[English] 日本語
Yorodumi
- PDB-7c2f: Crystal Structure of the Thorarchaeota ProGel/rabbit actin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c2f
TitleCrystal Structure of the Thorarchaeota ProGel/rabbit actin complex
Components
  • Actin, alpha skeletal muscle
  • Gelsolin-like domain-containing protein
KeywordsSTRUCTURAL PROTEIN / actin regulator
Function / homology
Function and homology information


cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / 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 / lamellipodium / 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
Severin / Severin / 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. ...Severin / Severin / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / Gelsolin-like domain-containing protein / 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: 2.03 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
B: Gelsolin-like domain-containing protein
C: Actin, alpha skeletal muscle
D: Gelsolin-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,89010
Polymers105,0364
Non-polymers1,8546
Water10,215567
1
A: Actin, alpha skeletal muscle
B: Gelsolin-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4455
Polymers52,5182
Non-polymers9273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Actin, alpha skeletal muscle
D: Gelsolin-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4455
Polymers52,5182
Non-polymers9273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.427, 108.626, 167.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 32 or resid 34...
21(chain C and (resid 5 through 32 or resid 34...
12(chain B and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))
22(chain D and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5 through 32 or resid 34...A5 - 32
121(chain A and (resid 5 through 32 or resid 34...A34 - 41
131(chain A and (resid 5 through 32 or resid 34...A51 - 59
141(chain A and (resid 5 through 32 or resid 34...A5 - 374
151(chain A and (resid 5 through 32 or resid 34...A5 - 374
161(chain A and (resid 5 through 32 or resid 34...A5 - 374
171(chain A and (resid 5 through 32 or resid 34...A298 - 374
181(chain A and (resid 5 through 32 or resid 34...A1376 - 1379
211(chain C and (resid 5 through 32 or resid 34...C5 - 32
221(chain C and (resid 5 through 32 or resid 34...C34 - 59
231(chain C and (resid 5 through 32 or resid 34...C5 - 374
241(chain C and (resid 5 through 32 or resid 34...C5 - 374
251(chain C and (resid 5 through 32 or resid 34...C142 - 2
261(chain C and (resid 5 through 32 or resid 34...C298 - 374
271(chain C and (resid 5 through 32 or resid 34...C1 - 374
281(chain C and (resid 5 through 32 or resid 34...C1376 - 1379
112(chain B and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))B1 - 49
122(chain B and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))B51 - 53
132(chain B and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))B55 - 88
212(chain D and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))D1 - 49
222(chain D and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))D51 - 53
232(chain D and (resid 1 through 49 or resid 51 through 53 or resid 55 through 88))D55 - 88

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ACBD

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


Mass: 41875.633 Da / Num. of mol.: 2
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 Gelsolin-like domain-containing protein


Mass: 10642.312 Da / Num. of mol.: 2
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: A0A135VMT5

-
Non-polymers , 4 types, 573 molecules

#3: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29NO5S
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M MES pH 6.0 0.2 M magnesium chloride hexahydrate 20% w/v polyethylene glycol 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→91.14 Å / Num. obs: 68445 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.048 / Rrim(I) all: 0.125 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1 / Resolution: 2.03→2.08 Å

Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
6.60.7942830.8930.3270.85693
5.70.0467670.9990.0210.05198.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBT

