-nucleated actin cable assembly / polarisome / bipolar cellular bud site selection / budding cell apical bud growth / secretory vesicle / vesicle targeting / pseudohyphal growth / prospore membrane / establishment or maintenance of actin cytoskeleton polarity ...cytoskeletal regulatory protein binding / positive regulation of formin-nucleated actin cable assembly / polarisome / bipolar cellular bud site selection / budding cell apical bud growth / secretory vesicle / vesicle targeting / pseudohyphal growth / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / positive regulation of actin nucleation / astral microtubule organization / incipient cellular bud site / cellular bud tip / cell tip / cellular bud neck / mating projection tip / spindle pole body / cytoskeletal motor activator activity / establishment of cell polarity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / enzyme activator activity / actin filament polymerization / filopodium / actin filament / regulation of actin cytoskeleton organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / regulation of protein localization / lamellipodium / actin binding / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Actin interacting protein 3, C-terminal / Actin interacting protein 3-like, C-terminal / Actin interacting protein 3 / Actin interacting protein 3 / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. ...Actin interacting protein 3, C-terminal / Actin interacting protein 3-like, C-terminal / Actin interacting protein 3 / Actin interacting protein 3 / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Bud site selection protein 6 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.493 Å
AuthorsEck, M.J. / Park, E. / Zheng, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071834 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM083137 United States
CitationJournal: Structure / Year: 2015
Title: Structure of a Bud6/Actin Complex Reveals a Novel WH2-like Actin Monomer Recruitment Motif.
Authors: Park, E. / Graziano, B.R. / Zheng, W. / Garabedian, M. / Goode, B.L. / Eck, M.J.
History
DepositionNov 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Data collection
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
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_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Bud site selection protein 6
C: Actin, alpha skeletal muscle
D: Bud site selection protein 6
E: Actin, alpha skeletal muscle
F: Bud site selection protein 6
G: Actin, alpha skeletal muscle
H: Bud site selection protein 6
I: Actin, alpha skeletal muscle
J: Bud site selection protein 6
K: Actin, alpha skeletal muscle
L: Bud site selection protein 6
M: Actin, alpha skeletal muscle
N: Bud site selection protein 6
O: Actin, alpha skeletal muscle
P: Bud site selection protein 6
Q: Actin, alpha skeletal muscle
R: Bud site selection protein 6
S: Actin, alpha skeletal muscle
T: Bud site selection protein 6
U: Actin, alpha skeletal muscle
V: Bud site selection protein 6
X: Actin, alpha skeletal muscle
Y: Bud site selection protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)638,21848
Polymers631,65124
Non-polymers6,56724
Water00
1
A: Actin, alpha skeletal muscle
B: Bud site selection protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1854
Polymers52,6382
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-33 kcal/mol
Surface area17820 Å2
MethodPISA
2
C: Actin, alpha skeletal muscle
D: Bud site selection protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1854
Polymers52,6382
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-35 kcal/mol
Surface area17640 Å2
MethodPISA
3
E: Actin, alpha skeletal muscle
F: Bud site selection protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1854
Polymers52,6382
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-34 kcal/mol
Surface area17470 Å2
MethodPISA
4
G: Actin, alpha skeletal muscle
H: Bud site selection protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1854
Polymers52,6382
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-35 kcal/mol
Surface area17430 Å2
MethodPISA
5
I: Actin, alpha skeletal muscle
J: Bud site selection protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1854
Polymers52,6382
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-35 kcal/mol
Surface area17560 Å2
MethodPISA
6
K: Actin, alpha skeletal muscle
L: Bud site selection protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1854
Polymers52,6382
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-35 kcal/mol
Surface area17640 Å2
MethodPISA
7
M: Actin, alpha skeletal muscle
N: Bud site selection protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1854
Polymers52,6382
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-36 kcal/mol
Surface area17490 Å2
MethodPISA
8
O: Actin, alpha skeletal muscle
P: Bud site selection protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1854
Polymers52,6382
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-34 kcal/mol
Surface area17560 Å2
MethodPISA
9
Q: Actin, alpha skeletal muscle
R: Bud site selection protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1854
Polymers52,6382
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-34 kcal/mol
Surface area17240 Å2
MethodPISA
10
S: Actin, alpha skeletal muscle
T: Bud site selection protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1854
Polymers52,6382
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-35 kcal/mol
Surface area17360 Å2
MethodPISA
11
U: Actin, alpha skeletal muscle
V: Bud site selection protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1854
Polymers52,6382
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-36 kcal/mol
Surface area17230 Å2
MethodPISA
12
X: Actin, alpha skeletal muscle
Y: Bud site selection protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1854
Polymers52,6382
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-36 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.753, 138.753, 356.651
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42096.953 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Details: ATP, Ca / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein
Bud site selection protein 6 / Actin-interacting protein 3


Mass: 10540.659 Da / Num. of mol.: 12 / Fragment: residues 699-788
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: BUD6, AIP3, YLR319C, L8543.5 / Plasmid: pET
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P41697
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.493→45.418 Å / Num. obs: 97910 / % possible obs: 99.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 4.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
Cootmodel building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MN7

3mn7


Resolution: 3.493→45.418 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2581 2017 2.1 %
Rwork0.2124 --
obs0.2134 95892 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.493→45.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37131 0 384 0 37515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00538309
X-RAY DIFFRACTIONf_angle_d1.0852025
X-RAY DIFFRACTIONf_dihedral_angle_d15.34414099
X-RAY DIFFRACTIONf_chiral_restr0.0495806
X-RAY DIFFRACTIONf_plane_restr0.0046652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4933-3.58070.34931400.29346503X-RAY DIFFRACTION95
3.5807-3.67740.34551400.2796841X-RAY DIFFRACTION100
3.6774-3.78560.36011490.27186747X-RAY DIFFRACTION100
3.7856-3.90770.26241490.25026761X-RAY DIFFRACTION100
3.9077-4.04730.31081490.23996779X-RAY DIFFRACTION100
4.0473-4.20920.25831510.21256840X-RAY DIFFRACTION100
4.2092-4.40070.20861470.19536711X-RAY DIFFRACTION99
4.4007-4.63250.25191410.18536802X-RAY DIFFRACTION99
4.6325-4.92240.21591440.19376757X-RAY DIFFRACTION99
4.9224-5.30190.26031470.21136679X-RAY DIFFRACTION99
5.3019-5.83450.30951400.21596725X-RAY DIFFRACTION99
5.8345-6.67650.26191450.21786690X-RAY DIFFRACTION98
6.6765-8.40290.20241420.18776598X-RAY DIFFRACTION97
8.4029-45.42140.23651330.18396442X-RAY DIFFRACTION94

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