[English] 日本語
Yorodumi
- PDB-6bz3: Complex structure of FAK FAT domain and DCC P3 motif -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bz3
TitleComplex structure of FAK FAT domain and DCC P3 motif
Components
  • Focal adhesion kinase 1
  • Netrin receptor DCC
KeywordsTRANSFERASE/MEMBRANE PROTEIN / 4-helix bundle / axon guidance / focal adhesion kinase / transferase-peptide complex / MEMBRANE PROTEIN / TRANSFERASE-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


Netrin-1 signaling / DCC mediated attractive signaling / Caspase activation via Dependence Receptors in the absence of ligand / DCC mediated attractive signaling / Apoptotic cleavage of cellular proteins / netrin receptor activity / MET activates PTK2 signaling / dorsal/ventral axon guidance / NCAM signaling for neurite out-growth / negative regulation of synapse assembly ...Netrin-1 signaling / DCC mediated attractive signaling / Caspase activation via Dependence Receptors in the absence of ligand / DCC mediated attractive signaling / Apoptotic cleavage of cellular proteins / netrin receptor activity / MET activates PTK2 signaling / dorsal/ventral axon guidance / NCAM signaling for neurite out-growth / negative regulation of synapse assembly / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / central nervous system neuron axonogenesis / EPHB-mediated forward signaling / RHO GTPases Activate WASPs and WAVEs / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Extra-nuclear estrogen signaling / RAF/MAP kinase cascade / negative regulation of axonogenesis / growth cone membrane / negative regulation of organ growth / Regulation of actin dynamics for phagocytic cup formation / corpus callosum development / regulation of modification of postsynaptic actin cytoskeleton / VEGFA-VEGFR2 Pathway / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / nuclear migration / organ growth / optic nerve development / regulation of osteoblast differentiation / blood vessel development / axon development / positive regulation of cardiac muscle hypertrophy / regulation of cell adhesion mediated by integrin / ephrin receptor signaling pathway / positive regulation of protein kinase activity / endothelial cell migration / postsynaptic modulation of chemical synaptic transmission / vasculogenesis / cellular response to transforming growth factor beta stimulus / extracellular matrix organization / response to amphetamine / negative regulation of autophagy / axonogenesis / axon guidance / integrin-mediated signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / postsynaptic density membrane / peptidyl-tyrosine phosphorylation / Schaffer collateral - CA1 synapse / cerebral cortex development / cell-cell adhesion / positive regulation of neuron projection development / microtubule cytoskeleton organization / neuron migration / cell migration / lamellipodium / regulation of cell shape / regulation of cell population proliferation / positive regulation of protein phosphorylation / cell cortex / protein autophosphorylation / protein tyrosine kinase activity / angiogenesis / transcription coactivator activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / ciliary basal body / positive regulation of cell migration / apical plasma membrane / axon / focal adhesion / apoptotic process / positive regulation of cell population proliferation / centrosome / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Neogenin, C-terminal / Neogenin C-terminus / Nucleotidyltransferases domain 2 / Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : ...Neogenin, C-terminal / Neogenin C-terminus / Nucleotidyltransferases domain 2 / Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM domain signature 2. / Immunoglobulin domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Focal adhesion kinase 1 / Netrin receptor DCC
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsXu, S. / Wang, J.-H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01HL103526 United States
CitationJournal: Cell Discov / Year: 2018
Title: The binding of DCC-P3 motif and FAK-FAT domain mediates the initial step of netrin-1/DCC signaling for axon attraction.
Authors: Xu, S. / Liu, Y. / Li, X. / Liu, Y. / Meijers, R. / Zhang, Y. / Wang, J.H.
History
DepositionDec 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Focal adhesion kinase 1
B: Netrin receptor DCC
C: Focal adhesion kinase 1
D: Netrin receptor DCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9585
Polymers32,9184
Non-polymers401
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-77 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.178, 36.130, 65.429
Angle α, β, γ (deg.)90.000, 104.300, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Focal adhesion kinase 1 / FADK 1 / Focal adhesion kinase-related nonkinase / FRNK / Protein-tyrosine kinase 2 / p125FAK / pp125FAK


Mass: 14006.386 Da / Num. of mol.: 2 / Fragment: FAT domain residues 959-1084
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptk2, Fadk, Fak, Fak1, Kiaa4203 / Plasmid: pET28Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P34152, non-specific protein-tyrosine kinase
#2: Protein/peptide Netrin receptor DCC / Tumor suppressor protein DCC


Mass: 2452.735 Da / Num. of mol.: 2 / Fragment: P3 motif residues 1421-1443 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q63155
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris pH8.5, 20% (w/v) PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.497→50 Å / Num. obs: 10318 / % possible obs: 98.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.2
Reflection shellResolution: 2.497→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2 / Num. unique obs: 978 / % possible all: 93.4

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.10_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OW6

1ow6


Resolution: 2.497→39.889 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.88
RfactorNum. reflection% reflection
Rfree0.2686 496 4.81 %
Rwork0.226 --
obs0.2278 10314 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.84 Å2 / Biso mean: 64.3044 Å2 / Biso min: 29.89 Å2
Refinement stepCycle: final / Resolution: 2.497→39.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 1 12 2230
Biso mean--81.48 53.76 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062243
X-RAY DIFFRACTIONf_angle_d0.5733017
X-RAY DIFFRACTIONf_chiral_restr0.03371
X-RAY DIFFRACTIONf_plane_restr0.005381
X-RAY DIFFRACTIONf_dihedral_angle_d17.7111433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4974-2.74870.32051250.28962336246195
2.7487-3.14630.34281260.297824462572100
3.1463-3.96340.2581300.231424722602100
3.9634-39.89440.23551150.190625642679100
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)
12.8764-0.4676-1.86241.32811.65423.55590.3230.0486-0.0287-0.0408-0.4711-0.59830.36750.44860.01190.45220.0895-0.03340.43090.09590.3948-25.38165.177826.1822
23.0832-0.979-0.59973.26420.22652.69420.21830.2834-0.0437-0.2031-0.07650.1487-0.1201-0.2097-0.14670.338-0.01520.04640.3024-0.0180.3401-6.3982-1.46687.4161
31.9281-0.3224-1.01286.4448-2.3642.539-0.02190.0715-0.78190.0002-0.40340.48990.6495-0.64420.16720.57190.00120.02760.6008-0.0090.8669-20.7631-6.64819.666
43.7667-2.0487-1.36631.46411.63562.1801-0.2505-0.3579-0.1450.09310.2332-0.2337-0.0779-0.5156-0.06240.46720.02590.03940.30530.0310.4139-14.8693-2.505914.7046
52.87210.53191.46211.9711.21884.31340.3136-0.1172-0.1614-0.016-0.08240.07670.3353-1.30440.04980.4114-0.0282-0.00530.57810.02150.396-36.05276.024829.8777
63.97930.8827-1.27511.78621.81695.90850.2220.85610.5353-0.6624-0.6999-1.1484-0.90860.8612-0.15660.7001-0.07980.19450.7576-0.02320.6969-23.75114.296924.9765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 922 through 946 )A922 - 946
2X-RAY DIFFRACTION2chain 'A' and (resid 947 through 1046 )A947 - 1046
3X-RAY DIFFRACTION3chain 'B' and (resid 1423 through 1440 )B0
4X-RAY DIFFRACTION4chain 'C' and (resid 922 through 946 )C922 - 946
5X-RAY DIFFRACTION5chain 'C' and (resid 947 through 1046 )C947 - 1046
6X-RAY DIFFRACTION6chain 'D' and (resid 1423 through 1441 )D0

+
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