3hbt


Resolution: 2.03→48.59 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 3407 5 %RANDOM
Rwork0.199 64785 --
obs0.2006 68192 99.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 236.79 Å2 / Biso mean: 55.0174 Å2 / Biso min: 14.07 Å2
Refinement stepCycle: final / Resolution: 2.03→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7064 0 184 567 7815
Biso mean--28.44 43.1 -
Num. residues----899
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3432X-RAY DIFFRACTION5.92TORSIONAL
12C3432X-RAY DIFFRACTION5.92TORSIONAL
21B825X-RAY DIFFRACTION5.92TORSIONAL
22D825X-RAY DIFFRACTION5.92TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.060.29611220.28032429255189
2.06-2.090.31251230.270826402763100
2.09-2.120.29291800.25426882868100
2.12-2.160.2491400.249426382778100
2.16-2.190.26971260.244627052831100
2.19-2.230.2531530.243826622815100
2.23-2.280.29771560.239426482804100
2.28-2.320.24481290.230826882817100
2.32-2.370.24721290.221627082837100
2.37-2.430.24791580.22426542812100
2.43-2.490.26531400.211526852825100
2.49-2.560.23621340.210626922826100
2.56-2.630.24081300.207527252855100
2.63-2.720.25081300.207727122842100
2.72-2.810.21841580.209926912849100
2.81-2.930.27761310.209627272858100
2.93-3.060.21531560.19926912847100
3.06-3.220.22241490.196727292878100
3.22-3.420.2141320.193127392871100
3.42-3.690.21551640.191227072871100
3.69-4.060.22231430.169227532896100
4.06-4.640.18961360.15262762289899
4.64-5.850.21341470.165728072954100
5.85-48.590.21891410.19672905304698
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)
11.33220.28110.26093.5440.46331.8585-0.00480.0778-0.1617-0.43750.1083-0.42830.12030.2552-0.04640.1963-0.02990.05660.2462-0.00190.226646.621718.0561.6129
21.5666-0.37171.00331.1316-0.38632.3706-0.1525-0.120.05960.04040.0945-0.0352-0.12780.04630.06110.0944-0.0299-0.00020.2480.00230.2850.535435.172980.6943
31.01030.00780.20812.62980.0121.0293-0.07830.03570.0858-0.3870.06230.247-0.1186-0.0970.0310.1886-0.0226-0.07410.26560.02360.251235.985438.629165.6765
42.87990.80240.32850.22540.09880.6025-0.06481.09960.4678-1.32940.236-0.0813-1.07290.2455-0.18231.2286-0.1474-0.02590.73210.0050.409640.929618.415342.8871
53.46190.8194-0.33741.07681.52922.97530.2292-0.2585-0.46840.5825-0.24790.01420.8515-0.29570.00591.0642-0.3876-0.05971.2125-0.1480.682811.993434.698247.7875
60.055-0.07290.0020.0954-0.0030.0007-0.147-0.43330.44630.0105-0.0070.2794-0.3459-0.16940.1730.7243-0.05370.02131.5109-0.03931.32826.183142.321651.4739
71.3244-0.26380.14963.4148-0.89873.5055-0.0502-1.20860.2610.2792-0.15620.6438-0.5168-1.34030.22720.5478-0.007-0.12651.1532-0.07020.503214.924243.284250.3701
80.7783-0.1187-0.55750.29440.45750.91450.2813-1.0126-0.29910.19810.06270.00420.3255-0.318-0.32880.4946-0.1219-0.14080.93160.00490.434219.335839.806755.0639
91.8915-0.59180.96842.0944-1.24973.29040.5313-0.4451-0.6422-0.05110.01540.27160.9092-0.7611-0.51010.6585-0.119-0.09420.52460.0690.442322.097932.779648.0556
101.1405-0.2910.02610.988-0.10062.53460.1499-0.58640.32440.4784-0.21620.0129-0.4015-0.09270.10540.5060.041-0.12580.6784-0.13110.407422.073345.939749.0414
111.1442-1.50150.74252.3587-0.8531.97010.1261-0.03910.1877-0.01090.15930.7199-0.423-0.71-0.28050.82630.3712-0.27720.9299-0.34151.01413.901451.853653.7354
123.4083-0.6333-0.22492.8575-0.03142.76770.1258-0.0261-0.59250.2618-0.05250.38940.6886-0.2756-0.08590.639-0.04160.06740.25220.0120.36799.214413.839418.1032
131.26390.20450.30931.87220.73682.1688-0.1316-0.1187-0.04630.35540.03630.0060.3230.00740.08660.29470.04520.02750.1736-0.00790.193815.514532.330216.1985
142.0858-0.2411-0.22280.4856-0.87531.79330.23880.3771-0.52180.0562-0.2981-0.05720.29090.43310.03161.08760.213-0.12481.36350.06130.703746.875435.19236.1154
151.5609-0.2392-0.64611.2540.47532.21250.2860.36980.1297-0.26560.0089-0.0038-0.1649-0.1493-0.26510.85730.0257-0.07851.87620.16961.292452.413242.714332.0055
161.80790.7210.24632.23910.52534.51650.50151.4320.1052-0.4751-0.382-0.4805-0.87081.151-0.06450.79850.0313-0.00371.38280.14950.553944.116143.592333.3844
174.11610.1395-0.69042.08590.62823.82850.26631.2109-0.7389-0.2134-0.3471-0.23450.74131.10320.0650.73240.2439-0.10190.95240.00550.596138.037635.802731.2021
182.8735-0.2119-0.5972.18260.18422.3545-0.18750.1541-0.28660.0163-0.2421-0.0755-0.56420.43410.44250.5466-0.1209-0.08910.48350.05320.333337.671742.037446.1071
190.4351-0.2248-0.37811.79690.06854.0772-0.2290.79350.6642-0.2834-0.085-0.6754-1.12361.10910.27540.8897-0.1846-0.05461.08620.35560.572540.054148.924529.7111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 165 )A5 - 165
2X-RAY DIFFRACTION2chain 'A' and (resid 166 through 273 )A166 - 273
3X-RAY DIFFRACTION3chain 'A' and (resid 274 through 354 )A274 - 354
4X-RAY DIFFRACTION4chain 'A' and (resid 355 through 374 )A355 - 374
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 14 )B1 - 14
6X-RAY DIFFRACTION6chain 'B' and (resid 15 through 22 )B15 - 22
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 37 )B23 - 37
8X-RAY DIFFRACTION8chain 'B' and (resid 38 through 48 )B38 - 48
9X-RAY DIFFRACTION9chain 'B' and (resid 49 through 65 )B49 - 65
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 80 )B66 - 80
11X-RAY DIFFRACTION11chain 'B' and (resid 81 through 88 )B81 - 88
12X-RAY DIFFRACTION12chain 'C' and (resid 5 through 97 )C5 - 97
13X-RAY DIFFRACTION13chain 'C' and (resid 98 through 374 )C98 - 374
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 14 )D1 - 14
15X-RAY DIFFRACTION15chain 'D' and (resid 15 through 22 )D15 - 22
16X-RAY DIFFRACTION16chain 'D' and (resid 23 through 37 )D23 - 37
17X-RAY DIFFRACTION17chain 'D' and (resid 38 through 61 )D38 - 61
18X-RAY DIFFRACTION18chain 'D' and (resid 62 through 69 )D62 - 69
19X-RAY DIFFRACTION19chain 'D' and (resid 70 through 88 )D70 - 90

+
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