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- PDB-6twn: Crystal structure of Talin1 R7R8 in complex with CDK1 (206-223) -

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Basic information

Entry
Database: PDB / ID: 6twn
TitleCrystal structure of Talin1 R7R8 in complex with CDK1 (206-223)
Components
  • Cyclin-dependent kinase 1
  • Talin-1
KeywordsCELL ADHESION / Talin / focal adhesions.
Function / homology
Function and homology information


regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly ...regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / ventricular cardiac muscle cell development / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / Depolymerization of the Nuclear Lamina / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / MASTL Facilitates Mitotic Progression / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / : / cyclin A2-CDK1 complex / Phosphorylation of Emi1 / LIM domain binding / Smooth Muscle Contraction / Platelet degranulation / Transcriptional regulation by RUNX2 / cortical microtubule organization / Phosphorylation of the APC/C / Nuclear Pore Complex (NPC) Disassembly / vinculin binding / integrin activation / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / protein localization to kinetochore / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity / RNA polymerase II CTD heptapeptide repeat S2 kinase activity / RNA polymerase II CTD heptapeptide repeat T4 kinase activity / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / RNA polymerase II CTD heptapeptide repeat S7 kinase activity / Initiation of Nuclear Envelope (NE) Reformation / cell-substrate junction assembly / response to copper ion / Golgi Cisternae Pericentriolar Stack Reorganization / Condensation of Prometaphase Chromosomes / centrosome cycle / chromosome condensation / [RNA-polymerase]-subunit kinase / cortical actin cytoskeleton organization / MAPK3 (ERK1) activation / phosphatidylserine binding / cyclin-dependent protein kinase activity / response to amine / G1/S-Specific Transcription / mitotic G2 DNA damage checkpoint signaling / : / Regulation of APC/C activators between G1/S and early anaphase / regulation of embryonic development / protein deubiquitination / response to axon injury / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin A/B1/B2 associated events during G2/M transition / response to cadmium ion / cyclin-dependent protein kinase holoenzyme complex / positive regulation of cardiac muscle cell proliferation / ruffle / positive regulation of G2/M transition of mitotic cell cycle / epithelial cell differentiation / RNA polymerase II CTD heptapeptide repeat kinase activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / peptidyl-threonine phosphorylation / ERK1 and ERK2 cascade / Recruitment of mitotic centrosome proteins and complexes / Hsp70 protein binding / phosphatidylinositol binding / APC/C:Cdc20 mediated degradation of Cyclin B / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / cyclin binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Condensation of Prophase Chromosomes / AURKA Activation by TPX2 / response to activity / positive regulation of DNA replication / integrin-mediated signaling pathway / adherens junction / spindle microtubule / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / regulation of circadian rhythm / MAPK6/MAPK4 signaling / PKR-mediated signaling / structural constituent of cytoskeleton / positive regulation of protein localization to nucleus / microtubule cytoskeleton organization
Similarity search - Function
Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain / Talin 1-like, rod segment domain ...Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain / Talin 1-like, rod segment domain / Talin, N-terminal F0 domain / : / N-terminal or F0 domain of Talin-head FERM / Talin IBS2B domain / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Alpha-catenin/vinculin-like superfamily / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / 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 / : / PH-like domain superfamily / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Cyclin-dependent kinase 1 / Talin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsZacharchenko, T. / Muench, S.P. / Goult, B.T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust204825/Z/16/Z United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Talin mechanosensitivity is modulated by a direct interaction with cyclin-dependent kinase-1.
Authors: Gough, R.E. / Jones, M.C. / Zacharchenko, T. / Le, S. / Yu, M. / Jacquemet, G. / Muench, S.P. / Yan, J. / Humphries, J.D. / Jorgensen, C. / Humphries, M.J. / Goult, B.T.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 24, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / database_2 / diffrn_source / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_proc / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_seq_map_depositor_info / pdbx_struct_ref_seq_depositor_info / pdbx_unobs_or_zero_occ_residues / struct / struct_asym / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_entity_id / _atom_site.label_seq_id ..._atom_site.label_entity_id / _atom_site.label_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_name_com.entity_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_src_syn.entity_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_seq_map_depositor_info.entity_id / _pdbx_struct_ref_seq_depositor_info.entity_id / _struct.pdbx_center_of_mass_x / _struct.pdbx_center_of_mass_y / _struct.pdbx_center_of_mass_z / _struct_asym.entity_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id ..._diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Talin-1
B: Talin-1
C: Cyclin-dependent kinase 1
D: Cyclin-dependent kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3307
Polymers69,1104
Non-polymers2203
Water3,009167
1
A: Talin-1
D: Cyclin-dependent kinase 1


