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- PDB-8as9: Crystal structure of the talin-KANK1 complex -

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Basic information

Entry
Database: PDB / ID: 8as9
TitleCrystal structure of the talin-KANK1 complex
Components
  • B-cell lymphoma 6 protein
  • KN-motif NCoR1 BBD fusion,Nuclear receptor corepressor 1
  • Talin-1
KeywordsCELL INVASION / Cell-Migration / Talin / KANK / Focal Adhesions
Function / homology
Function and homology information


negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / NR1D1 (REV-ERBA) represses gene expression / podocyte cell migration / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / Smooth Muscle Contraction / Loss of MECP2 binding ability to the NCoR/SMRT complex / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / NR1D1 (REV-ERBA) represses gene expression / podocyte cell migration / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / Smooth Muscle Contraction / Loss of MECP2 binding ability to the NCoR/SMRT complex / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / negative regulation of substrate adhesion-dependent cell spreading / MAP2K and MAPK activation / regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / LIM domain binding / negative regulation of androgen receptor signaling pathway / Platelet degranulation / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation / negative regulation of actin filament polymerization / plasma cell differentiation / vinculin binding / paraspeckles / germinal center formation / integrin activation / regulation of immune system process / pyramidal neuron differentiation / regulation of Rho protein signal transduction / negative regulation of JNK cascade / type 2 immune response / T-helper 2 cell differentiation / positive regulation of regulatory T cell differentiation / cell-substrate junction assembly / negative regulation of B cell apoptotic process / positive regulation of cell motility / negative regulation of glycolytic process / regulation of establishment of cell polarity / nuclear thyroid hormone receptor binding / negative regulation of Rho protein signal transduction / cortical actin cytoskeleton organization / FOXO-mediated transcription of cell death genes / negative regulation of cell-matrix adhesion / negative regulation of fatty acid metabolic process / positive regulation of wound healing / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / regulation of T cell proliferation / negative regulation of Notch signaling pathway / regulation of cell differentiation / Notch-HLH transcription pathway / B cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / phosphatidylserine binding / locomotor rhythm / negative regulation of cellular senescence / histone deacetylase complex / Rho protein signal transduction / Regulation of MECP2 expression and activity / positive regulation of Wnt signaling pathway / regulation of immune response / spindle assembly / erythrocyte development / positive regulation of B cell proliferation / Nuclear signaling by ERBB4 / negative regulation of insulin receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / ruffle / regulation of cytokine production / transcription repressor complex / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / phosphatidylinositol binding / cell-matrix adhesion / transcription corepressor binding / negative regulation of miRNA transcription / negative regulation of cell migration / integrin-mediated signaling pathway / nuclear receptor binding / cell motility / HDACs deacetylate histones / adherens junction / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Heme signaling / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / heterochromatin formation / PPARA activates gene expression / Cytoprotection by HMOX1 / negative regulation of cell growth / chromatin DNA binding / structural constituent of cytoskeleton / NOTCH1 Intracellular Domain Regulates Transcription / mitotic spindle / cell-cell adhesion / DNA-binding transcription repressor activity, RNA polymerase II-specific
Similarity search - Function
: / Kank N-terminal motif / KN motif / : / Talin, R4 domain / N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Vinculin-binding site-containing domain / Talin, central ...: / Kank N-terminal motif / KN motif / : / Talin, R4 domain / N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain / N-terminal or F0 domain of Talin-head FERM / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / Alpha-catenin/vinculin-like superfamily / FERM domain signature 1. / FERM conserved site / SANT domain profile. / FERM domain signature 2. / SANT domain / Myb domain / Myb-like DNA-binding domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / FERM central domain / SANT/Myb domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Homeobox-like domain superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Nuclear receptor corepressor 1 / Talin-1 / B-cell lymphoma 6 protein / KN motif and ankyrin repeat domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsZacharchenko, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: Open Biology / Year: 2023
Title: The structural basis of the talin-KANK1 interaction that coordinates the actin and microtubule cytoskeletons at focal adhesions.
Authors: Li, X. / Goult, B.T. / Ballestrem, C. / Zacharchenko, T.
History
DepositionAug 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 15, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B-cell lymphoma 6 protein
B: B-cell lymphoma 6 protein
D: KN-motif NCoR1 BBD fusion,Nuclear receptor corepressor 1
C: Talin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0399
Polymers69,5624
Non-polymers4765
Water00
1
A: B-cell lymphoma 6 protein
B: B-cell lymphoma 6 protein
D: KN-motif NCoR1 BBD fusion,Nuclear receptor corepressor 1
C: Talin-1
hetero molecules

