[English] 日本語
Yorodumi
- PDB-3edu: Crystal structure of the ankyrin-binding domain of human erythroi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3edu
TitleCrystal structure of the ankyrin-binding domain of human erythroid spectrin
ComponentsSpectrin beta chain, erythrocyte
KeywordsSTRUCTURAL PROTEIN / spectrin / ankyrin / ankyrin-binding domain / Actin capping / Actin-binding / Cytoskeleton / Disease mutation / Elliptocytosis / Hereditary hemolytic anemia / Phosphoprotein
Function / homology
Function and homology information


spectrin / spectrin-associated cytoskeleton / modification of postsynaptic actin cytoskeleton / actin filament capping / Interaction between L1 and Ankyrins / ankyrin binding / cortical actin cytoskeleton / COPI-mediated anterograde transport / NCAM signaling for neurite out-growth / cell projection ...spectrin / spectrin-associated cytoskeleton / modification of postsynaptic actin cytoskeleton / actin filament capping / Interaction between L1 and Ankyrins / ankyrin binding / cortical actin cytoskeleton / COPI-mediated anterograde transport / NCAM signaling for neurite out-growth / cell projection / cytoplasmic side of plasma membrane / structural constituent of cytoskeleton / actin filament binding / actin cytoskeleton / cell junction / actin binding / actin cytoskeleton organization / RAF/MAP kinase cascade / postsynapse / glutamatergic synapse / cell surface / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
Spectrin, beta subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain ...Spectrin, beta subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spectrin beta chain, erythrocytic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSimonovic, M. / Stabach, P. / Simonovic, I. / Steitz, T.A. / Morrow, J.S.
CitationJournal: Blood / Year: 2009
Title: The structure of the ankyrin-binding site of {beta}-spectrin reveals how tandem spectrin-repeats generate unique ligand-binding properties
Authors: Stabach, P.R. / Simonovic, I. / Ranieri, M.A. / Aboodi, M.S. / Steitz, T.A. / Simonovic, M. / Morrow, J.S.
History
DepositionSep 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Refinement description
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spectrin beta chain, erythrocyte


Theoretical massNumber of molelcules
Total (without water)24,8111
Polymers24,8111
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.823, 111.746, 127.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-62-

HOH

-
Components

#1: Protein Spectrin beta chain, erythrocyte / Beta-I spectrin


Mass: 24810.543 Da / Num. of mol.: 1 / Fragment: Spectrin 14-Spectrin 15 di-repeat
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTB, SPTB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P11277
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1M bis-tris-propane, pH 6.2, 0.2M KSCN, 20% PEG 3,350, 3-10mM spermine, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
2771
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-E10.9793
SYNCHROTRONAPS 24-ID-E20.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 5, 2008
ADSC QUANTUM 3152CCDJul 5, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→31 Å / Num. all: 15823 / Num. obs: 15696 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 48.2 Å2 / Rsym value: 0.08
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 3 / Rsym value: 0.52 / % possible all: 96.3

-
Processing

Software
NameClassification
CBASSdata collection
SHELXSphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→31 Å / SU ML: 0.29 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 1563 9.96 %
Rwork0.2103 --
obs0.2148 15692 99.2 %
all-15692 -
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.458 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 58.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 0 136 1635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071563
X-RAY DIFFRACTIONf_angle_d0.862127
X-RAY DIFFRACTIONf_dihedral_angle_d16.918569
X-RAY DIFFRACTIONf_chiral_restr0.053242
X-RAY DIFFRACTIONf_plane_restr0.003278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16780.25411390.22491209X-RAY DIFFRACTION95
2.1678-2.24530.28991340.22761270X-RAY DIFFRACTION98
2.2453-2.33520.2851500.23741231X-RAY DIFFRACTION99
2.3352-2.44140.27191160.20471298X-RAY DIFFRACTION100
2.4414-2.57010.26971350.21051305X-RAY DIFFRACTION100
2.5701-2.7310.27641400.21041282X-RAY DIFFRACTION100
2.731-2.94180.28891430.21461289X-RAY DIFFRACTION100
2.9418-3.23760.25141290.2111307X-RAY DIFFRACTION100
3.2376-3.70540.23231510.19491291X-RAY DIFFRACTION100
3.7054-4.66620.21751580.17841299X-RAY DIFFRACTION100
4.6662-32.26770.2351680.22041348X-RAY DIFFRACTION100
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)
10.02950.2333-0.09592.81131.31971.421-0.0194-0.02570.05370.3636-0.1870.1838-0.1863-0.2622-0.00010.28260.0604-0.01760.31030.00210.283816.523143.644811.7812
22.2970.94360.4139-0.09630.70530.7779-0.2504-0.66970.6526-1.1062-0.65261.3953-0.8605-0.8427-0.05910.66040.1612-0.4320.251-0.10120.57673.87918.7697-21.8315
31.5381-0.33130.53281.27211.17490.1028-0.21790.0287-0.1486-1.32530.23840.1706-0.47630.5586-0.16430.8551-0.1809-0.16520.284-0.00950.351212.046717.2665-22.3545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1resid 1690:1798
2X-RAY DIFFRACTION2resid 1799:1821
3X-RAY DIFFRACTION3resid 1835:1893

+
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