[English] 日本語
Yorodumi
- PDB-5x57: Structure of GAR domain of ACF7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x57
TitleStructure of GAR domain of ACF7
ComponentsMicrotubule-actin cross-linking factor 1, isoforms 1/2/3/5
KeywordsSIGNALING PROTEIN / functional class
Function / homology
Function and homology information


regulation of neuron projection arborization / hemidesmosome / microtubule minus-end binding / regulation of epithelial cell migration / intermediate filament cytoskeleton organization / Golgi to plasma membrane protein transport / regulation of microtubule-based process / intermediate filament / regulation of focal adhesion assembly / positive regulation of Wnt signaling pathway ...regulation of neuron projection arborization / hemidesmosome / microtubule minus-end binding / regulation of epithelial cell migration / intermediate filament cytoskeleton organization / Golgi to plasma membrane protein transport / regulation of microtubule-based process / intermediate filament / regulation of focal adhesion assembly / positive regulation of Wnt signaling pathway / positive regulation of axon extension / cytoplasmic microtubule organization / regulation of cell migration / wound healing / Wnt signaling pathway / ruffle membrane / actin filament binding / actin cytoskeleton / actin binding / microtubule / cytoskeleton / cadherin binding / calcium ion binding / structural molecule activity / Golgi apparatus / RNA binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Transcriptional regulator DELLA protein N terminal / GAR domain / GAR domain superfamily / Growth-Arrest-Specific Protein 2 Domain / GAR domain profile. / Growth-Arrest-Specific Protein 2 Domain / : / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat ...Transcriptional regulator DELLA protein N terminal / GAR domain / GAR domain superfamily / Growth-Arrest-Specific Protein 2 Domain / GAR domain profile. / Growth-Arrest-Specific Protein 2 Domain / : / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain / Plectin repeat / Plakin / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
NICKEL (II) ION / Microtubule-actin cross-linking factor 1, isoforms 1/2/3/4/5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.45 Å
AuthorsYang, F. / Wang, T. / Zhang, Y. / Wu, X.Y.
CitationJournal: Nat Commun / Year: 2017
Title: ACF7 regulates inflammatory colitis and intestinal wound response by orchestrating tight junction dynamics.
Authors: Ma, Y. / Yue, J. / Zhang, Y. / Shi, C. / Odenwald, M. / Liang, W.G. / Wei, Q. / Goel, A. / Gou, X. / Zhang, J. / Chen, S.Y. / Tang, W.J. / Turner, J.R. / Yang, F. / Liang, H. / Qin, H. / Wu, X.
History
DepositionFeb 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4802
Polymers9,4211
Non-polymers591
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5510 Å2
Unit cell
Length a, b, c (Å)74.040, 45.990, 25.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

-
Components

#1: Protein Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5 / Spectraplakin protein / 620 kDa actin-binding protein / ABP620 / Actin cross-linking family protein ...Spectraplakin protein / 620 kDa actin-binding protein / ABP620 / Actin cross-linking family protein 7 / Macrophin-1 / Trabeculin-alpha


Mass: 9420.826 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 7113-7193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MACF1, ABP620, ACF7, KIAA0465, KIAA1251
Production host: bacterial endosymbiont of Idas sp. (bacteria)
References: UniProt: Q9UPN3
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5 / Details: Sodium cacodylate trihydrate, (NH4)2SO4, PEG 4000

-
Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→28.84 Å / Num. obs: 16069 / % possible obs: 98 % / Redundancy: 4.4 % / Net I/σ(I): 30
Reflection shellRmerge(I) obs: 0.114 / Mean I/σ(I) obs: 3.5 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 1.45→28.838 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1652 1608 10.01 %
Rwork0.1261 --
obs0.1301 16069 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→28.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms657 0 1 126 784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023695
X-RAY DIFFRACTIONf_angle_d1.78934
X-RAY DIFFRACTIONf_dihedral_angle_d20.138279
X-RAY DIFFRACTIONf_chiral_restr0.10498
X-RAY DIFFRACTIONf_plane_restr0.012126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4501-1.49690.21440.11481286X-RAY DIFFRACTION98
1.4969-1.55040.16391420.10131290X-RAY DIFFRACTION100
1.5504-1.61250.161450.0991300X-RAY DIFFRACTION100
1.6125-1.68580.15171440.10011297X-RAY DIFFRACTION100
1.6858-1.77470.18541450.09691300X-RAY DIFFRACTION100
1.7747-1.88590.13811440.09651299X-RAY DIFFRACTION100
1.8859-2.03150.15271470.11231321X-RAY DIFFRACTION100
2.0315-2.23580.141480.11631324X-RAY DIFFRACTION100
2.2358-2.55920.17121480.11981340X-RAY DIFFRACTION100
2.5592-3.22360.17821490.1411336X-RAY DIFFRACTION99
3.2236-28.84360.17161520.16311368X-RAY DIFFRACTION95

+
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