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- PDB-5n7k: Crystal structure of the coiled-coil domain of human tricellulin -

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Basic information

Entry
Database: PDB / ID: 5n7k
TitleCrystal structure of the coiled-coil domain of human tricellulin
ComponentsMARVEL domain-containing protein 2
KeywordsCELL ADHESION / tight junction / CC domain / dimerization
Function / homology
Function and homology information


tricellular tight junction / paranodal junction / bicellular tight junction assembly / Schmidt-Lanterman incisure / cell-cell junction organization / establishment of endothelial barrier / tight junction / bicellular tight junction / sensory perception of sound / cell junction ...tricellular tight junction / paranodal junction / bicellular tight junction assembly / Schmidt-Lanterman incisure / cell-cell junction organization / establishment of endothelial barrier / tight junction / bicellular tight junction / sensory perception of sound / cell junction / cytoplasmic vesicle / basolateral plasma membrane / apical plasma membrane / cytoplasm
Similarity search - Function
Occludin homology domain / ELL/occludin family / Occludin homology domain / Occludin/ELL (OCEL) domain profile. / Marvel domain / Membrane-associating domain / MARVEL domain profile.
Similarity search - Domain/homology
MARVEL domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsSchuetz, A. / Heinemann, U.
CitationJournal: Ann. N. Y. Acad. Sci. / Year: 2017
Title: Crystal structure of the tricellulin C-terminal coiled-coil domain reveals a unique mode of dimerization.
Authors: Schuetz, A. / Radusheva, V. / Krug, S.M. / Heinemann, U.
History
DepositionFeb 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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: MARVEL domain-containing protein 2
B: MARVEL domain-containing protein 2
C: MARVEL domain-containing protein 2
D: MARVEL domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)55,9114
Polymers55,9114
Non-polymers00
Water00
1
A: MARVEL domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)13,9781
Polymers13,9781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MARVEL domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)13,9781
Polymers13,9781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MARVEL domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)13,9781
Polymers13,9781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MARVEL domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)13,9781
Polymers13,9781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.621, 82.621, 188.825
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
MARVEL domain-containing protein 2 / Tricellulin


Mass: 13977.784 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MARVELD2, TRIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N4S9

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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: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 55% (v/v) MPD, 0.1 M Mes pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.805→47.26 Å / Num. obs: 18866 / % possible obs: 99.43 % / Redundancy: 10.2 % / Biso Wilson estimate: 83.31 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.15
Reflection shellResolution: 2.805→2.906 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.9753 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 1787 / % possible all: 97.01

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N7H

5n7h


Resolution: 2.81→47.26 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.614 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.607 / SU Rfree Blow DPI: 0.3 / SU Rfree Cruickshank DPI: 0.305
RfactorNum. reflection% reflectionSelection details
Rfree0.242 941 5 %RANDOM
Rwork0.215 ---
obs0.217 18820 99.7 %-
Displacement parametersBiso mean: 96.71 Å2
Baniso -1Baniso -2Baniso -3
1--11.4847 Å20 Å20 Å2
2---11.4847 Å20 Å2
3---22.9694 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.81→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 0 0 3789
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013858HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.955150HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1490SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes132HARMONIC2
X-RAY DIFFRACTIONt_gen_planes531HARMONIC5
X-RAY DIFFRACTIONt_it3858HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.13
X-RAY DIFFRACTIONt_other_torsion16.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion469SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4411SEMIHARMONIC4
LS refinement shellResolution: 2.81→2.98 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2828 148 4.97 %
Rwork0.2403 2829 -
all0.2424 2977 -
obs--99.3 %
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)
12.25031.92771.58991.47580.3137.0845-0.36280.051-0.26370.2085-0.15540.422-0.2703-1.50950.5182-0.3596-0.14550.14630.0508-0.1701-0.313455.953435.0349181.752
2-0.10072.4078-2.59432.8139-3.306600.0524-0.1238-0.6134-0.03730.0941-0.57050.58320.5396-0.14650.449-0.23480.04910.27310.1950.004958.260915.1108214.886
3-0.1616-0.03491.19663.8178-1.6214.2163-0.2508-0.4587-0.44120.55290.04320.6386-0.4475-1.45370.2076-0.2133-0.09390.27780.5605-0.0222-0.161751.969434.2986185.884
44.01361.72631.48272.25761.31277.5377-0.92230.6151-0.08160.2712-0.00930.3574-0.0921-1.11460.93160.1126-0.22830.0296-0.1909-0.0975-0.366367.663539.3699181.318
51.1087-1.2944-3.68155.27244.247511.9256-0.2388-0.03160.3725-0.7316-0.08470.2053-1.87570.36170.32340.76110.1257-0.1343-0.3146-0.0052-0.297874.565855.7991213.576
61.86640.79074.86841.71821.73490-1.05330.643-0.15840.0913-0.0460.1076-0.157-0.42961.09930.2922-0.19160.0108-0.2026-0.028-0.257272.204239.6377184.19
71.4392-1.19983.45196.1884-3.41399.5229-0.5124-0.0298-0.14991.22350.110.8464-1.1228-0.38140.4024-0.187-0.03370.1081-0.4205-0.024-0.196584.545717.787199.413
86.38021.30819.96940.12161.3422.07170.07880.40040.25370.25290.0330.15781.0743-0.7413-0.11180.1342-0.2572-0.15910.3259-0.18730.308770.14298.1253166.939
92.55911.27642.134.9886-0.156710.5066-0.5055-0.0719-0.37820.7454-0.11790.4478-0.4295-0.67060.6234-0.09220.02810.121-0.2736-0.05750.057685.982913.973195.947
101.20420.12590.35273.6288-0.77716.6941-0.59870.0283-0.31870.4189-0.0369-0.39980.15390.78010.63550.1956-0.03620.1286-0.41330.0256-0.281282.525430.6696200.072
115.33962.5394-6.61183.27430.419215.8939-0.0460.29420.42280.3292-0.1572-0.2541-1.07760.5920.20320.2519-0.4767-0.06440.08710.203-0.242393.548244.5778167.659
121.79111.4308-1.1151.1688-5.59150-0.7950.0068-0.11890.386-0.0777-0.1455-0.01110.46890.87270.32860.00090.0838-0.27650.0297-0.171180.50934.6931197.055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|439 - 480}
2X-RAY DIFFRACTION2{A|481 - 517}
3X-RAY DIFFRACTION3{A|518 - 551}
4X-RAY DIFFRACTION4{B|437 - 480}
5X-RAY DIFFRACTION5{B|481 - 517}
6X-RAY DIFFRACTION6{B|518 - 551}
7X-RAY DIFFRACTION7{C|438 - 480}
8X-RAY DIFFRACTION8{C|481 - 517}
9X-RAY DIFFRACTION9{C|518 - 551}
10X-RAY DIFFRACTION10{D|438 - 480}
11X-RAY DIFFRACTION11{D|481 - 517}
12X-RAY DIFFRACTION12{D|518 - 551}

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