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- PDB-3e2u: Crystal structure of the zink-knuckle 2 domain of human CLIP-170 ... -

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Basic information

Entry
Database: PDB / ID: 3e2u
TitleCrystal structure of the zink-knuckle 2 domain of human CLIP-170 in complex with CAP-Gly domain of human dynactin-1 (p150-GLUED)
Components
  • CAP-Gly domain-containing linker protein 1
  • Dynactin subunit 1
KeywordsPROTEIN BINDING / STRUCTURAL PROTEIN MICROTUBULE BINDING / DYNACTIN / CYTOSKELETON ASSOCIATED PROTEIN / P150GLUED / CLIP-170/RESTIN / +TIP PROTEIN COMPLEX STRUCTURE / ZINC-KNUCKLE / AUTOINHIBITION / Cytoskeleton / Dynein / Microtubule / Motor protein / Phosphoprotein
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 / COPI-mediated anterograde transport / intercellular bridge / 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 / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / centriole / 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 / cytoplasmic vesicle membrane / regulation of mitotic spindle organization / 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 / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsWeisbrich, A. / Honnappa, S. / Capitani, G. / Steinmetz, M.O.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structure-function relationship of CAP-Gly domains
Authors: Weisbrich, A. / Honnappa, S. / Jaussi, R. / Okhrimenko, O. / Frey, D. / Jelesarov, I. / Akhmanova, A. / Steinmetz, M.O.
History
DepositionAug 6, 2008Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 19, 2008ID: 2PZO
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / 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 / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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 subunit 1
B: Dynactin subunit 1
C: Dynactin subunit 1
D: Dynactin subunit 1
E: CAP-Gly domain-containing linker protein 1
F: CAP-Gly domain-containing linker protein 1
G: CAP-Gly domain-containing linker protein 1
H: CAP-Gly domain-containing linker protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,71612
Polymers60,4548
Non-polymers2624
Water1,04558
1
A: Dynactin subunit 1
E: CAP-Gly domain-containing linker protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1793
Polymers15,1142
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-10 kcal/mol
Surface area5590 Å2
MethodPISA
2
B: Dynactin subunit 1
F: CAP-Gly domain-containing linker protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1793
Polymers15,1142
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-11 kcal/mol
Surface area5510 Å2
MethodPISA
3
C: Dynactin subunit 1
G: CAP-Gly domain-containing linker protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1793
Polymers15,1142
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-11 kcal/mol
Surface area5610 Å2
MethodPISA
4
D: Dynactin subunit 1
H: CAP-Gly domain-containing linker protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1793
Polymers15,1142
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-12 kcal/mol
Surface area5900 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-73 kcal/mol
Surface area18480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.220, 116.310, 79.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and backbone and (resseq 29:70 or resseq 75:93 )
21chain B and backbone and (resseq 29:70 or resseq 75:93 )
31chain C and backbone and (resseq 29:70 or resseq 75:93 )
41chain D and backbone and (resseq 29:70 or resseq 75:93 )
12chain E and backbone and (resseq 1406:1427 )
22chain F and backbone and (resseq 1406:1427 )
32chain G and backbone and (resseq 1406:1427 )
42chain H and backbone and (resseq 1406:1427 )

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALASPASPAA29 - 7015 - 56
121GLYGLYGLNGLNAA75 - 9361 - 79
211VALVALASPASPBB29 - 7015 - 56
221GLYGLYGLNGLNBB75 - 9361 - 79
311VALVALASPASPCC29 - 7015 - 56
321GLYGLYGLNGLNCC75 - 9361 - 79
411VALVALASPASPDD29 - 7015 - 56
421GLYGLYGLNGLNDD75 - 9361 - 79
112PROPROPHEPHEEE1406 - 142721 - 42
212PROPROPHEPHEFF1406 - 142721 - 42
312PROPROPHEPHEGG1406 - 142721 - 42
412PROPROPHEPHEHH1406 - 142721 - 42

NCS ensembles :
ID
1
2

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Components

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


Mass: 10309.413 Da / Num. of mol.: 4 / Fragment: CAP-Gly domain
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
#2: Protein/peptide
CAP-Gly domain-containing linker protein 1 / Restin / Cytoplasmic linker protein 170 alpha-2 / CLIP-170 / Reed-Sternberg intermediate filament- ...Restin / Cytoplasmic linker protein 170 alpha-2 / CLIP-170 / Reed-Sternberg intermediate filament-associated protein / Cytoplasmic linker protein 1


