[English] 日本語
Yorodumi
- PDB-7c2g: Crystal Structure of the Thorarchaeota 2DGel/rabbit actin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c2g
TitleCrystal Structure of the Thorarchaeota 2DGel/rabbit actin complex
Components
  • 2DGel3
  • Actin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / actin regulator
Function / homology
Function and homology information


actin filament severing / podosome / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly ...actin filament severing / podosome / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / 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 / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / lamellipodium / cell junction / 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
Adseverin / Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site ...Adseverin / Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Adseverin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Candidatus Thorarchaeota archaeon SMTZ1-83 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 Å
AuthorsRobinson, R.C. / Akil, C.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20H00476 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea
Authors: Akil, C. / Tran, L.T. / Orhant-Prioux, M. / Baskaran, Y. / Manser, E. / Blanchoin, L. / Robinson, R.C.
History
DepositionMay 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Jan 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Actin, alpha skeletal muscle
G: 2DGel3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,03410
Polymers65,2472
Non-polymers7888
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-100 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.854, 101.343, 55.765
Angle α, β, γ (deg.)90.000, 96.620, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 42109.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli) / References: UniProt: P68135
#2: Protein 2DGel3


Mass: 23136.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Skeletal muscle
Source: (gene. exp.) Candidatus Thorarchaeota archaeon SMTZ1-83 (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A135VHY8
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M Bis-Tris pH 5.5 0.2 M magnesium chloride hexahydrate 25% w/v polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 60879 / % possible obs: 98 % / Redundancy: 6.6 % / Biso Wilson estimate: 14.16 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.042 / Rrim(I) all: 0.108 / Χ2: 0.923 / Net I/σ(I): 12 / Num. measured all: 403297
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.734.50.91428930.6320.4551.0260.64492.5
1.73-1.765.10.81629340.7360.3810.9040.66796.2
1.76-1.795.60.7630230.7790.3390.8350.69696.2
1.79-1.836.10.65429880.8380.2840.7150.75297.1
1.83-1.876.40.58730090.880.2480.6380.79297.4
1.87-1.916.70.51130400.9230.2130.5540.84597.8
1.91-1.966.90.40630040.9390.1670.4390.90497.7
1.96-2.027.10.33930280.9580.1380.3660.98197.9
2.02-2.077.10.27230450.9670.1110.2941.02298.4
2.07-2.147.10.23330280.9740.0950.2511.08298.1
2.14-2.227.10.18730490.9810.0770.2021.08298.4
2.22-2.3170.15530620.9850.0650.1691.10698.5
2.31-2.4170.12630630.9880.0530.1361.03698.6
2.41-2.5470.10430610.9880.0440.1131.01998.9
2.54-2.770.08530640.9930.0360.0930.96999.1
2.7-2.96.90.07431210.9940.0310.0810.90299.3
2.9-3.26.90.06530730.9950.0270.0710.84299.5
3.2-3.666.90.05631060.9970.0240.0610.74699.7
3.66-4.66.90.06631220.9910.0270.0720.80899.7
4.6-206.90.08831660.9850.0360.0951.24199.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBT

3hbt


Resolution: 1.71→19.862 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.61
RfactorNum. reflection% reflection
Rfree0.2027 2802 4.82 %
Rwork0.1686 --
obs0.1703 58175 92.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.01 Å2 / Biso mean: 25.4049 Å2 / Biso min: 3.8 Å2
Refinement stepCycle: final / Resolution: 1.71→19.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4436 0 38 557 5031
Biso mean--15.57 34.55 -
Num. residues----557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7105-1.740.2644770.2241135446
1.74-1.77160.29931020.2197207869
1.7716-1.80560.22741170.2006233777
1.8056-1.84250.2321360.2068251486
1.8425-1.88250.25491320.2087277593
1.8825-1.92620.24261500.2286296
1.9262-1.97440.25941410.1821291298
1.9744-2.02770.20741550.1735292098
2.0277-2.08730.19151450.1691290198
2.0873-2.15460.22761400.1669296998
2.1546-2.23150.21571460.1706294599
2.2315-2.32070.2061550.1704294198
2.3207-2.42620.20581470.1728293699
2.4262-2.55380.22491520.1718294999
2.5538-2.71350.24361470.1692296199
2.7135-2.92240.19761570.173298899
2.9224-3.21540.20821360.1662980100
3.2154-3.67810.17781590.14743003100
3.6781-4.62430.14721620.13612997100
4.6243-19.8620.19021460.17283051100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.70080.2097-0.11210.89530.19131.65070.12370.05930.6435-0.34840.07760.229-0.471-0.2440.47480.16720.0377-0.01530.0790.07650.145455.316227.579313.0005
20.6087-0.1732-0.08440.72690.2420.4734-0.04270.08320.0674-0.16950.02030.2148-0.0665-0.2016-0.01190.10410.0049-0.04170.14770.03570.120250.592615.018816.3527
30.6550.4276-0.22821.4941-0.05690.71720.0042-0.08690.00330.0824-0.0042-0.08090.01050.0425-0.00490.04550.01110.00230.09940.00190.082572.791214.054227.8531
41.074-0.3439-0.50220.55660.00980.4816-0.07170.0788-0.2607-0.3005-0.05810.44770.1758-0.3417-0.39940.1309-0.0766-0.07210.1911-0.02210.234647.02296.657210.7448
50.87960.02330.05740.5403-0.04441.28720.09090.1189-0.3954-0.6116-0.003-0.29840.5293-0.06410.23990.3326-0.05680.11870.0917-0.05470.090662.5345-10.41057.6877
60.4639-0.0583-0.13760.6856-0.49590.4512-0.13650.46070.1662-0.76830.26410.1027-0.1052-0.13810.01750.4921-0.16940.01520.22250.07440.183369.455434.63931.5802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 68 )A5 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 165 )A69 - 165
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 334 )A166 - 334
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 372 )A335 - 372
5X-RAY DIFFRACTION5chain 'G' and (resid 2 through 106 )G2 - 106
6X-RAY DIFFRACTION6chain 'G' and (resid 107 through 197 )G107 - 197

+
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