[English] 日本語
Yorodumi
- PDB-5ypu: Crystal structure of an actin monomer in complex with the nucleat... -

+
Open data


ID or keywords:

Loading...

-
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 / embryonic axis specification / actin crosslink formation / notochord development / collateral sprouting in absence of injury / positive regulation of ruffle assembly / digestive tract development / positive regulation of dendrite development ...somite specification / floor plate development / actin filament network formation / embryonic axis specification / actin crosslink formation / notochord development / collateral sprouting in absence of injury / positive regulation of ruffle assembly / digestive tract development / positive regulation of dendrite development / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle / dendritic growth cone / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / axonal growth cone / stress fiber / skeletal muscle fiber development / ruffle / titin binding / actin filament polymerization / liver development / filopodium / actin filament / neural tube closure / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / actin cytoskeleton organization / cell cortex / cytoskeleton / 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 / identical protein binding / membrane / 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: _ / Refine code: _

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

-
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


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more