Theoretical massNumber of molelcules
Total (without water)34,5552
Polymers34,5552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-12 kcal/mol
Surface area17030 Å2
MethodPISA
2
B: Talin-1
C: Cyclin-dependent kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7755
Polymers34,5552
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-22 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.000, 97.870, 104.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROLYSLYS(chain 'A' and (resid 1354 through 1415 or resid 1417 through 1659))AA1354 - 14154 - 65
121GLYGLYLEULEU(chain 'A' and (resid 1354 through 1415 or resid 1417 through 1659))AA1417 - 165967 - 309
211PROPROLYSLYS(chain 'B' and (resid 1354 through 1415 or resid 1417 through 1659))BB1354 - 14154 - 65
221GLYGLYLEULEU(chain 'B' and (resid 1354 through 1415 or resid 1417 through 1659))BB1417 - 165967 - 309
132ASPASPPROPROchain 'C'CC207 - 2231 - 17
232ASPASPPROPROchain 'D'DD207 - 2231 - 17

NCS ensembles :
ID
1
2

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Components

#1: Protein Talin-1


Mass: 32574.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P26039
#2: Protein/peptide Cyclin-dependent kinase 1 / CDK1 / Cell division control protein 2 homolog / Cell division protein kinase 1 / p34 protein kinase


Mass: 1980.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P06493, UniProt: P26039*PLUS, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3 / References: UniProt: P06493*PLUS
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.09 % / Description: Stacked needles
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Na citrate pH 5.6, 20% Isopropanol and 20% PEG4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.28→46.15 Å / Num. obs: 32879 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 32.28 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.099 / Net I/σ(I): 7
Reflection shellResolution: 2.28→2.35 Å / Rmerge(I) obs: 1.309 / Num. unique obs: 2498 / CC1/2: 0.541 / Rpim(I) all: 0.652 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X0C

2x0c


Resolution: 2.28→46.15 Å / SU ML: 0.317 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8132
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 1634 4.98 %RANDOM
Rwork0.2144 31187 --
obs0.2167 32821 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.3 Å2
Refinement stepCycle: LAST / Resolution: 2.28→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 13 167 4988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274892
X-RAY DIFFRACTIONf_angle_d0.52056630
X-RAY DIFFRACTIONf_chiral_restr0.0371770
X-RAY DIFFRACTIONf_plane_restr0.0038891
X-RAY DIFFRACTIONf_dihedral_angle_d12.42161823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.350.3391380.30172498X-RAY DIFFRACTION98.51
2.35-2.420.31591430.28372548X-RAY DIFFRACTION99.59
2.42-2.510.35361380.27662578X-RAY DIFFRACTION99.6
2.51-2.610.34311200.25282571X-RAY DIFFRACTION99.01
2.61-2.730.31211350.23922571X-RAY DIFFRACTION99.56
2.73-2.870.24931350.23142584X-RAY DIFFRACTION99.82
2.87-3.050.27351280.23042597X-RAY DIFFRACTION99.74
3.05-3.290.26481440.2312566X-RAY DIFFRACTION99.23
3.29-3.620.25631220.21052640X-RAY DIFFRACTION99.86
3.62-4.140.23061500.18322609X-RAY DIFFRACTION99.75
4.14-5.220.2171230.18552666X-RAY DIFFRACTION99.57
5.22-46.150.23811580.17972759X-RAY DIFFRACTION99.39

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