[English] 日本語
Yorodumi
- PDB-3ud1: Crystal structure of ZU5A-ZU5B domains of human erythrocyte ankyrin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ud1
TitleCrystal structure of ZU5A-ZU5B domains of human erythrocyte ankyrin
ComponentsAnkyrin-1
KeywordsPROTEIN BINDING / Beta sandwich / ZU5 / Adapter protein / Spectrin binding / Cytoskeleton
Function / homology
Function and homology information


spectrin-associated cytoskeleton / positive regulation of organelle organization / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / Neurofascin interactions / ankyrin-1 complex / CHL1 interactions / cytoskeletal anchor activity / M band / Interaction between L1 and Ankyrins ...spectrin-associated cytoskeleton / positive regulation of organelle organization / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / Neurofascin interactions / ankyrin-1 complex / 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 / Z disc / cytoplasmic side of plasma membrane / ATPase binding / basolateral plasma membrane / protein phosphatase binding / postsynaptic membrane / transmembrane transporter binding / cytoskeleton / neuron projection / structural molecule activity / enzyme binding / signal transduction / plasma membrane / cytosol
Similarity search - Function
Chondroitinase Ac; Chain A, domain 3 - #30 / Ankyrin, UPA domain / UPA domain / Chondroitinase Ac; Chain A, domain 3 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Ankyrin repeat / Death domain profile. ...Chondroitinase Ac; Chain A, domain 3 - #30 / Ankyrin, UPA domain / UPA domain / Chondroitinase Ac; Chain A, domain 3 / 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 / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsYasunaga, M. / Ipsaro, J.J. / Mondragon, A.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structurally Similar but Functionally Diverse ZU5 Domains in Human Erythrocyte Ankyrin.
Authors: Yasunaga, M. / Ipsaro, J.J. / Mondragon, A.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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-1
B: Ankyrin-1
C: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,80915
Polymers108,2563
Non-polymers55312
Water12,358686
1
A: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3166
Polymers36,0851
Non-polymers2305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3166
Polymers36,0851
Non-polymers2305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1773
Polymers36,0851
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.123, 40.491, 178.104
Angle α, β, γ (deg.)90.00, 112.68, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Ankyrin-1 / ANK-1 / Ankyrin-R / Erythrocyte ankyrin


Mass: 36085.289 Da / Num. of mol.: 3 / Fragment: ZU5A-ZU5B Ankyrin-R, UNP residues 911-1233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANK1, ANK / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16157
#2: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% ethanol, 0.1 M Tris pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 283.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→29.68 Å / Num. all: 71819 / Num. obs: 71819 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.18 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 7.3
Reflection shellResolution: 2→2.09 Å / % possible all: 99.3

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 3F59

3f59


Resolution: 2→29.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3623 5.05 %RANDOM
Rwork0.171 ---
obs0.173 71813 --
all-71813 --
Displacement parametersBiso mean: 27.65 Å2
Baniso -1Baniso -2Baniso -3
1--3.1774 Å20 Å2-0.4731 Å2
2--2.4228 Å20 Å2
3---0.7546 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7527 0 36 686 8249
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018055HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0510978HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1218HARMONIC5
X-RAY DIFFRACTIONt_it8055HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion14.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1062SEMIHARMONIC5
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_contact9501SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2002 257 5.15 %
Rwork0.1906 4737 -
all0.1911 4994 -
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)
11.0354-0.3002-0.05791.50790.06651.7903-0.00110.04070.0080.0404-0.00830.017-0.05460.20.0094-0.0436-0.02710.0104-0.0107-0.008-0.1034-2.053422.8252-69.6267
20.93930.1063-0.44632.56470.19490.71210.03170.00010.0504-0.21620.04750.162-0.0238-0.0497-0.0792-0.0595-0.0180.0096-0.089-0.0164-0.0038-34.224312.648-62.7252
31.3343-0.3778-0.33651.49110.0512.83550.0557-0.03320.0352-0.06520.0224-0.0577-0.2353-0.0063-0.07810.0219-0.0079-0.0184-0.10420.0021-0.13862.06711.6347-15.3732
41.0561-0.4935-0.17435.39190.42920.51280.04110.0174-0.07930.4373-0.12780.1440.107800.0867-0.0241-0.00280.0005-0.1213-0.0142-0.0824-29.4866-6.5021-9.8874
51.00750.1192-0.11241.603-0.19781.5751-0.02920.0106-0.02040.12070.04370.0043-0.0180.0078-0.0144-0.02140.0072-0.0083-0.04510.0022-0.0913-6.37522.0287-39.2093
60.9987-0.1168-0.05862.16160.12910.7326-0.04190.0371-0.0914-0.0712-0.0751-0.080.1164-0.01050.117-0.0452-0.01340.0255-0.07550.0092-0.006125.119814.3438-43.6664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1A 912 A 1072
2X-RAY DIFFRACTION2A 1073 A 1233
3X-RAY DIFFRACTION3B 912 B 1072
4X-RAY DIFFRACTION4B 1073 B 1233
5X-RAY DIFFRACTION5C 912 C 1072
6X-RAY DIFFRACTION6C 1073 C 1233

+
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