[English] 日本語
Yorodumi
- PDB-5ybu: Structure of the KANK1 ankyrin domain in complex with KIF21A peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ybu
TitleStructure of the KANK1 ankyrin domain in complex with KIF21A peptide
Components
  • KN motif and ankyrin repeat domain-containing protein 1
  • Kinesin-like protein KIF21A
KeywordsCELL ADHESION
Function / homology
Function and homology information


regulation of microtubule depolymerization / negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / regulation of axon guidance / podocyte cell migration / negative regulation of substrate adhesion-dependent cell spreading / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / negative regulation of actin filament polymerization / cortical microtubule organization / regulation of Rho protein signal transduction ...regulation of microtubule depolymerization / negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / regulation of axon guidance / podocyte cell migration / negative regulation of substrate adhesion-dependent cell spreading / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / negative regulation of actin filament polymerization / cortical microtubule organization / regulation of Rho protein signal transduction / ankyrin repeat binding / anterograde axonal transport / plus-end-directed microtubule motor activity / Kinesins / kinesin complex / microtubule motor activity / regulation of establishment of cell polarity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / positive regulation of wound healing / negative regulation of Rho protein signal transduction / regulation of microtubule polymerization / positive regulation of Wnt signaling pathway / axonal growth cone / axon cytoplasm / negative regulation of insulin receptor signaling pathway / negative regulation of cell migration / beta-catenin binding / ruffle membrane / positive regulation of canonical Wnt signaling pathway / presynapse / negative regulation of neuron projection development / actin cytoskeleton organization / cell cortex / microtubule binding / protein-macromolecule adaptor activity / Estrogen-dependent gene expression / microtubule / cytoskeleton / cell population proliferation / dendrite / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / KIF21A-like domain / KIF21A-like domain / Kank N-terminal motif / KN motif / : / Kinesin-like protein / Ankyrin repeat-containing domain / Kinesin motor domain signature. ...: / : / KIF21A-like domain / KIF21A-like domain / Kank N-terminal motif / KN motif / : / Kinesin-like protein / Ankyrin repeat-containing domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor 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 / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
KN motif and ankyrin repeat domain-containing protein 1 / Kinesin-like protein KIF21A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsGuo, Q. / Liao, S. / Min, J. / Xu, C. / Structural Genomics Consortium (SGC)
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for the recognition of kinesin family member 21A (KIF21A) by the ankyrin domains of KANK1 and KANK2 proteins.
Authors: Guo, Q. / Liao, S. / Zhu, Z. / Li, Y. / Li, F. / Xu, C.
History
DepositionSep 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 2023Group: 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: KN motif and ankyrin repeat domain-containing protein 1
B: Kinesin-like protein KIF21A


Theoretical massNumber of molelcules
Total (without water)29,9652
Polymers29,9652
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-6 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.648, 51.624, 137.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein KN motif and ankyrin repeat domain-containing protein 1 / Ankyrin repeat domain-containing protein 15 / Kidney ankyrin repeat-containing protein


Mass: 27310.148 Da / Num. of mol.: 1 / Fragment: UNP residues 1080-1329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KANK1, ANKRD15, KANK, KIAA0172
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: Q14678
#2: Protein/peptide Kinesin-like protein KIF21A / Kinesin-like protein KIF2 / Renal carcinoma antigen NY-REN-62


Mass: 2655.081 Da / Num. of mol.: 1 / Fragment: UNP residues 1146-1167
Source method: isolated from a genetically manipulated source
Details: KIF21A (1146-1167) / Source: (gene. exp.) Homo sapiens (human) / Gene: KIF21A, KIAA1708, KIF2
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: Q7Z4S6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.05M magnesium formate, 21% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.89→48.335 Å / Num. obs: 22149 / % possible obs: 99.5 % / Redundancy: 13.9 % / Net I/σ(I): 29.3

-
Processing

Software
NameVersionClassification
PHENIXdev_2722refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HBD

4hbd


Resolution: 1.89→48.335 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35
RfactorNum. reflection% reflection
Rfree0.2529 1996 9.01 %
Rwork0.2221 --
obs0.2249 22149 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→48.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 0 95 2047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011995
X-RAY DIFFRACTIONf_angle_d1.2272705
X-RAY DIFFRACTIONf_dihedral_angle_d19.452714
X-RAY DIFFRACTIONf_chiral_restr0.074322
X-RAY DIFFRACTIONf_plane_restr0.006350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.93730.41721390.34651405X-RAY DIFFRACTION99
1.9373-1.98970.38331410.32241424X-RAY DIFFRACTION99
1.9897-2.04820.33911380.29631376X-RAY DIFFRACTION100
2.0482-2.11430.36891390.27721419X-RAY DIFFRACTION99
2.1143-2.18990.3241420.27711416X-RAY DIFFRACTION99
2.1899-2.27760.30291390.26851416X-RAY DIFFRACTION100
2.2776-2.38120.3151430.25641436X-RAY DIFFRACTION100
2.3812-2.50680.32231410.25981433X-RAY DIFFRACTION100
2.5068-2.66380.25341430.25771442X-RAY DIFFRACTION100
2.6638-2.86940.27421430.25271442X-RAY DIFFRACTION100
2.8694-3.15820.27311430.24061443X-RAY DIFFRACTION100
3.1582-3.6150.26461440.22281464X-RAY DIFFRACTION100
3.615-4.5540.20181480.17731493X-RAY DIFFRACTION100
4.554-100.19491530.18051541X-RAY DIFFRACTION97
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)
10.9421-0.3857-0.37642.6844-1.58913.07420.09120.46870.0521-0.1377-0.1039-0.0098-0.06210.3458-0.01460.15960.0244-0.00040.3668-0.03340.3937-6.21493.7855-53.9464
20.20920.2146-0.4680.2457-0.5381.15070.1408-0.34150.0788-0.2523-0.17180.07110.8374-0.59260.00080.3892-0.0215-0.0530.3644-0.05820.4601-15.8584-5.8241-52.0755
31.831.5917-1.30271.4821-0.51045.66410.121-0.0309-0.16040.137-0.3639-0.1164-0.10480.9889-0.02260.1762-0.01630.00680.38310.03420.3125-3.36870.8587-41.4666
40.331-0.6981-0.0021.5646-0.63213.8581-0.1760.05320.15380.509-0.06360.1273-1.25640.85050.00830.5335-0.2709-0.09350.45920.01770.3467-3.64665.2442-28.9492
50.08460.31691.26541.25841.58169.1132-0.1126-0.2475-0.02510.4109-0.1219-0.0756-1.4712-0.3521-0.04220.62050-0.0140.32710.00770.2906-7.57373.0749-7.6541
63.78231.58980.91131.01170.92431.06520.4458-0.2305-0.9495-0.11410.0385-0.11430.8996-0.33770.13871.1119-0.2542-0.08850.46120.0370.421-10.9043-7.5917-8.1854
70.26360.1786-0.3921.2053-0.14720.60751.31880.1280.20320.3005-0.5714-0.89730.27812.0660.08720.62510.05750.02590.60750.05810.3932-3.9456-9.2728-19.9055
80.21850.00740.02770.00310.02220.17130.1967-0.2415-0.89030.506-0.63510.11910.7747-0.3874-0.00050.5586-0.0203-0.01960.23580.00320.4418-7.3084-9.4224-26.8486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1079 through 1105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1106 through 1119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1120 through 1177 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1178 through 1222 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1223 through 1326 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1152 through 1155 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1156 through 1161 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1162 through 1166 )

+
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