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- PDB-6j07: Crystal structure of human TERB2 and TERB1 -

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Basic information

Entry
Database: PDB / ID: 6j07
TitleCrystal structure of human TERB2 and TERB1
Components
  • Telomere repeats-binding bouquet formation protein 1
  • Telomere repeats-binding bouquet formation protein 2
KeywordsDNA BINDING PROTEIN / telomere / meiosis / protein-protein complex / nuclear envelope attachment
Function / homology
Function and homology information


meiotic attachment of telomere to nuclear envelope / meiotic telomere clustering / shelterin complex / synaptonemal complex assembly / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / nuclear inner membrane / oogenesis / spermatogenesis / chromosome, telomeric region
Similarity search - Function
Telomere repeats-binding bouquet formation protein 2 / Telomere repeats-binding bouquet formation protein 1 / Telomere-associated protein TERB2 / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Telomere repeats-binding bouquet formation protein 1 / Telomere repeats-binding bouquet formation protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.298 Å
AuthorsWang, Y. / Chen, Y. / Wu, J. / Huang, C. / Lei, M.
CitationJournal: Nat Commun / Year: 2019
Title: The meiotic TERB1-TERB2-MAJIN complex tethers telomeres to the nuclear envelope.
Authors: Wang, Y. / Chen, Y. / Chen, J. / Wang, L. / Nie, L. / Long, J. / Chang, H. / Wu, J. / Huang, C. / Lei, M.
History
DepositionDec 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomere repeats-binding bouquet formation protein 2
B: Telomere repeats-binding bouquet formation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1483
Polymers19,0832
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-12 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.900, 126.900, 90.429
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Telomere repeats-binding bouquet formation protein 2


Mass: 12082.541 Da / Num. of mol.: 1 / Fragment: NTD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERB2, C15orf43 / Plasmid: pRSFDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NHR7
#2: Protein Telomere repeats-binding bouquet formation protein 1 / Coiled-coil domain-containing protein 79


Mass: 7000.225 Da / Num. of mol.: 1 / Fragment: TERB2 binding motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERB1, CCDC79 / Plasmid: pRSFDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NA31
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 5.51 Å3/Da / Density % sol: 77.67 % / Mosaicity: 0.13 °
Crystal growTemperature: 291 K / Method: evaporation / pH: 9
Details: 0.1 M Bicine pH 9.0, 2% (v/v) 1,4-Dioxane, 4% (w/v) Polyethylene glycol 20000

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL18U110.97853
SYNCHROTRONSSRF BL19U120.97853
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJan 13, 2017
DECTRIS PILATUS 6M2PIXELJan 13, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978531
20.978531
ReflectionResolution: 3.298→50 Å / Num. obs: 6870 / % possible obs: 99.6 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.021 / Rrim(I) all: 0.079 / Χ2: 0.966 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.429.90.8436380.9590.2570.8850.99196.1
3.42-3.5513.50.736770.970.2020.7580.97100
3.55-3.7216.10.5286700.9840.1360.5450.994100
3.72-3.9116.10.366680.9910.0930.3720.989100
3.91-4.1614.80.2066720.9970.0560.2130.952100
4.16-4.4816.60.1366790.9980.0350.1410.979100
4.48-4.9316.40.0856860.9990.0220.0880.981100
4.93-5.6415.70.0726950.9990.0190.0740.953100
5.64-7.114.70.0637160.9980.0170.0660.946100
7.1-5013.20.0427690.9990.0120.0440.90599.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
HKL-3000data collection
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.298→46.959 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.53
RfactorNum. reflection% reflection
Rfree0.3369 297 5.03 %
Rwork0.2885 --
obs0.291 5905 85.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 265.49 Å2 / Biso mean: 97.4008 Å2 / Biso min: 13.44 Å2
Refinement stepCycle: final / Resolution: 3.298→46.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1340 0 1 0 1341
Biso mean--126.8 --
Num. residues----167
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.420.37951220.31772276239872
3.42-46.96410.31481750.27323332350799
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)
10.01970.00670.00580.01760.00570.0017-0.0137-0.023-0.04550.08880.0087-0.0608-0.00750.0218-0.0351.0508-0.2236-0.11790.2283-0.07140.204261.884-13.434-9.2604
20.0087-0.0174-0.00820.03040.01250.01890.0234-0.02720.0244-0.07240.0236-0.0301-0.07710.03860.00450.9177-0.0942-0.20880.6033-0.07540.601769.4815-10.7255-10.8333
30.01760.0150.00980.01120.00860.04860.04840.02170.06290.0595-00.0493-0.044-0.03620.030.57740.0767-0.11850.0417-0.12670.46256.4553-11.5233-18.5056
40.00110.0033-0.00950.01790.01090.0206-0.07780.0320.044-0.03430.006-0.0022-0.0696-0.0005-0.09350.8927-0.4524-0.009-0.1273-0.0713-0.068861.3573-12.1511-21.8304
50.12780.10050.08770.07860.0680.05960.0466-0.0189-0.02320.01540.0198-0.0222-0.038-0.01870.10750.5695-0.16810.00040.68910.34860.618466.3932-29.3523-11.2356
60.00430.00850.01240.05670.02220.02380.0074-0.0197-0.09420.05440.02730.0255-0.1007-0.0242-0.00420.3981-0.27960.0445-0.0040.01040.134553.3869-20.1848-28.1234
70.02220.0150.01570.0498-0.01510.02760.0245-0.04060.0211-0.0050.00990.005-0.0185-0.02080.03270.3933-0.2896-0.02650.38490.10690.63547.5846-30.4389-39.9233
80.0038-0.0019-0.00390.00150.0020.00030.06590.00780.1166-0.0385-0.025-0.07620.07440.14610.00010.5319-0.17080.05080.63360.13270.675470.6372-24.8457-23.3568
90.07070.0118-0.00510.01970.02640.0534-0.0197-0.0037-0.0176-0.0005-0.0427-0.0150.0380.0074-0.04660.4477-0.37640.1940.28160.09450.616469.2137-22.4924-31.2619
100.0090.00360.01250.02260.00780.01540.00130.01520.0181-0.07670.02090.0101-0.1412-0.03730.01180.8976-0.61140.0997-0.1349-0.12970.21158.8442-12.9712-35.7895
110.01250.00970.02430.06750.02880.0485-0.0415-0.00020.0321-0.012-0.07630.00060.0208-0.0442-0.07880.4332-0.0107-0.11070.0064-0.00890.312758.85918.9956-44.8455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 23 )A4 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 35 )A24 - 35
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 45 )A36 - 45
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 73 )A46 - 73
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 82 )A74 - 82
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 102 )A83 - 102
7X-RAY DIFFRACTION7chain 'A' and (resid 103 through 110 )A103 - 110
8X-RAY DIFFRACTION8chain 'B' and (resid 590 through 605 )B590 - 605
9X-RAY DIFFRACTION9chain 'B' and (resid 606 through 618 )B606 - 618
10X-RAY DIFFRACTION10chain 'B' and (resid 619 through 641 )B619 - 641
11X-RAY DIFFRACTION11chain 'B' and (resid 642 through 649 )B642 - 649

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