Mass: 4804.103 Da / Num. of mol.: 4 / Fragment: Zn-knuckle 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIP1, CYLN1, RSN / Plasmid: pETG20 MTA / Production host: Escherichia coli (E. coli) / 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.: 58 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.2M Trisodium Citrate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.039 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 26, 2006 / 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: 1.039 Å / Relative weight: 1
Reflection twinOperator: -k,h,l / Fraction: 0.352
ReflectionResolution: 2.6→47.02 Å / Num. obs: 16917 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 33.3 Å2 / Rsym value: 0.13 / Net I/σ(I): 10
Reflection shellResolution: 2.6→2.8 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.3 / Num. measured obs: 17204 / Num. unique obs: 3307 / Rsym value: 0.563 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2PZO (SOLVED BY MOLECULAR REPLACEMENT USING MOLREP)

2pzo
PDB Unreleased entry


Resolution: 2.6→47.015 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.628 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.238 854 5.05 %random
Rwork0.191 ---
obs0.193 16915 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 84.11 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 163.85 Å2 / Biso mean: 72.982 Å2 / Biso min: 9.64 Å2
Baniso -1Baniso -2Baniso -3
1--33.12 Å2-0 Å2-0 Å2
2---45.173 Å20 Å2
3----4.369 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 4 58 3066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073104
X-RAY DIFFRACTIONf_angle_d1.1034164
X-RAY DIFFRACTIONf_chiral_restr0.065433
X-RAY DIFFRACTIONf_plane_restr0.004546
X-RAY DIFFRACTIONf_dihedral_angle_d18.7071086
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A244X-RAY DIFFRACTIONPOSITIONAL
12B244X-RAY DIFFRACTIONPOSITIONAL0.034
13C244X-RAY DIFFRACTIONPOSITIONAL0.037
14D244X-RAY DIFFRACTIONPOSITIONAL0.037
21E88X-RAY DIFFRACTIONPOSITIONAL
22F88X-RAY DIFFRACTIONPOSITIONAL0.037
23G84X-RAY DIFFRACTIONPOSITIONAL0.056
24H88X-RAY DIFFRACTIONPOSITIONAL0.045
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.7180.3631220.24119642086
2.718-2.8620.2821040.219802084
2.862-3.0410.2841010.20919862087
3.041-3.2760.261950.19520162111
3.276-3.6050.2491120.19119822094
3.605-4.1270.21960.16820052101
4.127-5.1980.2131080.16220232131
5.198-47.0230.1921150.20921062221
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)
10.2005-0.17590.35870.4154-0.09940.1625-0.05820.14020.14090.0071-0.1474-0.2137-0.04240.04940.18120.1528-0.01370.00340.18410.02220.5592106.247358.3484-20.1035
20.1951.03080.15674.33121.46321.54770.02050.01920.16040.15780.00210.77810.20950.1823-0.01550.05620.0026-0.05780.0953-0.05270.174568.016841.0341-19.7251
30.6182-0.0307-0.40220.1068-0.26460.3117-0.0804-0.08940.061-0.04470.03210.11020.16880.07340.02550.25710.0141-0.03850.236-0.07020.52395.840130.6405-19.5736
40.29710.00740.05790.03280.23020.2411-0.0830.02450.31360.0637-0.0470.46210.14980.00450.11970.29940.01510.01650.24-0.00610.818278.921369.1593-19.6725
50.0059-0.0172-0.3933-0.1386-0.09760.8908-0.3875-0.07660.1485-0.05060.0411-0.04510.284-0.08790.30370.40720.07790.00820.4474-0.04340.237393.077961.806-9.3974
60.3960.2108-0.3480.46370.04890.1205-0.03020.14540.1865-0.03150.23810.4102-0.0575-0.1093-0.12020.33240.03950.02630.37390.07590.663581.37437.4782-9.3684
70.73060.06220.57670.3546-0.07760.21550.14-0.2129-0.36130.06320.24980.3423-0.13480.2174-0.16450.1846-0.01290.02170.2266-0.04470.758699.593144.181-8.8662
80.05950.6329-0.29840.3549-0.3277-0.19460.0778-0.20270.0070.23330.0647-0.1530.0651-0.2219-0.210.39340.0105-0.04610.3485-0.00011.002774.852655.2545-8.8719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

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