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- PDB-2hqh: Crystal structure of p150Glued and CLIP-170 -

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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


cell cortex region / centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / microtubule anchoring at centrosome / maintenance of synapse structure / ventral spinal cord development / microtubule plus-end / nuclear membrane disassembly / positive regulation of microtubule nucleation ...cell cortex region / centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / microtubule anchoring at centrosome / maintenance of synapse structure / ventral spinal cord development / microtubule plus-end / nuclear membrane disassembly / positive regulation of microtubule nucleation / XBP1(S) activates chaperone genes / melanosome transport / microtubule bundle formation / microtubule plus-end binding / non-motile cilium assembly / dynein complex / retrograde transport, endosome to Golgi / COPI-independent Golgi-to-ER retrograde traffic / Signaling by LTK in cancer / intermediate filament / microtubule associated complex / neuromuscular process / nuclear migration / neuromuscular junction development / cell leading edge / motor behavior / establishment of mitotic spindle orientation / RHO GTPases activate IQGAPs / intercellular bridge / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / ruffle / cytoplasmic microtubule organization / positive regulation of microtubule polymerization / neuron projection maintenance / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / 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 / tubulin binding / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / regulation of mitotic spindle organization / cytoplasmic vesicle membrane / AURKA Activation by TPX2 / RHO GTPases Activate Formins / neuron cellular homeostasis / kinetochore / tau protein binding / spindle / spindle pole / mitotic spindle / Separation of Sister Chromatids / Signaling by ALK fusions and activated point mutants / Regulation of PLK1 Activity at G2/M Transition / nuclear envelope / nervous system development / mitotic cell cycle / microtubule cytoskeleton / cell cortex / microtubule binding / microtubule / neuron projection / cilium / ciliary basal body / axon / cell division / neuronal cell body / centrosome / protein kinase binding / zinc ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CLIP1, zinc knuckle / CLIP1 zinc knuckle / CAP Gly-rich-like domain / Dynein associated protein / Dynein associated protein / 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 / CAP Gly-rich-like domain / Dynein associated protein / Dynein associated protein / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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