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- PDB-5n7h: Crystal structure of the coiled-coil domain of human tricellulin -

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Basic information

Entry
Database: PDB / ID: 5n7h
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 / Schmidt-Lanterman incisure / bicellular tight junction assembly / cell-cell junction organization / establishment of endothelial barrier / tight junction / bicellular tight junction / sensory perception of sound / cell junction ...tricellular tight junction / paranodal junction / Schmidt-Lanterman incisure / bicellular tight junction assembly / 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/ELL (OCEL) domain profile. / Occludin homology domain / ELL/occludin family / Occludin homology domain / 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 / AB INITIO PHASING / Resolution: 2.2 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 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MARVEL domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)13,9781
Polymers13,9781
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.039, 44.039, 202.843
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 13977.784 Da / Num. of mol.: 1
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.03 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 10% (v/v) isopropanol, 0.1 M citrate 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: Jan 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.198→44.039 Å / Num. obs: 6591 / % possible obs: 99.65 % / Redundancy: 12.7 % / Biso Wilson estimate: 50.21 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 33.69
Reflection shellResolution: 2.198→2.276 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 616 / % possible all: 99.52

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.2→38.14 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.349 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.212
RfactorNum. reflection% reflectionSelection details
Rfree0.258 493 7.51 %RANDOM
Rwork0.248 ---
obs0.248 6565 99.7 %-
Displacement parametersBiso mean: 73.09 Å2
Baniso -1Baniso -2Baniso -3
1--4.2922 Å20 Å20 Å2
2---4.2922 Å20 Å2
3---8.5843 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: 1 / Resolution: 2.2→38.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 0 0 17 919
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01917HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.951222HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d356SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes125HARMONIC5
X-RAY DIFFRACTIONt_it917HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.34
X-RAY DIFFRACTIONt_other_torsion17.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion112SEMIHARMONIC5
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_contact1081SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.46 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2905 133 7.47 %
Rwork0.2525 1648 -
all0.2556 1781 -
obs--99.89 %
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)
12.0701-0.96691.05144.7407-0.8655.39570.04850.6193-0.1204-0.2221-0.049-0.45370.06640.52820.0005-0.38630.0265-0.00610.0053-0.0908-0.1157.43713.938890.8188
2-1.33060.0573-3.31523.7932-2.65963.90020.1569-0.191-0.14590.1095-0.48240.14860.0122-0.17090.32550.1746-0.1394-0.16440.11730.09850.155813.8718-0.3723125.17
31.8769-0.15832.28712.55071.138412.88020.12730.1822-0.5109-0.09890.0488-0.20760.2418-0.0883-0.176-0.29580.01740.0276-0.0216-0.0264-0.04824.665811.171296.362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|438 - 480}
2X-RAY DIFFRACTION2{A|481 - 515}
3X-RAY DIFFRACTION3{A|516 - 550}

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