[English] 日本語
Yorodumi
- PDB-4b1x: Structure of the Phactr1 RPEL-2 bound to G-actin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b1x
TitleStructure of the Phactr1 RPEL-2 bound to G-actin
Components
  • ACTIN, ALPHA SKELETAL MUSCLE
  • PHOSPHATASE AND ACTIN REGULATOR 1
KeywordsSTRUCTURAL PROTEIN / NUCLEOTIDE-BINDING / TRANSCRIPTION REGULATION / TRANSCRIPTION / MUSCLE PROTEIN / ATP-BINDING / CYTOSKELETON
Function / homology
Function and homology information


dendrite arborization / protein phosphatase 1 binding / regulation of neuron migration / actomyosin structure organization / regulation of phosphorylation / protein phosphatase inhibitor activity / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / stress fiber assembly ...dendrite arborization / protein phosphatase 1 binding / regulation of neuron migration / actomyosin structure organization / regulation of phosphorylation / protein phosphatase inhibitor activity / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / stress fiber assembly / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / stress fiber / skeletal muscle fiber development / titin binding / actin filament polymerization / filopodium / cell motility / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cerebral cortex development / calcium-dependent protein binding / lamellipodium / actin binding / cell body / actin cytoskeleton organization / hydrolase activity / protein domain specific binding / calcium ion binding / synapse / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. ...RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / 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 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / Phosphatase and actin regulator 1 / Actin, alpha skeletal muscle / Phosphatase and actin regulator 1
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMouilleron, S. / Wiezlak, M. / O'Reilly, N. / Treisman, R. / McDonald, N.Q.
CitationJournal: Structure / Year: 2012
Title: Structures of the Phactr1 RPEL domain and RPEL motif complexes with G-actin reveal the molecular basis for actin binding cooperativity.
Authors: Mouilleron, S. / Wiezlak, M. / O'Reilly, N. / Treisman, R. / McDonald, N.Q.
History
DepositionJul 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Apr 25, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4Jun 20, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: ACTIN, ALPHA SKELETAL MUSCLE
M: PHOSPHATASE AND ACTIN REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7615
Polymers45,8342
Non-polymers9273
Water3,801211
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-29.3 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.280, 77.280, 130.809
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules BM

#1: Protein ACTIN, ALPHA SKELETAL MUSCLE / ALPHA SKELETAL MUSCLE ACTIN / ALPHA-ACTIN-1


Mass: 41965.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: MUSCLE / References: UniProt: P68135
#2: Protein/peptide PHOSPHATASE AND ACTIN REGULATOR 1 / PHOSPHATASE AND ACTIN REGULATOR 1 / ISOFORM CRA_C


Mass: 3868.409 Da / Num. of mol.: 1 / Fragment: RESIDUES 524-555 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: G5E8P7, UniProt: Q2M3X8*PLUS

-
Non-polymers , 4 types, 214 molecules

#3: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29NO5S / Comment: toxin*YM
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: ID23-1 / Type: DIAMOND / Wavelength: 0.9763
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 69989 / % possible obs: 98.7 % / Observed criterion σ(I): 1.1 / Redundancy: 5.6 % / Biso Wilson estimate: 26.16 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.1 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V52

2v52


Resolution: 1.8→38.64 Å / SU ML: 0.19 / σ(F): 1.42 / Phase error: 21.06 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2127 2058 5.1 %
Rwork0.1688 --
obs0.171 40540 95.19 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 2 Å2 / ksol: 2 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→38.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 59 211 3265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073185
X-RAY DIFFRACTIONf_angle_d1.1284346
X-RAY DIFFRACTIONf_dihedral_angle_d19.8871260
X-RAY DIFFRACTIONf_chiral_restr0.077493
X-RAY DIFFRACTIONf_plane_restr0.005551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84190.32281160.2352335X-RAY DIFFRACTION88
1.8419-1.88790.28731420.23342384X-RAY DIFFRACTION90
1.8879-1.9390.27141330.20812409X-RAY DIFFRACTION92
1.939-1.9960.24471480.19612523X-RAY DIFFRACTION95
1.996-2.06050.25461490.19172556X-RAY DIFFRACTION96
2.0605-2.13410.2571420.18912543X-RAY DIFFRACTION96
2.1341-2.21950.24941270.18012604X-RAY DIFFRACTION97
2.2195-2.32050.23711100.18352631X-RAY DIFFRACTION98
2.3205-2.44290.20811320.17012639X-RAY DIFFRACTION98
2.4429-2.59590.24531480.17842584X-RAY DIFFRACTION97
2.5959-2.79630.23981420.17252643X-RAY DIFFRACTION97
2.7963-3.07760.2261530.17592615X-RAY DIFFRACTION97
3.0776-3.52260.18981510.16892656X-RAY DIFFRACTION97
3.5226-4.43710.18091280.13922626X-RAY DIFFRACTION96
4.4371-38.64890.16891370.15282734X-RAY DIFFRACTION94
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)
14.01830.32140.36616.3832-1.96885.4981-0.0096-0.2098-0.45220.0210.1613-0.58220.20280.295-0.15270.13950.02440.00240.2176-0.08370.28476.8176-43.902211.1065
24.5016-0.3895-3.44180.2092-0.02184.22110.49760.64770.5962-0.8218-0.1392-1.0099-0.34221.1673-0.34540.5070.01330.25660.4913-0.10840.456113.6855-34.9659-1.6975
32.7187-0.6217-0.60772.34780.40492.10090.11550.3418-0.2231-0.6239-0.0837-0.2545-0.1695-0.0017-0.02850.29050.01020.04590.2535-0.09860.2224.2873-40.9331.7019
44.23071.4403-1.10272.4553-0.35581.23980.01720.20140.385-0.33820.1265-0.1261-0.1773-0.0408-0.09410.20070.00690.04640.1751-0.05890.2318-0.0992-23.557210.4615
52.1686-0.1347-0.60691.19120.56251.15060.4488-0.02481.286-0.22040.04910.2481-0.47720.2326-0.0250.3486-0.07020.21050.2106-0.22620.56535.3359-11.08416.9436
65.8020.3785-0.51912.1862-0.00010.14920.0823-0.48610.15470.13980.03160.1911-0.0837-0.0246-0.11820.1554-0.00530.03920.2736-0.08110.1696-12.3639-27.514821.1628
72.0114-1.2772-0.48642.73331.01940.8470.0374-0.53610.1810.4026-0.10530.22450.0826-0.04730.0020.1596-0.00480.04610.3386-0.13230.2316-4.3272-30.307723.6135
84.61940.59243.18342.84192.9135.437-0.1204-0.1049-1.07850.3608-0.39770.69720.7965-0.70280.04970.3446-0.10660.03850.3145-0.16920.6451-8.7735-54.50846.9793
94.8786-0.4401-0.05613.93190.61512.2867-0.2156-0.4468-0.89430.1376-0.38470.41620.5796-0.09340.35280.218-0.00320.08160.35520.03410.3497-17.705-45.089219.3266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESSEQ 0:28)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 29:61)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 62:145)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 146:216)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 217:273)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 274:308)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 309:348)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 349:375)
9X-RAY DIFFRACTION9CHAIN M

+
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