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- PDB-7c5d: Crystal structure of TRF2 TRFH domain in complex with a MCPH1 peptide -

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Basic information

Entry
Database: PDB / ID: 7c5d
TitleCrystal structure of TRF2 TRFH domain in complex with a MCPH1 peptide
Components
  • Microcephalin
  • Telomeric repeat-binding factor 2
KeywordsPROTEIN BINDING / Telomere / shelterin complex / TRF2 / MCPH1 / DNA repair
Function / homology
Function and homology information


regulation of chromosome condensation / axonal transport of messenger ribonucleoprotein complex / negative regulation of beta-galactosidase activity / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / negative regulation of telomere capping ...regulation of chromosome condensation / axonal transport of messenger ribonucleoprotein complex / negative regulation of beta-galactosidase activity / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / negative regulation of telomere capping / protection from non-homologous end joining at telomere / negative regulation of t-circle formation / telomerase activity / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / neuronal stem cell population maintenance / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / regulation of centrosome cycle / positive regulation of telomere maintenance / nuclear telomere cap complex / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / anterograde axonal transport / G-rich strand telomeric DNA binding / telomere capping / regulation of telomere maintenance / protein localization to centrosome / negative regulation of telomere maintenance via telomere lengthening / protein localization to chromosome, telomeric region / telomeric DNA binding / establishment of mitotic spindle orientation / negative regulation of cellular senescence / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / axon cytoplasm / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / Condensation of Prophase Chromosomes / male germ cell nucleus / positive regulation of nitric-oxide synthase activity / bone development / DNA Damage/Telomere Stress Induced Senescence / cerebral cortex development / cellular senescence / mitotic cell cycle / regulation of inflammatory response / in utero embryonic development / chromosome, telomeric region / nuclear body / cell cycle / negative regulation of gene expression / centrosome / protein-containing complex binding / positive regulation of gene expression / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Microcephalin-like / Microcephalin, mammal / Microcephalin protein / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / twin BRCT domain / Telomere repeat-binding factor, dimerisation domain ...Microcephalin-like / Microcephalin, mammal / Microcephalin protein / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / twin BRCT domain / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
Telomeric repeat-binding factor 2 / Microcephalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.151 Å
AuthorsXiong, X. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970576 China
CitationJournal: Nat Commun / Year: 2020
Title: Microcephalin 1/BRIT1-TRF2 interaction promotes telomere replication and repair, linking telomere dysfunction to primary microcephaly.
Authors: Cicconi, A. / Rai, R. / Xiong, X. / Broton, C. / Al-Hiyasat, A. / Hu, C. / Dong, S. / Sun, W. / Garbarino, J. / Bindra, R.S. / Schildkraut, C. / Chen, Y. / Chang, S.
History
DepositionMay 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Telomeric repeat-binding factor 2
B: Telomeric repeat-binding factor 2
C: Microcephalin
D: Microcephalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4936
Polymers52,3094
Non-polymers1842
Water2,522140
1
A: Telomeric repeat-binding factor 2
C: Microcephalin


Theoretical massNumber of molelcules
Total (without water)26,1542
Polymers26,1542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-7 kcal/mol
Surface area11200 Å2
MethodPISA
2
B: Telomeric repeat-binding factor 2
D: Microcephalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3384
Polymers26,1542
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-7 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.737, 74.941, 98.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Telomeric repeat-binding factor 2 / / TRF2


Mass: 23724.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q15554
#2: Protein/peptide Microcephalin /


Mass: 2429.638 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCPH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q8NEM0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 30% PEG400, 100 mM CHES-NaOH, pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 25033 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 34.18 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.022 / Rrim(I) all: 0.08 / Χ2: 0.476 / Net I/σ(I): 4.4 / Num. measured all: 326030
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.1911.80.59912360.9210.1810.6260.44799.6
2.19-2.2313.20.57312130.9360.1630.5970.447100
2.23-2.2713.50.62212260.9090.1750.6470.779100
2.27-2.3213.60.47812350.9480.1340.4970.53499.8
2.32-2.3713.60.36812200.9760.1040.3830.445100
2.37-2.4213.40.33512470.9720.0940.3480.456100
2.42-2.4813.40.28312350.9860.080.2950.469100
2.48-2.5513.40.26412370.9850.0750.2740.54399.8
2.55-2.6213.30.21212290.9890.060.2210.483100
2.62-2.7112.80.20212390.9910.0580.210.559100
2.71-2.8111.50.14712440.9930.0450.1530.48100
2.81-2.9213.30.13512370.9950.0380.140.462100
2.92-3.0513.80.11112560.9960.0310.1150.467100
3.05-3.2113.70.09712600.9970.0270.10.472100
3.21-3.4113.40.07412450.9980.0210.0770.50299.8
3.41-3.6813.30.06412480.9990.0180.0670.55299.8
3.68-4.05120.04812710.9990.0140.0510.48599.2
4.05-4.6312.90.03612760.9990.010.0380.38199.7
4.63-5.8313.30.033128710.0090.0340.30699.8
5.83-5011.70.024139210.0070.0250.23899.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
HKL-3000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H6P

1h6p


Resolution: 2.151→31.89 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 1249 5 %
Rwork0.1888 23713 -
obs0.1911 24962 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.13 Å2 / Biso mean: 40.3202 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.151→31.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 12 140 3583
Biso mean--32.35 42.9 -
Num. residues----421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053491
X-RAY DIFFRACTIONf_angle_d0.6454685
X-RAY DIFFRACTIONf_chiral_restr0.036534
X-RAY DIFFRACTIONf_plane_restr0.004595
X-RAY DIFFRACTIONf_dihedral_angle_d17.992170
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1514-2.23760.29671380.2149255699
2.2376-2.33940.29231400.22742612100
2.3394-2.46270.27191370.2112594100
2.4627-2.61690.26631450.20182584100
2.6169-2.81880.25761360.19642634100
2.8188-3.10230.24081250.19442640100
3.1023-3.55070.21361540.18152631100
3.5507-4.47150.20811250.16742685100
4.4715-31.890.2221490.1874277799

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