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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kbu
TitleCrystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK), EMTS derivative
Components
  • Ankyrin-1
  • Spectrin beta chain, erythrocyte
KeywordsSTRUCTURAL PROTEIN / complex / spectrin / spectrin repeat / three helix bundle / ankyrin binding / disease mutation / ankyrin / ZU5 / beta sandwich / spectrin binding / cytoskeleton / membrane skeleton / Actin capping / Actin-binding / Elliptocytosis / Hereditary hemolytic anemia / Phosphoprotein / Alternative promoter usage / ANK repeat / Lipoprotein / Membrane / Sarcoplasmic reticulum
Function / homology
Function and homology information


spectrin / spectrin-associated cytoskeleton / positive regulation of organelle organization / modification of postsynaptic actin cytoskeleton / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / Neurofascin interactions / ankyrin-1 complex / CHL1 interactions / cytoskeletal anchor activity ...spectrin / spectrin-associated cytoskeleton / positive regulation of organelle organization / modification of postsynaptic actin cytoskeleton / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / Neurofascin interactions / ankyrin-1 complex / CHL1 interactions / cytoskeletal anchor activity / actin filament capping / M band / Interaction between L1 and Ankyrins / ankyrin binding / cortical actin cytoskeleton / spectrin binding / exocytosis / axolemma / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / cytoskeleton organization / NCAM signaling for neurite out-growth / sarcoplasmic reticulum / protein localization to plasma membrane / cell projection / sarcolemma / structural constituent of cytoskeleton / Z disc / cytoplasmic side of plasma membrane / actin filament binding / cell junction / actin cytoskeleton / actin binding / ATPase binding / actin cytoskeleton organization / RAF/MAP kinase cascade / protein phosphatase binding / basolateral plasma membrane / transmembrane transporter binding / postsynaptic membrane / cytoskeleton / postsynapse / neuron projection / glutamatergic synapse / structural molecule activity / enzyme binding / cell surface / signal transduction / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
Chondroitinase Ac; Chain A, domain 3 - #30 / Spectrin, beta subunit / Ankyrin, UPA domain / UPA domain / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Chondroitinase Ac; Chain A, domain 3 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain ...Chondroitinase Ac; Chain A, domain 3 - #30 / Spectrin, beta subunit / Ankyrin, UPA domain / UPA domain / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Chondroitinase Ac; Chain A, domain 3 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Ankyrin repeat / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Death-like domain superfamily / Ankyrin repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Spectrin beta chain, erythrocytic / Ankyrin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsIpsaro, J.J. / Mondragon, A.
CitationJournal: Blood / Year: 2010
Title: Structural basis for spectrin recognition by ankyrin.
Authors: Ipsaro, J.J. / Mondragon, A.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spectrin beta chain, erythrocyte
B: Spectrin beta chain, erythrocyte
C: Ankyrin-1
D: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,81512
Polymers110,2104
Non-polymers1,6058
Water00
1
A: Spectrin beta chain, erythrocyte
D: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9076
Polymers55,1052
Non-polymers8024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-7 kcal/mol
Surface area25200 Å2
MethodPISA
2
B: Spectrin beta chain, erythrocyte
C: Ankyrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9076
Polymers55,1052
Non-polymers8024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-7 kcal/mol
Surface area26400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.130, 98.540, 137.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14C
24D
15C
25D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1587 - 1691
2112B1587 - 1691
1122A1692 - 1800
2122B1692 - 1800
1132A1801 - 1889
2132B1801 - 1889
1142C910 - 1000
2142D910 - 1000
1152C1006 - 1068
2152D1006 - 1068

NCS ensembles :
ID
1
2
3
4
5

-
Components

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


Mass: 37219.352 Da / Num. of mol.: 2 / Fragment: UNP residues 1583-1906 / Mutation: E1680C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTB, SPTB1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11277
#2: Protein Ankyrin-1 / Erythrocyte ankyrin / Ankyrin-R


Mass: 17885.594 Da / Num. of mol.: 2 / Fragment: UNP residues 911-1068
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANK, ANK1 / Plasmid: pICANTE / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P16157
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Hg
Sequence detailsEL TO DV SEQUENCE CONFLICT IN UNP ENTRY P16157

