[English] 日本語
Yorodumi
- PDB-1n11: D34 REGION OF HUMAN ANKYRIN-R AND LINKER -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n11
TitleD34 REGION OF HUMAN ANKYRIN-R AND LINKER
ComponentsAnkyrin
KeywordsSTRUCTURAL PROTEIN / ANKYRIN / CLATHRIN / BAND 3 / ANION EXCHANGER
Function / homology
Function and homology information


positive regulation of organelle organization / spectrin-associated cytoskeleton / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / ankyrin-1 complex / Neurofascin interactions / CHL1 interactions / cytoskeletal anchor activity / M band / Interaction between L1 and Ankyrins ...positive regulation of organelle organization / spectrin-associated cytoskeleton / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / ankyrin-1 complex / Neurofascin interactions / CHL1 interactions / cytoskeletal anchor activity / M band / Interaction between L1 and Ankyrins / spectrin binding / exocytosis / axolemma / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / cytoskeleton organization / sarcoplasmic reticulum / protein localization to plasma membrane / sarcolemma / structural constituent of cytoskeleton / cytoplasmic side of plasma membrane / Z disc / ATPase binding / postsynaptic membrane / basolateral plasma membrane / protein phosphatase binding / transmembrane transporter binding / cytoskeleton / neuron projection / structural molecule activity / enzyme binding / signal transduction / plasma membrane / cytosol
Similarity search - Function
Ankyrin, UPA domain / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Ankyrin repeat / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain ...Ankyrin, UPA domain / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Ankyrin repeat / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Ankyrin repeat-containing domain / Ankyrin repeats (many copies) / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Ankyrin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsMichaely, P. / Tomchick, D.R. / Machius, M. / Anderson, R.G.W.
CitationJournal: Embo J. / Year: 2002
Title: Crystal structure of a 12 ANK repeat stack from human ankyrinR
Authors: Michaely, P. / Tomchick, D.R. / Machius, M. / Anderson, R.G.W.
History
DepositionOct 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ankyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,85911
Polymers46,4601
Non-polymers39910
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.329, 137.329, 197.801
Angle α, β, γ (deg.)90, 90, 120
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein Ankyrin /


Mass: 46459.898 Da / Num. of mol.: 1 / Fragment: D34 region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ank-1 / Plasmid: pGEX-kg / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P16157
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, HEPES, NaBr, CaCl2, acetonitrile, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
220 mMHEPES-Na1droppH7.5
3500 mM1dropNaBr
41 mMEDTA1drop
51 mMdithiothreitol1drop
6100 mMHEPES1reservoirpH7.5
7500 mM1reservoirCaCl2
87-10 %(v/v)PEG4001reservoir
95 %(v/v)acetonitrile1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97925 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jan 31, 2001
RadiationMonochromator: Graphite Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 421780 / Num. obs: 415031 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 22.6
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.3 / % possible all: 93
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 37994 / Num. measured all: 415031
Reflection shell
*PLUS
% possible obs: 93 %

-
Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
MLPHAREphasing
CNSrefinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→30 Å / Isotropic thermal model: individual isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.303 1155 random
Rwork0.319 --
all0.318 30300 -
obs0.318 30300 -
Displacement parametersBiso mean: 67 Å2
Baniso -1Baniso -2Baniso -3
1--37.037 Å2-30.296 Å20 Å2
2---37.037 Å20 Å2
3---74.075 Å2
Refine analyzeLuzzati sigma a obs: 1.07 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 0 0 3073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.62
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 3.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.01

+
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://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