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- PDB-6xz4: Crystal structure of TLNRD1 -

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Basic information

Entry
Database: PDB / ID: 6xz4
TitleCrystal structure of TLNRD1
ComponentsTalin rod domain-containing protein 1
KeywordsCELL ADHESION / Actin binding protein / Protein complex / Cytoskeleton
Function / homologyTalin rod domain-containing protein 1 / : / Talin IBS2B domain / stress fiber / actin binding / identical protein binding / Talin rod domain-containing protein 1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCowell, A. / Singh, A.K. / Brown, D.G. / Goult, B.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N007336/1 United Kingdom
Human Frontier Science Program (HFSP)RGP00001/2016
Citation
Journal: J.Cell Biol. / Year: 2021
Title: Talin rod domain-containing protein 1 (TLNRD1) is a novel actin-bundling protein which promotes filopodia formation.
Authors: Cowell, A.R. / Jacquemet, G. / Singh, A.K. / Varela, L. / Nylund, A.S. / Ammon, Y.C. / Brown, D.G. / Akhmanova, A. / Ivaska, J. / Goult, B.T.
#1: Journal: Biorxiv / Year: 2020
Title: Talin Rod Domain Containing Protein 1 (TLNRD1) is a novel actin- bundling protein which promotes filopodia formation.
Authors: Cowell, A. / Jacquemet, G. / Singh, A.K. / Ammon, Y.-K. / Brown, D.G. / Akhmanova, A. / Ivaska, J. / Goult, B.T.
History
DepositionFeb 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Talin rod domain-containing protein 1
B: Talin rod domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)76,8662
Polymers76,8662
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-24 kcal/mol
Surface area28700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.170, 58.043, 84.324
Angle α, β, γ (deg.)90.000, 106.100, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1CYSCYSALAALAchain AAA40 - 34346 - 349
2HISHISGLNGLNchain BBB39 - 34245 - 348

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Components

#1: Protein Talin rod domain-containing protein 1 / Mesoderm development candidate 1


Mass: 38432.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Full length TLNRD1 residues 1-362 / Source: (gene. exp.) Homo sapiens (human) / Gene: TLNRD1, MESDC1 / Plasmid: pET151 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H1K6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 250 mM sodium thiocyanate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.3→60.22 Å / Num. obs: 28327 / % possible obs: 98.4 % / Redundancy: 2.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.063 / Rrim(I) all: 0.108 / Net I/σ(I): 5.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2810 / CC1/2: 0.831 / Rpim(I) all: 0.487 / Rrim(I) all: 0.841 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XZ3

6xz3


Resolution: 2.3→60.218 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 42.21
Details: Hydrogens have been added in riding positions. U values refined individually.
RfactorNum. reflection% reflection
Rfree0.3152 1385 4.95 %
Rwork0.2618 --
obs0.2645 27997 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 273.15 Å2 / Biso mean: 74.024 Å2 / Biso min: 24.66 Å2
Refinement stepCycle: final / Resolution: 2.3→60.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4461 0 0 70 4531
Biso mean---50.47 -
Num. residues----608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044514
X-RAY DIFFRACTIONf_angle_d0.7926100
X-RAY DIFFRACTIONf_chiral_restr0.03728
X-RAY DIFFRACTIONf_plane_restr0.004801
X-RAY DIFFRACTIONf_dihedral_angle_d14.981668
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3266X-RAY DIFFRACTION11.935TORSIONAL
12B3266X-RAY DIFFRACTION11.935TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.38220.45581400.3774266997
2.3822-2.47760.4481280.3493261797
2.4776-2.59040.36981290.3277264697
2.5904-2.72690.45071420.3038266898
2.7269-2.89780.39371300.2905266597
2.8978-3.12150.32271600.2866262697
3.1215-3.43560.32041340.2792265898
3.4356-3.93270.29041340.2479266697
3.9327-4.95440.25911560.2211268697
4.9544-60.2180.29291320.231271196

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