[English] 日本語
Yorodumi
- PDB-5n7i: Crystal structure of the coiled-coil domain of human tricellulin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n7i
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 / tight junction / establishment of endothelial barrier / 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 / tight junction / establishment of endothelial barrier / 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 / MOLECULAR REPLACEMENT / Resolution: 2.88 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: Data collection / Database references / Category: citation / reflns_shell
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.percent_possible_all
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MARVEL domain-containing protein 2
B: MARVEL domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)27,6112
Polymers27,6112
Non-polymers00
Water00
1
A: MARVEL domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)13,8061
Polymers13,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MARVEL domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)13,8061
Polymers13,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.711, 95.711, 34.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

-
Components

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


Mass: 13805.552 Da / Num. of mol.: 2
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8.5% (w/v) PEG4000, 20% 2-propanol, 0.1 M HEPES-NaOH pH 7.0

-
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: 2.879→47.86 Å / Num. obs: 7271 / % possible obs: 98.38 % / Redundancy: 5.4 % / Biso Wilson estimate: 97.28 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.62
Reflection shellResolution: 2.88→3.22 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.332 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 711 / % possible all: 98.78

-
Processing

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

5n7h


Resolution: 2.88→47.86 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 1.004 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.92 / SU Rfree Blow DPI: 0.321 / SU Rfree Cruickshank DPI: 0.329
RfactorNum. reflection% reflectionSelection details
Rfree0.238 538 7.41 %RANDOM
Rwork0.21 ---
obs0.212 7259 98.5 %-
Displacement parametersBiso mean: 116.58 Å2
Baniso -1Baniso -2Baniso -3
1--8.5749 Å20 Å20 Å2
2---8.5749 Å20 Å2
3---17.1498 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.88→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 0 0 1663
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011692HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.982261HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d640SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes229HARMONIC5
X-RAY DIFFRACTIONt_it1692HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion17.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion208SEMIHARMONIC5
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_contact2008SEMIHARMONIC4
LS refinement shellResolution: 2.88→3.22 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2429 150 7.42 %
Rwork0.2295 1871 -
all0.2304 2021 -
obs--98.78 %
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)
14.97070.86590.19968.0565-1.31234.1053-0.2082-0.44251.2312-0.03150.15240.9052-0.4474-1.1590.0558-0.46170.17210.0197-0.1208-0.2187-0.399721.509810.01115.4364
27.97961.3557-0.78920.94940.34573.33070.5431-0.15390.48530.6812-0.3154-0.56180.0731-0.105-0.2276-0.2903-0.01750.0073-0.1833-0.0147-0.266539.01913.291711.2114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more