[English] 日本語
Yorodumi
- PDB-3tq7: EB1c/EB3c heterodimer in complex with the CAP-Gly domain of P150glued -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tq7
TitleEB1c/EB3c heterodimer in complex with the CAP-Gly domain of P150glued
Components
  • Dynactin subunit 1
  • Microtubule-associated protein RP/EB family member 1
  • Microtubule-associated protein RP/EB family member 3
KeywordsPROTEIN BINDING / CAP-Gly domain / protein-protein interaction / microtubule binding / cytoskeleton
Function / homology
Function and homology information


protein localization to astral microtubule / cell cortex region / protein localization to mitotic spindle / neuron to neuron synapse / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / centriolar subdistal appendage / centriole-centriole cohesion / positive regulation of neuromuscular junction development / microtubule anchoring at centrosome ...protein localization to astral microtubule / cell cortex region / protein localization to mitotic spindle / neuron to neuron synapse / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / centriolar subdistal appendage / centriole-centriole cohesion / positive regulation of neuromuscular junction development / microtubule anchoring at centrosome / maintenance of synapse structure / ventral spinal cord development / protein localization to microtubule / mitotic nuclear membrane disassembly / dynein complex / cell projection membrane / microtubule plus-end / mitotic spindle microtubule / XBP1(S) activates chaperone genes / positive regulation of microtubule nucleation / attachment of mitotic spindle microtubules to kinetochore / positive regulation of dendritic spine morphogenesis / melanosome transport / microtubule plus-end binding / microtubule bundle formation / non-motile cilium assembly / protein localization to centrosome / retrograde transport, endosome to Golgi / COPI-independent Golgi-to-ER retrograde traffic / microtubule associated complex / nuclear migration / perinuclear theca / neuromuscular process / mitotic spindle pole / spindle midzone / negative regulation of microtubule polymerization / establishment of mitotic spindle orientation / neuromuscular junction development / motor behavior / cell leading edge / microtubule polymerization / microtubule organizing center / regulation of microtubule polymerization / regulation of microtubule polymerization or depolymerization / intercellular bridge / positive regulation of microtubule polymerization / COPI-mediated anterograde transport / cytoplasmic microtubule / spindle assembly / behavioral response to cocaine / neuron projection maintenance / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Mitotic Prometaphase / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / EML4 and NUDC in mitotic spindle formation / acrosomal vesicle / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / regulation of mitotic spindle organization / protein serine/threonine kinase activator activity / protein serine/threonine kinase binding / centriole / tubulin binding / RHO GTPases Activate Formins / neuron cellular homeostasis / kinetochore / tau protein binding / spindle / spindle pole / The role of GTSE1 in G2/M progression after G2 checkpoint / mitotic spindle / Signaling by ALK fusions and activated point mutants / Separation of Sister Chromatids / intracellular protein localization / Regulation of PLK1 Activity at G2/M Transition / nuclear envelope / nervous system development / mitotic cell cycle / cell migration / microtubule cytoskeleton / midbody / cell cortex / microtubule binding / microtubule / neuron projection / cilium / ciliary basal body / cadherin binding / axon / cell division / focal adhesion / neuronal cell body / centrosome / protein kinase binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / CAP Gly-rich-like domain / Dynein associated protein / Dynein associated protein / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / CAP-Gly domain signature. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / CAP Gly-rich-like domain / Dynein associated protein / Dynein associated protein / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Dynactin subunit 1 / Microtubule-associated protein RP/EB family member 1 / Microtubule-associated protein RP/EB family member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDe Groot, C.O. / Scharer, M.A. / Capitani, G. / Steinmetz, M.O.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Interaction of mammalian end binding proteins with CAP-Gly domains of CLIP-170 and p150(glued).
Authors: Bjelic, S. / De Groot, C.O. / Scharer, M.A. / Jaussi, R. / Bargsten, K. / Salzmann, M. / Frey, D. / Capitani, G. / Kammerer, R.A. / Steinmetz, M.O.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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: Microtubule-associated protein RP/EB family member 1
B: Microtubule-associated protein RP/EB family member 3
P: Dynactin subunit 1
Q: Dynactin subunit 1


Theoretical massNumber of molelcules
Total (without water)34,1494
Polymers34,1494
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-45 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.150, 103.560, 48.130
Angle α, β, γ (deg.)90.00, 113.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN P AND (RESSEQ 27:97 ) AND (NOT ELEMENT H)
211CHAIN Q AND (RESSEQ 27:97 ) AND (NOT ELEMENT H)
112CHAIN A AND (RESSEQ 203:207 OR RESSEQ 210:218 OR RESSEQ...
212CHAIN B AND (RESSEQ 212:216 OR RESSEQ 219:227 OR RESSEQ...

