[English] 日本語
Yorodumi
- PDB-2hl3: Crystal structure of the A49M mutant CAP-Gly domain of human Dyna... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hl3
TitleCrystal structure of the A49M mutant CAP-Gly domain of human Dynactin-1 (p150-Glued) in complex with human EB1 C-terminal hexapeptide
Components
  • Dynactin-1
  • Microtubule-associated protein RP/EB family member 1
KeywordsSTRUCTURAL PROTEIN / microtubule binding / dynactin / cytoskeleton associated protein / p150Glued / EB1 / +TIP protein Complex structure / EEY/F-COO- sequence motif / CLIP-170 / alpha-tubulin
Function / homology
Function and homology information


positive regulation of neuromuscular junction development / centriolar subdistal appendage / cell cortex region / protein localization to astral microtubule / cortical microtubule cytoskeleton / centriole-centriole cohesion / mitotic spindle astral microtubule end / ventral spinal cord development / microtubule anchoring at centrosome / maintenance of synapse structure ...positive regulation of neuromuscular junction development / centriolar subdistal appendage / cell cortex region / protein localization to astral microtubule / cortical microtubule cytoskeleton / centriole-centriole cohesion / mitotic spindle astral microtubule end / ventral spinal cord development / microtubule anchoring at centrosome / maintenance of synapse structure / melanosome transport / protein localization to microtubule / nuclear membrane disassembly / microtubule plus-end / positive regulation of microtubule nucleation / cell projection membrane / XBP1(S) activates chaperone genes / dynein complex / attachment of mitotic spindle microtubules to kinetochore / COPI-independent Golgi-to-ER retrograde traffic / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation / retrograde transport, endosome to Golgi / nuclear migration / protein localization to centrosome / microtubule associated complex / motor behavior / microtubule organizing center / neuromuscular process / negative regulation of microtubule polymerization / neuromuscular junction development / intercellular bridge / mitotic spindle pole / cytoplasmic microtubule / cell leading edge / microtubule polymerization / establishment of mitotic spindle orientation / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / positive regulation of microtubule polymerization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Signaling by ALK fusions and activated point mutants / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / MHC class II antigen presentation / centriole / neuron projection maintenance / tubulin binding / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / tau protein binding / protein localization / spindle / kinetochore / mitotic spindle / spindle pole / neuron cellular homeostasis / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / cell migration / mitotic cell cycle / nuclear envelope / nervous system development / cell cortex / microtubule binding / microtubule / molecular adaptor activity / neuron projection / cadherin binding / axon / cell division / focal adhesion / centrosome / neuronal cell body / protein kinase binding / Golgi apparatus / RNA binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Dynein associated protein / Dynein associated protein / CAP Gly-rich-like domain / 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 ...Dynein associated protein / Dynein associated protein / CAP Gly-rich-like domain / 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. / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Dynactin subunit 1 / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsHonnappa, S. / Winkler, F.K. / Steinmetz, M.O.
CitationJournal: Mol.Cell / Year: 2006
Title: Key interaction modes of dynamic +TIP networks.
Authors: Honnappa, S. / Okhrimenko, O. / Jaussi, R. / Jawhari, H. / Jelesarov, I. / Winkler, F.K. / Steinmetz, M.O.
History
DepositionJul 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2015Group: Database references / Structure summary
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). IN THE CRYSTAL STRUCTURE, THE BIOLOGICAL UNIT IS COMPRISED OF CHAINS A, B AND C. HOWEVER, THE ACTIVE BIOLOGICAL UNIT IS A COMPLEX OF CHAINS A AND C.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dynactin-1
B: Dynactin-1
C: Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)21,5653
Polymers21,5653
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.062, 55.068, 66.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Dynactin-1 / / 150 kDa dynein-associated polypeptide / DP-150 / DAP-150 / p150-glued / p135


Mass: 10369.531 Da / Num. of mol.: 2 / Fragment: CAP-Gly domain / Mutation: A49M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCTN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14203
#2: Protein/peptide Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 825.773 Da / Num. of mol.: 1 / Fragment: C-terminal hexapeptide / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: Q15691
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.82 Å3/Da / Density % sol: 32.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 25% PEG 3350, 0.05M Sodium Citrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 8, 2005 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→42.33 Å / Num. all: 10303 / Num. obs: 10303 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.03→2.085 Å / % possible all: 92.17

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→42.33 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.683 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.197 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22339 488 4.7 %RANDOM
Rwork0.18302 ---
obs0.18483 9814 97.03 %-
all-9814 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.088 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2---0.49 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.03→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 0 67 1236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221213
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9311622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5515149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.20422.85756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56715209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9181510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02906
X-RAY DIFFRACTIONr_nbd_refined0.1890.2504
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.212
X-RAY DIFFRACTIONr_mcbond_it1.9592761
X-RAY DIFFRACTIONr_mcangle_it3.1231182
X-RAY DIFFRACTIONr_scbond_it4.8254.5512
X-RAY DIFFRACTIONr_scangle_it7.156440
LS refinement shellResolution: 2.03→2.085 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 32 -
Rwork0.188 674 -
obs--92.17 %

+
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