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- PDB-4z6g: Structure of NT domain -

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Basic information

Entry
Database: PDB / ID: 4z6g
TitleStructure of NT domain
ComponentsMicrotubule-actin cross-linking factor 1, isoforms 1/2/3/5
KeywordsCELL ADHESION / cytoskeleton / cell migration / microtubule / Focal adhesion
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
PHOSPHATE ION / Microtubule-actin cross-linking factor 1, isoforms 1/2/3/4/5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.654 Å
AuthorsYang, F. / Zhang, Y.
CitationJournal: Nat Commun / Year: 2016
Title: In vivo epidermal migration requires focal adhesion targeting of ACF7.
Authors: Jiping Yue / Yao Zhang / Wenguang G Liang / Xuewen Gou / Philbert Lee / Han Liu / Wanqing Lyu / Wei-Jen Tang / Shao-Yu Chen / Feng Yang / Hong Liang / Xiaoyang Wu /
Abstract: Turnover of focal adhesions allows cell retraction, which is essential for cell migration. The mammalian spectraplakin protein, ACF7 (Actin-Crosslinking Factor 7), promotes focal adhesion dynamics by ...Turnover of focal adhesions allows cell retraction, which is essential for cell migration. The mammalian spectraplakin protein, ACF7 (Actin-Crosslinking Factor 7), promotes focal adhesion dynamics by targeting of microtubule plus ends towards focal adhesions. However, it remains unclear how the activity of ACF7 is regulated spatiotemporally to achieve focal adhesion-specific guidance of microtubule. To explore the potential mechanisms, we resolve the crystal structure of ACF7's NT (amino-terminal) domain, which mediates F-actin interactions. Structural analysis leads to identification of a key tyrosine residue at the calponin homology (CH) domain of ACF7, whose phosphorylation by Src/FAK (focal adhesion kinase) complex is essential for F-actin binding of ACF7. Using skin epidermis as a model system, we further demonstrate that the phosphorylation of ACF7 plays an indispensable role in focal adhesion dynamics and epidermal migration in vitro and in vivo. Together, our findings provide critical insights into the molecular mechanisms underlying coordinated cytoskeletal dynamics during cell movement.
History
DepositionApr 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,0043
Polymers40,8141
Non-polymers1902
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.088, 94.088, 192.634
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 40813.672 Da / Num. of mol.: 1 / Fragment: NT domain (UNP RESIDUES 74-421)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MACF1, ABP620, ACF7, KIAA0465, KIAA1251 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UPN3
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.22 Å3/Da / Density % sol: 76.45 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES, (NH4)2SO4, (NH4)2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. obs: 27500 / % possible obs: 98 % / Redundancy: 4 % / Net I/σ(I): 4.6

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Processing

Software
NameVersionClassification
PHENIX1.6_289refinement
SHELXLdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F7P, 2ODV

3f7p

2odv


Resolution: 2.654→24.175 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 1305 5.1 %
Rwork0.2084 --
obs0.2101 25589 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.373 Å2 / ksol: 0.299 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4517 Å20 Å2-0 Å2
2--1.4517 Å20 Å2
3----2.9034 Å2
Refinement stepCycle: LAST / Resolution: 2.654→24.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 10 24 2791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082820
X-RAY DIFFRACTIONf_angle_d1.0813802
X-RAY DIFFRACTIONf_dihedral_angle_d17.7531072
X-RAY DIFFRACTIONf_chiral_restr0.079414
X-RAY DIFFRACTIONf_plane_restr0.004485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.654-2.76010.34591280.30852601X-RAY DIFFRACTION97
2.7601-2.88550.32211250.27772669X-RAY DIFFRACTION100
2.8855-3.03740.31081570.26052658X-RAY DIFFRACTION100
3.0374-3.22730.28831500.25872660X-RAY DIFFRACTION100
3.2273-3.47580.27881360.23752684X-RAY DIFFRACTION100
3.4758-3.82440.23191580.1962671X-RAY DIFFRACTION100
3.8244-4.37490.22171530.17092687X-RAY DIFFRACTION99
4.3749-5.50120.19541570.17032758X-RAY DIFFRACTION100
5.5012-24.17620.22551410.20732896X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -33.3917 Å / Origin y: 1.3079 Å / Origin z: -33.2468 Å
111213212223313233
T0.5982 Å2-0.0538 Å20.0243 Å2-0.4001 Å2-0.0303 Å2--0.4506 Å2
L1.076 °2-0.3131 °20.8761 °2-0.6726 °2-1.239 °2--1.4686 °2
S-0.0274 Å °0.0739 Å °-0.036 Å °-0.1793 Å °0.1455 Å °-0.0511 Å °0.2755 Å °-0.1032 Å °-0.1072 Å °
Refinement TLS groupSelection details: ALL

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