A: B-cell lymphoma 6 protein
B: B-cell lymphoma 6 protein
D: KN-motif NCoR1 BBD fusion,Nuclear receptor corepressor 1
C: Talin-1
hetero molecules

A: B-cell lymphoma 6 protein
B: B-cell lymphoma 6 protein
D: KN-motif NCoR1 BBD fusion,Nuclear receptor corepressor 1
C: Talin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,11627
Polymers208,68712
Non-polymers1,42915
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area41040 Å2
ΔGint-439 kcal/mol
Surface area80460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.022, 207.022, 151.859
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11C-1702-

SO4

21C-1702-

SO4

31C-1703-

SO4

41C-1703-

SO4

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Components

#1: Protein B-cell lymphoma 6 protein / BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing ...BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing protein 27 / Zinc finger protein 51


Mass: 15602.981 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Recombinant Protein / Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P41182
#2: Protein KN-motif NCoR1 BBD fusion,Nuclear receptor corepressor 1 / N-CoR / N-CoR1


Mass: 5781.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8BRZ8, UniProt: O75376
#3: Protein Talin-1


Mass: 32574.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Production host: Escherichia coli (E. coli) / References: UniProt: P26039
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestN

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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: 4.9 Å3/Da / Density % sol: 73.6 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1M Ammonium sulfate, 0.1M CHES 9.5, 0.2M Sodium chloride, 6 % (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.4→61.89 Å / Num. obs: 17332 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 107.38 Å2 / CC1/2: 0.9 / Net I/σ(I): 2.9
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 21.8 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2505 / CC1/2: 0.289 / Rpim(I) all: 1.356 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XYX

6xyx


Resolution: 3.4→59.76 Å / SU ML: 0.66 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2855 866 5.03 %
Rwork0.2451 16356 -
obs0.2472 17222 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 357.18 Å2 / Biso mean: 127.6639 Å2 / Biso min: 57.24 Å2
Refinement stepCycle: final / Resolution: 3.4→59.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4649 0 26 0 4675
Biso mean--121.78 --
Num. residues----602
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.610.40271370.39322634277197
3.61-3.890.3181450.318927032848100
3.89-4.280.29681280.24927312859100
4.28-4.90.24461370.206327502887100
4.9-6.170.29311580.256527282886100
6.18-59.760.26511610.207328102971100
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)
13.44660.02480.20773.42391.37213.9384-0.0671-0.17720.1925-0.0780.3348-0.2572-0.170.6668-0.25150.67310.05180.06680.687-0.05840.856830.0931-36.210955.1051
23.2048-1.0371-0.18011.7738-0.06552.14990.0692-0.0956-0.17820.11550.11260.2152-0.0311-0.5248-0.21090.70140.01780.03060.5615-0.0580.865310.4701-36.199258.8752
31.0889-0.72520.06881.31830.15330.0446-0.2441-0.05550.046-0.2070.4712-0.69640.1028-0.4076-0.19361.49370.16120.28361.7382-0.06411.520519.9066-27.652936.6773
40.78750.2951-0.00071.7449-1.17433.335-0.22940.1997-0.3393-0.46440.16290.51640.059-1.21930.090.94910.09150.01651.2111-0.15811.1172-9.0384-20.637844.7821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 127)A7 - 127
2X-RAY DIFFRACTION2(chain 'B' and resid -4 through 128)B-4 - 128
3X-RAY DIFFRACTION3(chain 'D' and resid 1 through 51)D1 - 51
4X-RAY DIFFRACTION4(chain 'C' and resid 1354 through 1659)C1354 - 1659

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