NCS ensembles :
ID
1
2

-
Components

#1: Protein Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 9067.903 Da / Num. of mol.: 1 / Fragment: EB1 c-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPRE1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q15691
#2: Protein Microtubule-associated protein RP/EB family member 3 / EB1 protein family member 3 / EBF3 / End-binding protein 3 / EB3 / RP3


Mass: 9517.311 Da / Num. of mol.: 1 / Fragment: EB3 c-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPRE3 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UPY8
#3: Protein Dynactin subunit 1 / 150 kDa dynein-associated polypeptide / DAP-150 / DP-150 / p135 / p150-glued


Mass: 7781.931 Da / Num. of mol.: 2 / Fragment: CAP-Gly domain of P150glued / Mutation: A49M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCTN1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q14203
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% PEG 4000, 0.1M Tris-HCl, 0.2M Magnesium chloride hexahydrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2009 / Details: dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→44.095 Å / Num. obs: 15694 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 59.999 Å2 / Net I/σ(I): 27.64
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.3-2.414.25.42193842199.1
2.4-2.514.18.22162926.2199
2.5-2.813.613.31366215.6199.5
2.8-313.322.0317009.3199.7
3-412.936.8535815.5183.6
4-201357.8831303.6199.2

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1wu9

1wu9


Resolution: 2.3→44.09 Å / SU ML: 0.39 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 34.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2811 971 6.2 %random
Rwork0.2255 ---
obs0.229 15666 95.34 %-
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.324 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso mean: 69.585 Å2
Baniso -1Baniso -2Baniso -3
1--9.9429 Å2-0 Å26.9514 Å2
2---19.8847 Å20 Å2
3---29.8277 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 0 36 2052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072047
X-RAY DIFFRACTIONf_angle_d1.0272745
X-RAY DIFFRACTIONf_dihedral_angle_d14.13761
X-RAY DIFFRACTIONf_chiral_restr0.071306
X-RAY DIFFRACTIONf_plane_restr0.003352
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11P547X-RAY DIFFRACTIONPOSITIONAL
12Q547X-RAY DIFFRACTIONPOSITIONAL0.041
21A29X-RAY DIFFRACTIONPOSITIONAL
22B29X-RAY DIFFRACTIONPOSITIONAL0.13
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.42130.35251440.30242174X-RAY DIFFRACTION99
2.4213-2.5730.3071430.24732181X-RAY DIFFRACTION99
2.573-2.77160.35061450.25592188X-RAY DIFFRACTION100
2.7716-3.05050.33741430.24752166X-RAY DIFFRACTION100
3.0505-3.49170.32961290.25281946X-RAY DIFFRACTION88
3.4917-4.39830.26421200.20631819X-RAY DIFFRACTION83
4.3983-40.57370.23461470.20572221X-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)
10.632-0.1247-0.94240.00670.29481.6081-0.5936-0.03150.14670.9870.5037-0.2663-0.4012-1.3815-0.03430.92380.1379-0.11610.5392-0.00430.148614.320624.378522.6289
22.38810.3582-1.64321.54560.83291.9408-0.1091-0.22060.8826-0.25520.27040.8001-0.1503-0.0482-0.19360.44830.0542-0.03210.36550.11810.42558.403731.7904-1.8058
35.0322-1.5259-4.95739.0471-6.28022.00630.78541.6095-0.56570.42450.28632.049-0.3372-1.19311.4130.45420.01310.23150.7743-0.56521.433.281746.42712.4173
41.4196-0.01230.92680.3503-0.54171.1853-0.50940.16240.1930.752-0.18750.73810.11270.081-0.02150.86780.06450.29780.3416-0.03070.46095.831426.812624.2107
52.5967-0.2665-1.89654.3871-0.69731.4851-0.585-0.285-0.4569-0.88180.46660.33330.34910.30610.02290.56780.0001-0.04710.43780.01370.356311.393621.0551-2.0226
63.0407-3.0551-1.23783.07491.07362.45220.55470.28270.29810.82090.5598-1.0232-0.0971-0.210.41930.78830.1633-0.28930.33040.26881.70616.73564.909311.0112
71.93011.05630.49742.3894-1.65812.33930.10210.2819-1.03970.4970.1965-0.54940.06510.1469-0.13630.34660.07170.00820.4281-0.04910.62698.58533.10914.4401
81.8155-0.31790.76821.8420.31642.5499-0.07920.28421.16820.2811-0.0958-0.1855-0.05160.15810.10480.3962-0.009-0.02210.43070.11530.732211.90248.93677.0244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 198:219)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 220:251)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 265:268)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 204:228)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 229:259)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 278:281)
7X-RAY DIFFRACTION7(CHAIN P AND RESID 27:97)
8X-RAY DIFFRACTION8(CHAIN Q AND RESID 27:97)

+
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