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- PDB-5ypu: Crystal structure of an actin monomer in complex with the nucleat... -

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Basic information

Entry
Database: PDB / ID: 5ypu
TitleCrystal structure of an actin monomer in complex with the nucleator Cordon-Bleu MET72NLE WH2-motif peptide
Components
  • Actin, alpha skeletal muscle
  • Cordon-Bleu WH2 motif
KeywordsPEPTIDE BINDING PROTEIN / WH2 / nucleation / actin-binding
Function / homology
Function and homology information


somite specification / floor plate development / actin filament network formation / terminal web / embryonic axis specification / notochord development / actin crosslink formation / digestive tract development / collateral sprouting in absence of injury / positive regulation of ruffle assembly ...somite specification / floor plate development / actin filament network formation / terminal web / embryonic axis specification / notochord development / actin crosslink formation / digestive tract development / collateral sprouting in absence of injury / positive regulation of ruffle assembly / positive regulation of dendrite development / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / dendritic growth cone / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / axonal growth cone / stress fiber / titin binding / ruffle / actin filament polymerization / liver development / filopodium / neural tube closure / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / cell cortex / actin cytoskeleton organization / hydrolase activity / protein domain specific binding / axon / neuronal cell body / dendrite / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Cordon-bleu, ubiquitin-like domain / Protein cordon-bleu-like / Cordon-bleu ubiquitin-like domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH2 domain / WH2 domain profile. / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain ...Cordon-bleu, ubiquitin-like domain / Protein cordon-bleu-like / Cordon-bleu ubiquitin-like domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH2 domain / WH2 domain profile. / 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 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin, alpha skeletal muscle / Protein cordon-bleu
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsScipion, C.P.M. / Wongsantichon, J. / Ferrer, F.J. / Yuen, T.Y. / Robinson, R.C.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural evidence for the roles of divalent cations in actin polymerization and activation of ATP hydrolysis
Authors: Scipion, C.P.M. / Ghoshdastider, U. / Ferrer, F.J. / Yuen, T.Y. / Wongsantichon, J. / Robinson, R.C.
History
DepositionNov 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.formula_weight
Revision 1.3Nov 22, 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_conn_type / struct_ncs_dom_lim
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Cordon-Bleu WH2 motif
C: Actin, alpha skeletal muscle
D: Cordon-Bleu WH2 motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,07413
Polymers86,7794
Non-polymers1,2959
Water11,079615
1
A: Actin, alpha skeletal muscle
B: Cordon-Bleu WH2 motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0176
Polymers43,3892
Non-polymers6274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-44 kcal/mol
Surface area16170 Å2
MethodPISA
2
C: Actin, alpha skeletal muscle
D: Cordon-Bleu WH2 motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0577
Polymers43,3892
Non-polymers6675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-47 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.861, 40.832, 109.000
Angle α, β, γ (deg.)90.000, 101.760, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRARGARGAA5 - 3721 - 368
21THRTHRARGARGCC5 - 3721 - 368
12SERSERVALVALBB66 - 871 - 22
22SERSERVALVALDD66 - 871 - 22

NCS ensembles :
ID
1
2

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Components

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


Mass: 40994.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein/peptide Cordon-Bleu WH2 motif


Mass: 2394.774 Da / Num. of mol.: 2 / Mutation: MET72NLE / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q5NBX1*PLUS
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / 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.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 615 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 20mM MES pH 4.9, 0.2mM CaCl2,2H2O, 20%(w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→29.82 Å / Num. obs: 51425 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.054 / Rrim(I) all: 0.103 / Χ2: 0.893 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.10.52925170.80.3530.6390.84597.4
2.03-2.073.20.47725210.850.3160.5750.94699.3
2.07-2.113.30.42325300.8860.2730.5050.88699.6
2.11-2.153.50.36425660.9230.2280.4310.87399.7
2.15-2.23.50.36825240.9140.230.4360.91499.9
2.2-2.253.60.30325910.9350.1860.3571.0199.8
2.25-2.313.70.27425350.9570.1670.3220.96199.7
2.31-2.373.70.23125780.9710.1390.270.91499.9
2.37-2.443.70.22225300.9710.1340.260.88899.6
2.44-2.523.70.1825670.9860.1090.2110.8899.9
2.52-2.613.70.1625690.9850.0970.1880.87699.7
2.61-2.713.70.13225890.9870.080.1550.85399.8
2.71-2.843.70.10225360.9930.0620.120.83899.5
2.84-2.993.70.08625880.9950.0520.1010.84799.8
2.99-3.173.70.06625860.9960.040.0780.84899.8
3.17-3.423.70.05625950.9970.0340.0660.99799.7
3.42-3.763.60.04725790.9970.0290.0551.11399.7
3.76-4.313.60.03325730.9990.020.0390.8399.2
4.31-5.423.50.02926140.9990.0180.0340.71498.9
5.42-303.60.0327370.9980.0190.0360.82499.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JHD

4jhd


Resolution: 2→29.82 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.219 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.183
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 2490 5 %RANDOM
Rwork0.193 ---
obs0.1954 47762 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.64 Å2 / Biso mean: 29.67 Å2 / Biso min: 14.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 69 615 6522
Biso mean--19.13 35.34 -
Num. residues----749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196056
X-RAY DIFFRACTIONr_bond_other_d0.0030.025735
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9788219
X-RAY DIFFRACTIONr_angle_other_deg0.944313242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6655751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74723.984256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.487151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9891536
X-RAY DIFFRACTIONr_chiral_restr0.080.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216731
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021323
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A215790.09
12C215790.09
21B10430.13
22D10430.13
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 149 -
Rwork0.28 2840 -
all-2989 -
obs--78.18 %

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