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 283K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 7, 2008
RadiationMonochromator: Diamond laue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. all: 32653 / Num. obs: 32570 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 27.8 Å2 / Rsym value: 0.058 / Net I/σ(I): 16
Reflection shellResolution: 2.75→2.87 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.288 / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345data collection
SHARPphasing
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: PDB entries 3F57, 3F59

3f57

3f59


Resolution: 2.75→37.82 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.889 / SU B: 30.686 / SU ML: 0.295 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.108 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27724 1676 5.2 %RANDOM
Rwork0.2253 ---
obs0.22797 30815 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.628 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.75→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7117 0 8 0 7125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227249
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.969768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6486.7982771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17724.032377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.195151297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3061567
X-RAY DIFFRACTIONr_chiral_restr0.1110.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215531
X-RAY DIFFRACTIONr_mcbond_it0.9381.5477
X-RAY DIFFRACTIONr_mcangle_it2.0252757
X-RAY DIFFRACTIONr_scbond_it3.2943305
X-RAY DIFFRACTIONr_scangle_it5.3014.5298
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A420TIGHT POSITIONAL0.120.05
1A434MEDIUM POSITIONAL0.120.5
1A420TIGHT THERMAL0.230.5
1A434MEDIUM THERMAL0.252
2A436TIGHT POSITIONAL0.070.05
2A448MEDIUM POSITIONAL0.10.5
2A436TIGHT THERMAL0.260.5
2A448MEDIUM THERMAL0.242
3A272TIGHT POSITIONAL0.050.05
3A281MEDIUM POSITIONAL0.070.5
3A272TIGHT THERMAL0.150.5
3A281MEDIUM THERMAL0.162
4C352TIGHT POSITIONAL0.080.05
4C303MEDIUM POSITIONAL0.090.5
4C352TIGHT THERMAL0.220.5
4C303MEDIUM THERMAL0.232
5C244TIGHT POSITIONAL0.070.05
5C255MEDIUM POSITIONAL0.080.5
5C244TIGHT THERMAL0.150.5
5C255MEDIUM THERMAL0.162
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 140 -
Rwork0.307 2207 -
obs-2347 100 %
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)
12.5532-4.53830.622213.4582-1.7241.0931-0.08130.1144-0.144-0.16710.0979-0.462-0.03690.1522-0.01650.0357-0.00420.05880.1821-0.01070.125620.647-23.27128.058
21.9717-1.1211-0.013815.2353-5.90623.3044-0.3505-0.02920.39160.29940.2238-0.1292-0.23480.0060.12660.3804-0.0034-0.16110.13670.03220.124411.40122.0087.381
31.0742.62310.054212.58622.47233.98550.01550.05920.35940.11860.3563-0.5176-0.73970.3131-0.37180.6621-0.0206-0.20790.39170.2630.779810.61859.946-8.73
413.3607-3.48861.03543.4309-0.09822.78720.10170.2041.0277-0.2347-0.00670.3343-0.6133-0.4395-0.09490.29410.07310.00190.44810.03970.2423-45.24451.2810.241
514.2972-0.07541.40310.5059-0.58311.64680.03040.61480.0814-0.0878-0.0436-0.1030.07870.03910.01320.03410.01720.02210.07690.00620.04131.36441.35225.334
611.44023.89780.52032.3977-0.24991.53370.2984-0.02410.03840.2629-0.0613-0.0263-0.17680.1253-0.23710.09920.0735-0.00030.2586-0.09260.084943.74442.6939.856
78.04551.6535-1.25546.0405-0.45171.76380.0176-0.4736-1.59250.0669-0.3405-0.68150.6777-0.01620.3230.3009-0.04140.01150.06010.08010.37923.3419.61839.34
86.05020.35631.44068.5018-0.59212.7418-0.33420.89630.1650.16780.21680.7031-0.1347-0.05920.11730.0238-0.03360.00670.29670.06930.0849-6.94222.115-11.647
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1584 - 1691
2X-RAY DIFFRACTION2A1692 - 1800
3X-RAY DIFFRACTION3A1801 - 1889
4X-RAY DIFFRACTION4B1587 - 1691
5X-RAY DIFFRACTION5B1692 - 1800
6X-RAY DIFFRACTION6B1801 - 1893
7X-RAY DIFFRACTION7C911 - 1068
8X-RAY DIFFRACTION8D910 - 1068

+
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