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- PDB-6j08: Crystal structure of human MAJIN and TERB2 -

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Basic information

Entry
Database: PDB / ID: 6j08
TitleCrystal structure of human MAJIN and TERB2
Components
  • Membrane-anchored junction protein
  • 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 / synaptonemal complex assembly / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / nuclear inner membrane / oogenesis / spermatogenesis / chromosome, telomeric region / DNA binding
Similarity search - Function
Membrane-anchored junction protein / Membrane-anchored junction protein / Telomere repeats-binding bouquet formation protein 2 / Telomere-associated protein TERB2
Similarity search - Domain/homology
Membrane-anchored junction protein / Telomere repeats-binding bouquet formation protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 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
Revision 1.1Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane-anchored junction protein
D: Telomere repeats-binding bouquet formation protein 2
B: Membrane-anchored junction protein
E: Telomere repeats-binding bouquet formation protein 2
C: Membrane-anchored junction protein
F: Telomere repeats-binding bouquet formation protein 2


Theoretical massNumber of molelcules
Total (without water)51,1856
Polymers51,1856
Non-polymers00
Water0
1
A: Membrane-anchored junction protein
D: Telomere repeats-binding bouquet formation protein 2


Theoretical massNumber of molelcules
Total (without water)17,0622
Polymers17,0622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-14 kcal/mol
Surface area8900 Å2
MethodPISA
2
B: Membrane-anchored junction protein
E: Telomere repeats-binding bouquet formation protein 2


Theoretical massNumber of molelcules
Total (without water)17,0622
Polymers17,0622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-14 kcal/mol
Surface area8270 Å2
MethodPISA
3
C: Membrane-anchored junction protein
F: Telomere repeats-binding bouquet formation protein 2


Theoretical massNumber of molelcules
Total (without water)17,0622
Polymers17,0622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-14 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.737, 128.767, 86.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Membrane-anchored junction protein


Mass: 13014.044 Da / Num. of mol.: 3 / Fragment: NTD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAJIN, C11orf85 / Plasmid: pRSFDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3KP22
#2: Protein/peptide Telomere repeats-binding bouquet formation protein 2


Mass: 4047.547 Da / Num. of mol.: 3 / Fragment: TERB2 binding motif
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
Sequence detailsSequence of chain A,B,C was based on isoform 1 of UNP database Q3KP22 (MAJIN_HUMAN).

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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: 2.94 Å3/Da / Density % sol: 58.22 % / Mosaicity: 0.369 °
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.8
Details: 100 mM HEPES pH 6.8, 0.2 M Potassium thiocyanate, 22% (w/v) Polyethylene glycol 3350, 25% (v/v) Glycerol

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL18U110.97776
SYNCHROTRONSSRF BL19U120.97776
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELSep 14, 2016
DECTRIS PILATUS 6M2PIXELSep 14, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.977761
21
ReflectionResolution: 2.9→100 Å / Num. obs: 13769 / % possible obs: 99.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.022 / Rrim(I) all: 0.08 / Χ2: 1.428 / Net I/σ(I): 7.3 / Num. measured all: 182312
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-313.50.65513540.9310.1840.6810.508100
3-3.1213.80.41513380.9680.1160.4310.486100
3.12-3.2713.40.27213600.9820.0770.2830.522100
3.27-3.4412.80.18513540.9910.0530.1920.599100
3.44-3.6513.30.12313790.9950.0350.1280.665100
3.65-3.9413.80.08713600.9980.0240.090.849100
3.94-4.3313.40.06713750.9980.0190.071.2100
4.33-4.96130.05913840.9980.0170.0621.402100
4.96-6.2513.40.06713910.9980.0190.073.0599.9
6.25-10012.10.06514740.9950.020.0685.06199.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
HKL-3000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.9→32.192 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 662 4.82 %
Rwork0.2117 13067 -
obs0.2142 13729 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 189.98 Å2 / Biso mean: 91.3919 Å2 / Biso min: 45.59 Å2
Refinement stepCycle: final / Resolution: 2.9→32.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 0 0 3432
Num. residues----411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9001-3.12380.34431220.262625592681
3.1238-3.43790.28811370.238625722709
3.4379-3.93460.27181330.223425942727
3.9346-4.95420.22731470.187626142761
4.9542-32.19370.26971230.211727282851
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)
11.5501-0.66341.53162.9333-1.28711.59830.1009-0.0889-0.00010.10450.0260.374-0.135-0.007500.53450.12850.02110.5582-0.07430.518920.684444.332541.1332
20.4094-1.0472-0.5165-0.3222-0.76692.26390.3218-0.30880.14080.0767-0.06650.134-0.0739-0.0487-00.70280.0849-0.15860.5603-0.02390.894917.328748.419435.4964
31.27420.79490.38393.561-0.84152.24510.0843-0.0711-0.09740.043-0.0361-0.10060.17420.257100.49540.0863-0.01760.5792-0.03280.44733.542358.21617.7406
41.2562.03981.29640.8228-1.64232.51950.3269-0.0673-0.22450.5108-0.1558-0.29130.42980.5451-00.78970.1919-0.05850.65210.01370.645833.271952.145321.6876
52.4562-0.2518-0.53311.2886-0.03112.7141-0.1437-0.0502-0.0878-0.0030.15310.2032-0.3799-0.054300.49450.05230.08580.45040.00580.534816.350678.062510.5881
61.56720.7938-0.41221.60660.43160.97460.64510.47440.3579-0.4969-0.30360.166-0.8046-0.3729-00.72090.20140.00390.8629-0.00320.71348.107278.83511.0017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 109
2X-RAY DIFFRACTION2chain DD174 - 209
3X-RAY DIFFRACTION3chain BB1 - 109
4X-RAY DIFFRACTION4chain EE175 - 205
5X-RAY DIFFRACTION5chain CC1 - 109
6X-RAY DIFFRACTION6chain FF175 - 208

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