[English] 日本語
Yorodumi
- PDB-2hqh: Crystal structure of p150Glued and CLIP-170 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hqh
TitleCrystal structure of p150Glued and CLIP-170
Components
  • Dynactin-1
  • Restin
KeywordsSTRUCTURAL PROTEIN / PROTEIN BINDING / beta/beta structure / zinc finger motif
Function / homology
Function and homology information


positive regulation of neuromuscular junction development / centriolar subdistal appendage / cell cortex region / centriole-centriole cohesion / ventral spinal cord development / microtubule anchoring at centrosome / maintenance of synapse structure / melanosome transport / cell tip / nuclear membrane disassembly ...positive regulation of neuromuscular junction development / centriolar subdistal appendage / cell cortex region / centriole-centriole cohesion / ventral spinal cord development / microtubule anchoring at centrosome / maintenance of synapse structure / melanosome transport / cell tip / nuclear membrane disassembly / microtubule plus-end / positive regulation of microtubule nucleation / XBP1(S) activates chaperone genes / dynein complex / 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 / motor behavior / microtubule associated complex / intermediate filament / neuromuscular process / neuromuscular junction development / intercellular bridge / cell leading edge / establishment of mitotic spindle orientation / RHO GTPases activate IQGAPs / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / cytoplasmic microtubule organization / 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 / ruffle / 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 / Signaling by ALK fusions and activated point mutants / cytoplasmic vesicle membrane / tau protein binding / spindle / mitotic spindle / kinetochore / spindle pole / neuron cellular homeostasis / Separation of Sister Chromatids / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / nuclear envelope / mitotic cell cycle / nervous system development / cell cortex / microtubule binding / microtubule / neuron projection / cell division / axon / centrosome / neuronal cell body / protein kinase binding / zinc ion binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CLIP1, zinc knuckle / CLIP1 zinc knuckle / Dynein associated protein / Dynein associated protein / CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. ...CLIP1, zinc knuckle / CLIP1 zinc knuckle / Dynein associated protein / Dynein associated protein / CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
CAP-Gly domain-containing linker protein 1 / Dynactin subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsHayashi, I. / Ikura, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: CLIP170 autoinhibition mimics intermolecular interactions with p150Glued or EB1.
Authors: Hayashi, I. / Plevin, M.J. / Ikura, M.
History
DepositionJul 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Dynactin-1
B: Dynactin-1
C: Dynactin-1
D: Dynactin-1
E: Restin
F: Restin
G: Restin
H: Restin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,68712
Polymers51,4258
Non-polymers2624
Water9,008500
1
A: Dynactin-1
E: Restin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9223
Polymers12,8562
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Dynactin-1
F: Restin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9223
Polymers12,8562
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-11 kcal/mol
Surface area5480 Å2
MethodPISA, PQS
3
C: Dynactin-1
G: Restin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9223
Polymers12,8562
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-11 kcal/mol
Surface area5450 Å2
MethodPISA, PQS
4
D: Dynactin-1
H: Restin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9223
Polymers12,8562
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-12 kcal/mol
Surface area5490 Å2
MethodPISA, PQS
5
C: Dynactin-1
G: Restin
hetero molecules

C: Dynactin-1
G: Restin
hetero molecules

A: Dynactin-1
B: Dynactin-1
D: Dynactin-1
E: Restin
F: Restin
H: Restin
hetero molecules

A: Dynactin-1
B: Dynactin-1
D: Dynactin-1
E: Restin
F: Restin
H: Restin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,37324
Polymers102,85016
Non-polymers5238
Water28816
TypeNameSymmetry operationNumber
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/21
crystal symmetry operation6_455x-1/2,-y+1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area19070 Å2
ΔGint-154 kcal/mol
Surface area33750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.8, 122.8, 68.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11F-222-

HOH

DetailsThe biological assembly is a dimer of chain A and E, or B and F, or C and G, or D and H

-
Components

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


Mass: 9928.076 Da / Num. of mol.: 4 / Fragment: CAP-Gly domain, residues 15-107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCTN1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q14203
#2: Protein/peptide
Restin / Cytoplasmic linker protein 170 alpha-2 / CLIP-170 / Reed- Sternberg intermediate filament- ...Cytoplasmic linker protein 170 alpha-2 / CLIP-170 / Reed- Sternberg intermediate filament-associated protein / Cytoplasmic linker protein 1


Mass: 2928.173 Da / Num. of mol.: 4 / Fragment: second zinc finger domain, residues 1405-1427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RSN, CYLN1 / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30622
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 4M sodium formate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791, 1.2826, 1.2830, 1.2694
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 5, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
21.28261
31.2831
41.26941
ReflectionResolution: 1.8→45.7 Å / Num. all: 48867 / Num. obs: 49011 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14 Å2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
SnBphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→45.68 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 41271 -RANDOM
Rwork0.194 ---
all-48921 --
obs-45911 93.8 %-
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 4 500 3429

+
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